diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 000000000..5aeec088a --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,32 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: bug +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (if applicable, please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 000000000..249f8b03f --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,27 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: feature +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**How important is this feature?** Select from the options below: +• Low - it's an enhancement but not crucial for work +• Medium - can do work without it; but it's important (e.g. to save time or for convenience) +• Important - it's a blocker and can't do work without it + +**When will use cases depending on this become relevant?** Select from the options below: +• Short-term - 2-4 weeks +• Mid-term - 2-4 months +• Long-term - 6 months - 1 year + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 000000000..261eeb9e9 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 11ddf3314..a0f81655f 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# HTAN Data Ingress Pipeline +# Schematic ## Usage @@ -6,9 +6,15 @@ Python 3 has built-in support for virtual environments (using `venv` module). Perform the following steps: -_Note: It is assumed that you are running all the below commands from the main/root (`HTAN-data-pipeline`) directory._ +_Note: It is assumed that you are running all the below commands from the main/root (`schematic`) directory._ -After cloning the git repository, navigate into the `HTAN-data-pipeline` directory and run the command as below: +Clone this branch of the git repository + +``` +git clone --single-branch --branch main https://github.com/ncihtan/schematic.git +``` + +Navigate into the `schematic` directory and run the command as below: ```bash python[3] -m venv .venv @@ -88,9 +94,9 @@ _Note: You can get your Synapse API key by: **logging into Synapse > Settings > Clone a copy of the repository here: ```bash -git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/HTAN-data-pipeline.git +git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git ``` Modify your files, add them to the staging area, use a descriptive commit message and push to the same branch as a pull request for review. -* Please consult [CONTRIBUTION.md](https://github.com/Sage-Bionetworks/HTAN-data-pipeline/blob/develop/CONTRIBUTION.md) for further reference. +* Please consult [CONTRIBUTION.md](https://github.com/Sage-Bionetworks/schematic/blob/develop/CONTRIBUTION.md) for further reference. diff --git a/data/csv/HTAN.csv b/data/csv/HTAN.csv index bee4785e1..d2452e435 100644 --- a/data/csv/HTAN.csv +++ b/data/csv/HTAN.csv @@ -1,481 +1,723 @@ -Attribute,Description,Valid Values,Requires,Properties,Required,Parent,Requires Component,Source,Validation Rules -Assay,"A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]",,,,FALSE,,,http://purl.obolibrary.org/obo/OBI_0000070, -Device,"A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment""",,,,FALSE,Assay,,https://w3id.org/biolink/vocab/Device, -Sequencing,Module for next generation sequencing assays,,,,FALSE,Assay,,http://example.org/htan/Sequencing, -Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",,,,TRUE,,,https://w3id.org/biolink/vocab/category, -Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy",http://example.org/htan/Patient, -File,A type of Information Content Entity specific to OS,,,"Filename, File Format",FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, -Filename,Name of a file ,,,,TRUE,,,http://example.org/htan/filename, -File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe ",,,TRUE,,,http://example.org/htan/fileFormat, -Checksum,MD5 checksum of the fasta file,,,,TRUE,Information Content Entity,,, -HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, -HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, -HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, -HTAN Parent ID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, -HTAN Parent Biospecimen ID,HTAN Biospecimen Identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, -HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,,, -Demographics,Individual biomedical demographics attributes,,"Component, HTAN Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Age Is Obfuscated, Year Of Birth, Occupation Duration Years, Premature At Birth, Weeks Gestation at Birth",,FALSE,Patient,,, -Family History,Individual's family cancer history,,"Component, HTAN Participant ID, Relative with Cancer History",,FALSE,Patient,,, -Exposure,Individual's exposure to carcenogens,,"Component, HTAN Participant ID, Smoking Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica Exposure",,FALSE,Patient,,, -Follow Up,Individual's follow up exams,,"Component, HTAN Participant ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year, Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight",,FALSE,Patient,,, -Therapy,Individual's first line of therapy or treatment,,"Component, HTAN Participant ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type",,FALSE,Patient,,, -Diagnosis,Individual's diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status, Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition",,FALSE,Patient,,, -Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subsamples of those",,"Component, HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen ID, Biospecimen Type, Acquisition Method Type, Fixative Type, Site of Resection or Biopsy, Storage Method, Processing Days from Index, Protocol Link, Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method, Preinvasive Morphology, Lysis Buffer, Method of Nucleic Acid Isolation",,FALSE,Biosample,Patient,http://example.org/htan/Biospecimen, -Other Assay,Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,, -Assay Type,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",,,,TRUE,Assay,,, -scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Date, Single Cell Dissociation Date, Sequencing Library Construction Date, Nucleic Acid Capture Date, Protocol Link, Technical Replicate Group",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913, -scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, scRNA-seq Workflow Type, Workflow Version, Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, White-list Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,scRNA-seq Level 1,, -scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNA-seq Workflow Type, scRNA-seq Workflow Parameters Description, Workflow Link, Workflow Start Date-time, Workflow End Date-time",,FALSE,Sequencing,scRNA-seq Level 2,, -scRNA-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, scRNA-seq Workflow Type, scRNA-seq Workflow Parameters Description, Workflow Version, Workflow Link, Workflow Start Date-time, Workflow End Date-time",,FALSE,Sequencing,scRNA-seq Level 3,, -Bulk RNA-seq Level 1,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Nucleic Acid Source, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Date, Spike In, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow, Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Transcript Integrity Number (TIN), RIN, DV200, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link ",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0003738, -Bulk RNA-seq Level 2,Bulk RNA-seq alignment protocol description,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, HTAN Parent Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion, Targets No Coverage, Proportion Base Mismatch, Short Reads",,FALSE,Sequencing,Bulk RNA-seq Level 1,, -Bulk RNA-seq Level 3,Bulk RNA-seq gene expression matrices,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Pseudo Alignment Used, Data Category, Expression Units, Matrix Type, Fusion Gene Detected, Fusion Gene Identity",,FALSE,Sequencing,Bulk RNA-seq Level 2,, -Bulk WES Level 1,Bulk Whole Exome Sequencing raw files,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Library Selection Method, Read Length, Target Capture Kit, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Sequencing Platform, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Multiplex Barcode, Library Preparation Date, Size Selection Range, Target Depth, To Trim Adapter Sequence",,FALSE,Sequencing,Biospecimen,, -Bulk WES Level 2,Bulk Whole Exome Sequencing aligned files and QC,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Adapter Content, Basic Statistics, Encoding, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, QC Workflow Type, QC Workflow Version, QC Workflow Link, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X",,FALSE,Sequencing,Bulk WES Level 1,, -Bulk WES Level 3,Bulk Whole Exome Sequencing called variants,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Genomic Reference, Genomic Reference URL, Germline Variants Workflow URL, Germline Variants Workflow Type, Germline Variants Workflow Type, Somatic Variants Workflow URL, Somatic Variants Workflow Type, Somatic Variants Sample Type, Structural Variant Workflow URL, Structural Variant Workflow Type",,FALSE,Sequencing,Bulk WES Level 2,, -scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATAC-seq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATAC-seq Read1, scATAC-seq Read2, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks - FRIP, Median Fraction of Reads in Annotated cis-DNA Elements - FRIADE, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Sequencing,Biospecimen,, -Imaging Level 2,Raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Workflow Start Date-time, Workflow End Date-time, Software and Version, Image Acquisition Date, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance,WorkingDistanceUnit, Immersion, Pyramid, Z-stack, T-series, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType",,FALSE,Assay,"Biospecimen, Imaging Level 1 and 2 Channels",, -Imaging Level 2 Channels,Channel-level Metadata Attributes,,"Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub-Cycle Number, Target Name, Cycle Number, Sub-Cycle Number, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope - Element, Metal Isotope - Mass, Oligo Barcode - Upper Strand, Oligo Barcode - Lower Strand, Dilution, Concentration",,FALSE,Imaging Level 2,,, -Channel ID,"This must match the corresponding field in the OME-XML / TIFF header. (eg ""Channel:0:1"")",,,,TRUE,Imaging Level 2 Channels,,, -Channel Name,This must match the corresponding field in the OME-XML / TIFF header. (eg “Blue” or “CD45” or “E-cadherin”),,,,TRUE,Imaging Level 2 Channels,,, -Channel Passed QC,Identify stains that did not pass QC but are included in the dataset.,"Yes, No",,,TRUE,Imaging Level 2 Channels,,, -Cycle Number,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),,,,FALSE,Imaging Level 2 Channels,,, -Sub-Cycle Number,Sub-cycle number,,,,FALSE,Imaging Level 2 Channels,,, -Target Name,Short descriptive name (abbreviation) for this target (antigen),,,,FALSE,Imaging Level 2 Channels,,, -Antibody Name,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",,,,FALSE,Imaging Level 2 Channels,,, -RRID identifier,Research Resource Identifier (eg “RRID: AB_394606”),,,,FALSE,Imaging Level 2 Channels,,https://scicrunch.org/resources, -Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),,,,FALSE,Imaging Level 2 Channels,,http://purl.obolibrary.org/obo/MI_0857, -Clone,Clone,,,,FALSE,Imaging Level 2 Channels,,, -Lot,Lot number from vendor,,,,FALSE,Imaging Level 2 Channels,,, -Vendor,Vendor,,,,FALSE,Imaging Level 2 Channels,,, -Catalog Number,Catalog Number,,,,FALSE,Imaging Level 2 Channels,,, -Excitation Wavelength,Center/peak of the excitation spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, -Emission Wavelength,Center/peak of the emission spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, -Excitation Bandwidth,Nominal width of excitation spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, -Emission Bandwidth,Nominal width of emission spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, -Metal Isotope - Element,Element abbreviation. eg “La” or “Nd”,,,,FALSE,Imaging Level 2 Channels,,, -Metal Isotope - Mass,Element mass number,,,,FALSE,Imaging Level 2 Channels,,, -Oligo Barcode - Upper Strand,Oligo Barcode - Upper Strand,,,,FALSE,Imaging Level 2 Channels,,, -Oligo Barcode - Lower Strand,Oligo Barcode - Lower Strand,,,,FALSE,Imaging Level 2 Channels,,, -Dilution,Dilution (eg 1:1000),,,,FALSE,Imaging Level 2 Channels,,, -Concentration,Concentration (eg 10ug/mL),,,,FALSE,Imaging Level 2 Channels,,, -Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI",,,TRUE,Imaging Level 2,,, -Channel Metadata Filename,Full path of uploaded companion CSV file containing channel-level metadata details,,,,TRUE,Imaging Level 2,,, -Image Acquisition Date,Date of image acquisition,,,,FALSE,Imaging Level 2,,, -Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",,,,TRUE,Imaging Level 2,,http://purl.obolibrary.org/obo/OBI_0400169, -Objective,Objective,,,,FALSE,Imaging Level 2,,, -NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),,,,TRUE,Imaging Level 2,,, -LensNA,The numerical aperture of the lens. Floating point value > 0.,,,,FALSE,Imaging Level 2,,, -WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",,WorkingDistanceUnit,,FALSE,Imaging Level 2,,, -WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, -Immersion,Immersion medium,"Air, Oil, Other",,,FALSE,Imaging Level 2,,, -Pyramid,Does data file contain pyramid of images,"Yes, No",,,TRUE,Imaging Level 2,,, -Z-stack,Does data file contain a Z-stack of images,"Yes, No",,,TRUE,Imaging Level 2,,, -T-series,Does data file contain a time-series of images,"Yes, No",,,TRUE,Imaging Level 2,,, -Passed QC,Did all channels pass QC (if not add free text Comment),"Yes, No - Channels QC",,,TRUE,Imaging Level 2,,, -No - Channels QC,Not all channels passed QC,,Comment,,FALSE,Imaging Level 2,,, -Comment,Free text field (generally for QC comment),,,,FALSE,Imaging Level 2,,, -FOV number,Index of FOV (as it pertains to its sequence order). Integer >= 1,,,,FALSE,Imaging Level 2,,, -FOVX,Field of view X dimension. Floating point,,FOVXUnit,,FALSE,Imaging Level 2,,, -FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging Level 2,,, -FOVY,Field of view Y dimension. Floating point value,,FOVYUnit,,FALSE,Imaging Level 2,,, -FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging Level 2,,, -Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",,,,FALSE,Imaging Level 2,,, -Image ID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",,,,TRUE,Imaging Level 2,,, -DimensionOrder,The order in which the individual planes of data are interleaved.,"XYZCT, XYZTC, XYCTZ, XYCZT, XYTZC",,,TRUE,Imaging Level 2,,, -PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,,PhysicalSizeXUnit,,TRUE,Imaging Level 2,,, -PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, -PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,,PhysicalSizeYUnit,,TRUE,Imaging Level 2,,, -PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, -PhysicalSizeYUnit,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,,PhysicalSizeZUnit,,TRUE,Imaging Level 2,,, -PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, -Pixels BigEndian,Boolean (True/False),"True, False",,,TRUE,Imaging Level 2,,, -PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",,,,TRUE,Imaging Level 2,,, -SizeC,Number of channels. Integer >= 1,,,,TRUE,Imaging Level 2,,, -SizeT,Number of time points. Integer >= 1,,,,TRUE,Imaging Level 2,,, -SizeX,Size of image: X dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, -SizeY,Size of image: Y dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, -SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, -PixelType,"Data type for each pixel value. E.g. ""uint16""","int8, int16, int32, uint8, uint16, uint32, float, double, bit",,,TRUE,Imaging Level 2,,, -Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,http://example.org/htan/NucleicAcidSource, -Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x",,,TRUE,scRNA-seq Level 1,,, -Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion",,,TRUE,scRNA-seq Level 1,,, -Library Layout,Sequencing read type,"Paired End, Single Read",,,TRUE,Sequencing,,, -Nucleus Identifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,Nuclei Barcode,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode,Nuclei Barcode,"Nuclei Barcode Read, Nuclei Barcode Length",,,FALSE,scATAC-seq Level 1,,, -scATAC-seq Library Layout,Sequencing read type,scATAC-seq Paired End,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Read,Nuclei Barcode Read,,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Length,Nuclei Barcode Length,,,,TRUE,scATAC-seq Level 1,,, -scATAC-seq Paired End,A library layout type,"scATAC-seq Read1, scATAC-seq Read2",,,FALSE,scATAC-seq Level 1,,, -scATAC-seq Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert",,,TRUE,scATAC-seq Level 1,,, -scATAC-seq Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert",,,TRUE,scATAC-seq Level 1,,, -Threshold for Minimum Passing Reads,Threshold for calling cells,,,,TRUE,scATAC-seq Level 1,,, -Total Number of Passing Nuclei,Number of nuclei sequenced,,,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Peaks - FRIP,Median fraction of reads in peaks (FRIP),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Annotated cis-DNA Elements - FRIADE,Median fraction of reads in annotated cis-DNA elements (FRIADE),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,, -Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,, -Peaks Calling Software,Generic name of peaks calling tool,,,,TRUE,scATAC-seq Level 1,,, -Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,, -Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,, -cDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",,"cDNA Offset, cDNA Length",,FALSE,Sequencing,,, -cDNA Offset,Offset in sequence for cDNA read (in bp): number,,,,TRUE,Sequencing,,, -cDNA Length,Length of cDNA read (in bp): number,,,,TRUE,Sequencing,,, -Cell Barcode and UMI,Cell and transcript identifiers,,"UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number",,FALSE,scRNA-seq Level 1,,, -Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, -Cell Barcode Length,Length of cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, -Valid Barcodes Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,, -UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",,,,TRUE,scRNA-seq Level 1,,https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html, -UMI Barcode Length,Length of UMI barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, -Median UMIs per Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,, -Cell Median Number Reads,Median number of reads per cell. Number,,,,TRUE,scRNA-seq Level 3,,, -Cell Median Number Genes,Median number of genes detected per cell. Number,,,,TRUE,scRNA-seq Level 3,,, -Cell Total,Number of sequenced cells. Applies to raw counts matrix only.,,,,TRUE,scRNA-seq Level 3,,, -Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711, -Library Selection Method,How the molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Other",,,TRUE,Sequencing,,, -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,scRNA-seq Level 1,,, -CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,,"Empty Well Barcode, Well Index",,FALSE,scRNA-seq Level 1,,, -Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,,,,TRUE,scRNA-seq Level 1,,, -Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,"Yes, No",,,FALSE,scRNA-seq Level 1,,, -Library Preparation Date,"The date that the libraries were prepared for sequencing (in number of days since sample received in lab). A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] or ""null""",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Single Cell Dissociation Date,The date when the sample was dissociated and cells were isolated (date format),,,,TRUE,scRNA-seq Level 1,,, -Sequencing Library Construction Date,Date of sequencing library construction part of library construction (in number of days since sample received in lab),,,,TRUE,Sequencing,,, -Nucleic Acid Capture Date,Date of nucleic acid capture part of library construction (in number of days since sample received in lab),,,,TRUE,Sequencing,,, -Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,scRNA-seq Level 1,,, -End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript",,,TRUE,scRNA-seq Level 1,,, -Reverse Transcription Primer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA","Oligo-dT, Poly-dT, Feature barcoding, Random",,,TRUE,scRNA-seq Level 1,,http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer, -Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],,Feature Reference Id,,FALSE,scRNA-seq Level 1,,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc, -Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",,,,TRUE,scRNA-seq Level 1,,, -Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX",,,TRUE,scRNA-seq Level 1,,, -ERCC,The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization,,"Spike In Concentration, Spike In Mix 1, Spike In Mix 2, Both Spike in Mixes",,FALSE,Spike In,,, -Spike In Concentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],,,,TRUE,ERCC,,https://www.ncbi.nlm.nih.gov/pubmed/21816910, -Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4 AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, Other, Unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,,, -Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Sequencing,,, -Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,, -Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni",,,TRUE,scATAC-seq Level 1,,, -Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, In-House",,,TRUE,scATAC-seq Level 1,,, -Read Length,"The length of the sequencing reads. Can be integer, null",,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Target Capture Kit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.","Not Applicable, Custom Targets File Provided, Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes, Custom GENIE-DFCI OncoPanel - 275 Genes, Custom GENIE-DFCI Oncopanel - 300 Genes, Custom GENIE-DFCI Oncopanel - 447 Genes, Custom HaloPlex DLBCL Panel - 370 Genes, Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes, Custom Large Construct Capture TARGET-OS Panel - 8 Genes, Custom MSK IMPACT Panel - 341 Genes, Custom MSK IMPACT Panel - 410 Genes, Custom MSK IMPACT Panel - 468 Genes, Custom Myeloid GENIE-VICC Panel - 37 Genes, Custom Personalis ACEcp VAREPOP-APOLLO Panel v2, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2, Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb, Custom Solid Tumor GENIE-VICC Panel - 34 Genes, Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb, Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb, Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb, Custom SureSelect GENIE-UHN Panel - 555 Genes, Custom SureSelect Human All Exon v1.1 Plus 3 Boosters, Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb, Custom Twist Broad Exome v1.0 - 35.0 Mb, Custom Twist Broad PanCancer Panel - 396 Genes, Foundation Medicine T5a Panel - 322 Genes, Foundation Medicine T7 Panel - 429 Genes, Ion AmpliSeq Cancer Hotspot Panel v2, Ion AmpliSeq Comprehensive Cancer Panel, Nextera DNA Exome, Nextera Rapid Capture Exome v1.2, SeqCap EZ HGSC VCRome v2.1, SeqCap EZ Human Exome v2.0, SeqCap EZ Human Exome v3.0, SureSelect Human All Exon v3, SureSelect Human All Exon v4, SureSelect Human All Exon v5, SureSelect Human All Exon v5 + UTR, TruSeq Amplicon Cancer Panel, TruSeq Exome Enrichment - 62 Mb, TruSeq RNA Exome, TruSight Myeloid Sequencing Panel, xGen Exome Research Panel v1.0, Unknown",,,TRUE,Sequencing,,, -Library Selection Method,How RNA molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Poly-T Enrichment, Random, rRNA Depletion, miRNA Size Fractionation, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Adapter Name,Name of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Adapter Sequence,Base sequence of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Base Caller Name,Name of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Base Caller Version,Version of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Flow Cell Barcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Fragment Maximum Length,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Fragment Mean Length,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Fragment Minimum Length,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Fragment Standard Deviation Length,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Lane Number,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Strand,Library stranded-ness.,"Unstranded, First Stranded, Second Stranded, Not Applicable",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Multiplex Barcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Size Selection Range,Range of size selection. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Target Depth,The targeted read depth prior to sequencing. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -To Trim Adapter Sequence,Does the user suggest adapter trimming?,"Yes - Trim Adapter Sequence, No",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Yes - Trim Adapter Sequence,Trim adapter sequence,"Adapter Trimmer Name, Adapter Trimmer Version, Adapter Trimmer Options",,,FALSE,Sequencing,,, -Adapter Trimmer Name,Name of adapter trimmer,,,,FALSE,Sequencing,,, -Adapter Trimmer Version,Version of the adapter trimmer,,,,FALSE,Sequencing,,, -Adapter Trimmer Options,Options used by adapter trimmer,,,,FALSE,Sequencing,,, -Transcript Integrity Number (TIN),"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Adapter Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Basic Statistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Encoding,Version of ASCII encoding of quality values found in the file. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Kmer Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Overrepresented Sequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Base N Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Base Sequence Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Base Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Sequence GC Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Sequence Quality Score,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Per Tile Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Percent GC Content,The overall %GC of all bases in all sequences. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Sequence Duplication Levels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Sequence Length Distribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Total Reads,Total number of reads per sample. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -White-list Cell Barcode File Link,Link to file listing all possible cell barcodes. URL,,,,TRUE,Sequencing,,, -Cell Barcode Tag,SAM tag for cell barcode field; please provide a valid cell barcode tag,,,,TRUE,Sequencing,,, -UMI Tag,"SAM tag for UMI field; please provide a valid UB, UMI",,,,TRUE,Sequencing,,, -Applied Hard Trimming,"Yes - Applied Hard Trimming, No",,,,TRUE,Sequencing,,, -Yes - Applied Hard Trimming,,,Aligned Read Length,,FALSE,Sequencing,,, -Aligned Read Length,Read length used for alignment if hard trimming was applied,,,,TRUE,Sequencing,,, -scRNA-seq Workflow Type,Generic name for the workflow used to analyze a data set.,"CellRanger, STARsolo, HCA Optimus, dropEST, SEQC, Cufflinks, DEXSeq, HTSeq - FPKM, Cell annotation, Differentiation trajectory analysis, Other",,,TRUE,Sequencing,,, -Workflow Type,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,, -Workflow Version,Major version of the workflow (e.g. Cell Ranger v3.1),,,,TRUE,Sequencing,,, -scRNA-seq Workflow Parameters Description,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",,,,TRUE,Sequencing,,, -Workflow Parameters Description,Parameters used to run the workflow.,,,,TRUE,Sequencing,,, -Workflow Link,Link to workflow or command. DockStore.org recommended. URL,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow, -Workflow Start Date-time,A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm],,,,FALSE,Sequencing,,, -Workflow End Date-time,A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm],,,,FALSE,Sequencing,,, -QC Workflow Type,Generic name for the workflow used to analyze a data set. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -QC Workflow Version,Major version for a workflow. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -QC Workflow Link,Link to workflow used. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Germline Variants Workflow URL,"Link to workflow document, e.g. Github, DockStore.org recommended",,,,TRUE,Sequencing,,, -Germline Variants Workflow Type,Generic name for the workflow used to analyze a data set,"GATK4, Other",,,TRUE,Sequencing,,, -Somatic Variants Workflow URL,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,, -Somatic Variants Workflow Type,Generic name for the workflow used to analyze a data set.,"CaVEMan, GATK4, MuTect2, MuSE, MuTect2, Pindel, SomaticSniper, VarScan2",,,TRUE,Sequencing,,, -Somatic Variants Sample Type,Is the sample case or control in somatic variant analysis,"Case Sample, Control Sample",,,TRUE,Sequencing,,, -Structural Variant Workflow URL,Link to workflow document. DockStore.org recommended. URL,,,,TRUE,Sequencing,,, -Structural Variant Workflow Type,Generic name for the workflow used to analyze a data set.,"BRASS, GATK4, CNV, CNVkit",,,TRUE,Sequencing,,, -Alignment Workflow Url,Link to workflow used for read alignment. DockStore.org recommended. String,,,,TRUE,Sequencing,,, -Alignment Workflow Type,Generic name for the workflow used to analyze a data set.,"BWA, BWA with BQSR, BWA-aln, BWA-mem, BWA with Mark Duplicates and BQSR, STAR 2-Pass, STAR 2-Pass Chimeric, STAR 2-Pass Genome, STAR 2-Pass Transcriptome",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, -MSI Workflow Link,Link to method workflow (or command) used in estimating the MSI. URL,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -MSI Score,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,,,,FALSE,Sequencing,,, -MSI Status,MSIsensor determination of either microsatellite stability or instability.,"MSI, MSI-low, MSI-high, MSS",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). URL,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, -Genomic Reference URL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),,,,TRUE,Sequencing,,, -Genome Annotation URL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),,,,TRUE,Sequencing,,, -Index File Name,The name (or part of a name) of a file (of any type). String,,,,TRUE,Sequencing,,, -Average Base Quality,Average base quality collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads_index, -Average Insert Size,Average insert size collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Average Read Length,Average read length collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Contamination Error,Estimation error of cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Mean Coverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Pairs On Diff CHR,Pairs on different chromosomes collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Total Uniquely Mapped,Number of reads that map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Total Unmapped reads,Number of reads that did not map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Proportion Reads Duplicated,Proportion of duplicated reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Proportion Reads Mapped,Proportion of mapped reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Proportion Targets No Coverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Proportion Base Mismatch,Proportion of mismatched bases collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Proportion Coverage 10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",,,,FALSE,Sequencing,,, -Proportion Coverage 30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",,,,FALSE,Sequencing,,, -Short Reads,Number of reads that were too short. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, -Pseudo Alignment Used,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,"Yes - Pseudo Alignment Used, No",,,TRUE,Sequencing,,, -Software and Version,Name of software used to generate expression values. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow, -Yes - Pseudo Alignment Used,Pseudo aligner was used,,"Workflow Link, Software and Version, Genomic Reference, Genomic Reference URL",,FALSE,Sequencing,,, -Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),,,,TRUE,Sequencing,,, -Genomic Reference URL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],,,,TRUE,Sequencing,,, -Data Category,Specific content type of the data file.,"Gene Expression, Transcript Expression, Exon Expression Quantification, Gene Expression Quantification, Isoform Expression Quantification, Splice Junction Quantification, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=gene_expression, -Expression Units,How quantities are corrected for gene length,"TPM, RPKM, FPKM, Counts, Other, NA",,,TRUE,Sequencing,,, -Fusion Gene Detected,Was a fusion gene identified?,"Yes - Fusion Gene Detected, No, Unknown",,,FALSE,Sequencing,,, -Yes - Fusion Gene Detected,A fusion gene was detected,,Fusion Gene Identity,,FALSE,Sequencing,,, -Fusion Gene Identity,The gene symbols of fused genes.,"EWS-FLI, EWS-ERG, SYT-SSX1, SYT-SSX2, EWS-WT1, Other Fusion Gene",,,FALSE,Sequencing,,,list -Other Fusion Gene,Other fusion gene detected.,,Specify Other Fusion Gene,,FALSE,Sequencing,,, -Specify Other Fusion Gene,"Specify fusion gene detected, if not in list",,,,FALSE,Sequencing,,, -Matrix Type,Type of data stored in matrix.,"Raw Counts, Normalized Counts, Scaled Counts, Batch Corrected Counts",,,TRUE,Sequencing,,, -Linked Matrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,,,,FALSE,Sequencing,,, -Biospecimen Type,Biospecimen Type,"Tissue Biospecimen Type, Blood Biospecimen Type, Analyte Biospecimen Type, Mouth Rinse Biospecimen Type, Stool Biospecimen Type, Urine Biospecimen Type, Ascites Biospecimen Type, Sputum Biospecimen Type, Fluids Biospecimen Type, Bone Marrow Biospecimen Type, Cells Biospecimen Type",,,TRUE,Biospecimen,,, -Analyte Biospecimen Type,A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,,"Analyte Type, Fixation Duration, Slide Charge Type, Section Thickness Value, Sectioning Days from Index, Shipping Condition Type, Ischemic Time, Ischemic Temperature",,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0, -Tissue Biospecimen Type,Tissue biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, -Bone Marrow Biospecimen Type,Bone Marrow biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, -Urine Biospecimen Type,Urine biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, -Blood Biospecimen Type,Blood biospecimen,,Shipping Condition Type,,FALSE,Biospecimen,,, -Timepoint Label,"Label to identify the time point at which the biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",,,,TRUE,Biospecimen,,, -Collection Days from Index,Number of days from the research participant's index date that the biospecimen was obtained.,,,,TRUE,Biospecimen,,, -Protocol Link,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",,,,TRUE,Information Content Entity,,, -Adjacent Biospecimen ID,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",,,,FALSE,Biospecimen,,, -Mounting Medium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media","Aqueous water based, Non-Aqueous Solvent based, Xylene,Toluene,Antifade with DAPI,Antifade without DAPI,PBS,Unknown,Not Reported",,,FALSE,Biospecimen,,, -Analyte Type,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0, -Acquisition Method Type,Records the method of acquisition or source for the specimen under consideration.,"Autopsy, Biopsy, Fine Needle Aspirate, Surgical Resection, Punch Biopsy, Shave Biopsy, Excision, Re-excision, Sentinel Node Biopsy, Lymphadenectomy - Regional Nodes, Other Acquisition Method, Not specified",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6626651&version=1.0, -Other Acquisition Method,A custom acquisition method,,Acquisition Method Other Specify,,FALSE,Biospecimen,,, -Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],,,,TRUE,Biospecimen,,, -Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, Unknown, Not Reported",,,TRUE,Biospecimen,,, -Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Other, None, Unknown",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=65078&version=3.0, -Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5230144&version=1.0, -Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",,,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, -Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20 Deg C Dry Ice, Liquid Nitrogen",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, -Collection Media,Material Specimen is collected into post procedure,"DMEM, DMEM+Serum, RPMI, RPMI+Serum, PBS, PBS+Serum",,,FALSE,Biospecimen,,, -Specimen Laterality,"For tumors in paired organs, designates the side on which the specimen was obtained.","Bilateral, Left, Right, Unknown, Not Reported, Not Applicable",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=1.0, -Portion Weight,"Numeric value that represents the sample portion weight, measured in milligrams.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432593&version=1.0, -Total Volume,"Numeric value for the total amount of sample or specimen, measured in milliliters (mL).",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3005019&version=1.0, -Tumor Tissue Type,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0, -Histologic Morphology Code,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0, -Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other",,,FALSE,Biospecimen,,, -Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5227611&version=1.0, -Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3024951&version=1.0, -Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection,,,,TRUE,Biospecimen,,, -Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Raraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, Unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method, -Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed,,,,TRUE,Biospecimen,,, -Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Other Shipping Environment, Specimen at Room Temperature",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5495533&version=1.0, -Site Data Source,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",,,,FALSE,Biospecimen,,, -Processing Location,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",,,,FALSE,Biospecimen,,, -Histology Assessment By,Text term describing who (in what role) made the histological assessments of the sample,"Pathologist, Research Scientist, Other, Unknown",,,FALSE,Biospecimen,,, -Histology Assessment Medium,The method of assessment used to characterize histology,"Digital, Microscope, Other, Unknown",,,FALSE,Biospecimen,,, -Tumor Infiltrating Lymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],,,,FALSE,Biospecimen,,, -Degree of Dysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,"Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, Unknown",,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5543188&version=1.0, -Dysplasia Fraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2390593&version=1.0, -Number Proliferating Cells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432636&version=1.0, -Percent Eosinophil Infiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897700&version=2.0, -Percent Granulocyte Infiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897705&version=2.0, -Percent Inflam Infiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897695&version=1.0, -Percent Lymphocyte Infiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897710&version=2.0, -Percent Monocyte Infiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5455535&version=1.0, -Percent Necrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841237&version=1.0, -Percent Neutrophil Infiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0, -Percent Normal Cells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0, -Percent Stromal Cells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841241&version=1.0, -Percent Tumor Cells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432686&version=1.0, -Percent Tumor Nuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841225&version=1.0, -Fiducial Marker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,"Nuclear Stain - DAPI, Fluorescent Beads, Grid Slides - Hemocytometer, Adhesive Markers, Other, Unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi, -Slicing Method,Imaging specific: the method by which the tissue was sliced.,"Vibratome, Cryosectioning, Tissue molds, Sliding microtome, Sectioning, Other, Unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi, -Antigen Retrieval ,"Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64676&version=3.0, -Biospecimen Slide Location,Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable,,,,FALSE,Biospecimen,,, -Staining Markers,Imaging specific: text to identify proteins/ antibodies selected for staining,,,,FALSE,Biospecimen,,, -Lysis Buffer,scRNA-seq specific: Type of lysis buffer used,,,,FALSE,Biospecimen,,, -Method of Nucleic Acid Isolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",,,,FALSE,Biospecimen,,, -Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, Unknown, not reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0, -Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, not reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0, -Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, Unknown, not reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0, -Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, Unknown, Not Reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5&version=5.0, -Dead,This indicates the participant is dead and defines further required metadata,,"Year of Death, Cause of Death, Cause of Death Source, Days to Death",,FALSE,Demographics,,, -Days to Birth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,,,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154723&version=1.0, -Year of Death,Numeric value to represent the year of the death of an individual.,Not Applicable,,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897030&version=1.0, -Age at Index,For GDC submission only - this is going to be always 0 since HTAN's index is the date of birth,null,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6028530&version=1.0, -Age Is Obfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,"true, false",,,FALSE,Demographics,,, -Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,null,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896954&version=1.0, -Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, Unknown, Not Applicable",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2554674&version=3.0, -Cause of Death Source,The text term used to describe the source used to determine the patient's cause of death.,"Autopsy, Death Certificate, Medical Record, Social Security Death Index, Unknown, Not Reported",,,FALSE,Demographics,,, -Days to Death,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154724&version=1.0, -Occupation Duration Years,The number of years a patient worked in a specific occupation.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2435424&version=1.0, -Premature At Birth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,"Yes, No, Unknown, Not Reported",,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6010765&version=1.0, -Weeks Gestation at Birth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2737369&version=1.0, -Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161021&version=1.0, -Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,,,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5300571&version=1.0, -Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, Unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161022&version=1.0, -Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son, Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister, Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, Unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2690165&version=2.0, -Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, Unknown, Not reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161023&version=1.0, -Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,,,,FALSE,Family History,,, -Yes - Cancer History Relative,Individual has a relative with cancer history,,"Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis",,FALSE,Family History,,, -Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported",,,TRUE,Exposure,,, -Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,,"Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used",,FALSE,Exposure,,, -Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2955385&version=1.0, -Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3137957&version=1.0, -Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported",,,TRUE,Exposure,,, -Yes - Alcohol Exposure,,,"Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity",,FALSE,Exposure,,, -Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3114013&version=1.0, -Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3124961&version=1.0, -Alcohol History,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2201918&version=1.0, -Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3457767&version=1.0, -Asbestos Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=1253&version=3.0, -Cigarettes per Day,The average number of cigarettes smoked per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2001716&version=4.0, -Coal Dust Exposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,"Yes, No, Unknown",,,FALSE,Exposure,,, -Environmental Tobacco Smoke Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.","Yes, No, Unknown",,,FALSE,Exposure,,, -Radon Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2816352&version=1.0, -Respirable Crystalline Silica Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.","Yes, No, Unknown",,,FALSE,Exposure,,, -Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, Unknown",,,FALSE,Exposure,,, -Time Between Waking and First Smoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,"Within 5 Minutes, 6-30 Minutes, 31-60 Minutes, After 60 Minutes, Unknown",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3279220&version=1.0, -Tobacco Smoking Onset Year,The year in which the participant began smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228604&version=1.0, -Tobacco Smoking Quit Year,The year in which the participant quit smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228610&version=1.0, -Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2181650&version=1.0, -Type of Smoke Exposure,The text term used to describe the patient's specific type of smoke exposure.,"Accidental building fire smoke,Accidental grass fire smoke, Accidental fire smoke NOS,Accidental forest fire smoke,Accidental vehicle fire smoke,Aircraft smoke,Burning tree smoke,Coal smoke NOS, Cooking related smoke NOS,Electronic cigarette smoke NOS,Electrical fire smoke,Environmental tobacco smoke,Factory smokestack smoke,Field burning smoke,Fire smoke NOS,Furnace or boiler smoke,Gas burning smoke propane,Grease fire smoke,Grilling smoke,Hashish smoke,Indoor coal burning stove or fireplace smoke,Indoor stove or fireplace smoke NOS,Indoor wood burning stove or fireplace smoke,Machine smoke,Marijuana smoke,No Smoke Exposure,Oil burning smoke Kerosene,Oil burning smoke NOS,Recreational fire smoke,Smoke exposure NOS,Smokehouse smoke,Tobacco smoke cigar,Tobacco smoke cigarettes,Tobacco smoke pipe,Unknown,Volcanic smoke,Waste burning smoke,Wood burning smoke factory,Wood burning smoke NOS, Workrelated smoke artificial smoke machines, Workrelated smoke fire fighting,Workrelated smoke foundry,Workrelated smoke generators,Workrelated smoke military,Workrelated smoke NOS,Workrelated smoke paint baking,Workrelated smoke plastics factory,Workrelated smoke plumbing,Workrelated smoke soldering/welding",,,FALSE,Exposure,,, -Type of Tobacco Used,The text term used to describe the specific type of tobacco used by the patient.,"Cigarettes, Cigar, Electronic Cigarette, Other, Pipe, Smokeless Tobacco",,,FALSE,Exposure,,, -Days to Follow Up,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154727&version=1.0, -Adverse Event,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,"Abdominal Distension, Abdominal Infection,Abdominal Pain,Abdominal Soft Tissue Necrosis,Abducens Nerve Disorder,Accessory Nerve Disorder,Acidosis,Acoustic Nerve Disorder NOS,Activated Partial Thromboplastin Time Prolonged,Acute Coronary Syndrome,Acute Kidney Injury,Adrenal Insufficiency,Adult Respiratory Distress Syndrome, Agitation, Akathisia, Alanine Aminotransferase Increased,Alcohol Intolerance,Alkaline Phosphatase Increased,Alkalosis,Allergic Reaction,Allergic Rhinitis, Alopecia, Amnesia,Anal Fistula,Anal Hemorrhage,Anal Mucositis, Anal Necrosis,Anal Pain,Anal Stenosis,Anal Ulcer,Anaphylaxis,Anemia,Ankle Fracture,Anorectal Infection,Anorexia,Anorgasmia,Anxiety,Aortic Injury,Aortic Valve Disease,Aphonia,Apnea,Appendicitis,Appendicitis Perforated,Arachnoiditis,Arterial Injury,Arteritis Infective,Arthralgia,Arthritis,Ascites,Aspartate Aminotransferase Increased,Aspiration,Asystole,Ataxia,Atelectasis,Atrial Fibrillation,Atrial Flutter,Atrioventricular Block Complete,Atrioventricular Block First Degree,Autoimmune Disorder,Avascular Necrosis,Azoospermia,Back Pain,Bile Duct Stenosis,Biliary Anastomotic Leak,Biliary Fistula,Biliary Tract Infection,Bladder Anastomotic Leak,Bladder Infection,Bladder Perforation,Bladder Spasm,Bloating,Blood and Lymphatic System Disorders Other,Blood Antidiuretic Hormone Abnormal,Blood Bilirubin Increased,Blood Corticotrophin Decreased,Blood Gonadotrophin Abnormal,Blood Prolactin Abnormal,Blurred Vision,Body Odor,Bone Infection,Bone Marrow Hypocellular,Bone Pain,Brachial Plexopathy,Breast Atrophy,Breast Infection,Breast Pain,Bronchial Fistula,Bronchial Infection,Bronchial Obstruction,Bronchial Stricture,Bronchopleural Fistula,Bronchopulmonary Hemorrhage,Bronchospasm,Bruising,Bullous Dermatitis,Burn,Buttock Pain,Capillary Leak Syndrome,Carbon Monoxide Diffusing Capacity Decreased,Cardiac Arrest,Cardiac Disorders Other,Cardiac Troponin I Increased,Cardiac Troponin T Increased,Cataract,Catheter Related Infection,CD4 Lymphocytes Decreased,Cecal Hemorrhage,Cecal Infection,Central Nervous System Necrosis,Cerebrospinal Fluid Leakage,Cervicitis Infection,Cheilitis,Chest Pain Cardiac,Chest Wall Pain,Chills,Cholecystitis,Cholesterol High,Chronic Kidney Disease,Chylothorax,Cognitive Disturbance,Colitis,Colonic Fistula,Colonic Hemorrhage,Colonic Obstruction,Colonic Perforation,Colonic Stenosis,Colonic Ulcer,Concentration Impairment,Conduction Disorder,Confusion,Congenital, Familial and Genetic Disorders Other,Conjunctivitis,Conjunctivitis Infective,Constipation,Constrictive Pericarditis,Corneal Infection,Corneal Ulcer,Cough,CPK Increased,Cranial Nerve Infection,Creatinine Increased,Cushingoid,Cystitis Noninfective,Cytokine Release Syndrome,Death Neonatal,Death NOS,Dehydration,Delayed Orgasm,Delayed Puberty,Delirium,Delusions,Dental Caries,Depressed Level of Consciousness,Depression,Dermatitis Radiation,Device Related Infection,Diarrhea,Disseminated Intravascular Coagulation,Dizziness,Dry Eye,Dry Mouth,Dry Skin,Duodenal Fistula,Duodenal Hemorrhage,Duodenal Infection,Duodenal Obstruction,Duodenal Perforation,Duodenal Stenosis,Duodenal Ulcer,Dysarthria,Dysesthesia,Dysgeusia,Dysmenorrhea,Dyspareunia,Dyspepsia,Dysphagia,Dysphasia,Dyspnea,Ear and Labyrinth Disorders Other,Ear Pain,Edema Cerebral,Edema Face,Edema Limbs,Edema Trunk,Ejaculation Disorder,Ejection Fraction Decreased,Electrocardiogram QT Corrected Interval Prolonged,Encephalitis Infection,Encephalomyelitis Infection,Encephalopathy,Endocarditis Infective,Endocrine Disorders Other,Endophthalmitis,Enterocolitis,Enterocolitis Infectious,Enterovesical Fistula,Epistaxis,Erectile Dysfunction,Erythema Multiforme,Erythroderma,Esophageal Anastomotic Leak,Esophageal Fistula,Esophageal Hemorrhage,Esophageal Infection,Esophageal Necrosis,Esophageal Obstruction,Esophageal Pain,Esophageal Perforation,Esophageal Stenosis,Esophageal Ulcer,Esophageal Varices Hemorrhage,Esophagitis,Euphoria,Exostosis,External Ear Inflammation,External Ear Pain,Extraocular Muscle Paresis,Extrapyramidal Disorder,Eye Disorders Other,Eye Infection,Eye Pain,Eyelid Function Disorder,Facial Muscle Weakness,Facial Nerve Disorder,Facial Pain,Fall,Fallopian Tube Anastomotic Leak,Fallopian Tube Obstruction,Fallopian Tube Perforation,Fallopian Tube Stenosis,Fat Atrophy,Fatigue,Febrile Neutropenia,Fecal Incontinence,Female Genital Tract Fistula,Feminization Acquired,Fetal Death,Fetal Growth Retardation,Fever,Fibrinogen Decreased,Fibrosis Deep Connective Tissue,Flank Pain,Flashing Lights,Flatulence,Floaters,Flu Like Symptoms,Flushing,Forced Expiratory Volume Decreased,Fracture,Gait Disturbance,Gallbladder Fistula,Gallbladder Infection,Gallbladder Necrosis,Gallbladder Obstruction,Gallbladder Pain,Gallbladder Perforation,Gastric Anastomotic Leak,Gastric Fistula,Gastric Hemorrhage,Gastric Necrosis,Gastric Perforation,Gastric Stenosis,Gastric Ulcer,Gastritis,Gastroesophageal Reflux Disease,Gastrointestinal Anastomotic Leak,Gastrointestinal Disorders Other,Gastrointestinal Fistula,Gastrointestinal Pain,Gastrointestinal Stoma Necrosis,Gastroparesis,General Disorders and Administration Site Conditions Other,Generalized Muscle Weakness,Genital Edema,GGT Increased,Gingival Pain,Glaucoma,Glossopharyngeal Nerve Disorder,Glucose Intolerance,Growth Accelerated,Growth Hormone Abnormal,Growth Suppression,Gum Infection,Gynecomastia,Hallucinations,Haptoglobin Decreased,Head Soft Tissue Necrosis,Headache,Hearing Impaired,Heart Failure,Hematoma,Hematosalpinx,Hematuria,Hemoglobin Increased,Hemoglobinuria,Hemolysis,Hemolytic Uremic Syndrome,Hemorrhoidal Hemorrhage,Hemorrhoids,Hepatic Failure,Hepatic Hemorrhage,Hepatic Infection,Hepatic Necrosis,Hepatic Pain,Hepatitis Viral,Hepatobiliary Disorders Other,Hiccups,Hip Fracture,Hirsutism,Hoarseness,Hot Flashes,Hydrocephalus,Hypercalcemia,Hyperglycemia,Hyperhidrosis,Hyperkalemia,Hypermagnesemia,Hypernatremia,Hyperparathyroidism,Hypersomnia,Hypertension,Hyperthyroidism,Hypertrichosis,Hypertriglyceridemia,Hyperuricemia,Hypoalbuminemia,Hypocalcemia,Hypoglossal Nerve Disorder,Hypoglycemia,Hypohidrosis,Hypokalemia,Hypomagnesemia,Hyponatremia,Hypoparathyroidism,Hypophosphatemia,Hypotension,Hypothermia,Hypothyroidism,Hypoxia,Ileal Fistula,Ileal Hemorrhage,Ileal Obstruction,Ileal Perforation,Ileal Stenosis,Ileal Ulcer,Ileus,Immune System Disorders Other,Infections and Infestations Other,Infective Myositis,Infusion Related Reaction,Infusion Site Extravasation,Injection Site Reaction,Injury to Carotid Artery,Injury to Inferior Vena Cava,Injury to Jugular Vein,Injury to Superior Vena Cava,Injury, Poisoning and Procedural Complications Other,INR Increased,Insomnia,Intestinal Stoma Leak,Intestinal Stoma Obstruction,Intestinal Stoma Site Bleeding,Intra-Abdominal Hemorrhage,Intracranial Hemorrhage,Intraoperative Arterial Injury,Intraoperative Breast Injury,Intraoperative Cardiac Injury,Intraoperative Ear Injury,Intraoperative Endocrine Injury,Intraoperative Gastrointestinal Injury,Intraoperative Head and Neck Injury,Intraoperative Hemorrhage,Intraoperative Hepatobiliary Injury,Intraoperative Musculoskeletal Injury,Intraoperative Neurological Injury,Intraoperative Ocular Injury,Intraoperative Renal Injury,Intraoperative Reproductive Tract Injury,Intraoperative Respiratory Injury,Intraoperative Skin Injury,Intraoperative Splenic Injury,Intraoperative Urinary Injury,Intraoperative Venous Injury,Investigations Other,Iron Overload,Irregular Menstruation,Irritability,Ischemia Cerebrovascular,IVth Nerve Disorder,Jejunal Fistula,Jejunal Hemorrhage,Jejunal Obstruction,Jejunal Perforation,Jejunal Stenosis,Jejunal Ulcer,Joint Effusion,Joint Infection,Joint Range of Motion Decreased,Joint Range of Motion Decreased Cervical Spine,Joint Range of Motion Decreased Lumbar Spine,Keratitis,Kidney Anastomotic Leak,Kidney Infection,Kyphosis,Lactation Disorder,Large Intestinal Anastomotic Leak,Laryngeal Edema,Laryngeal Fistula,Laryngeal Hemorrhage,Laryngeal Inflammation,Laryngeal Mucositis,Laryngeal Obstruction,Laryngeal Stenosis,Laryngitis,Laryngopharyngeal Dysesthesia,Laryngospasm,Left Ventricular Systolic Dysfunction,Lethargy,Leukemia Secondary to Oncology Chemotherapy,Leukocytosis,Leukoencephalopathy,Libido Decreased,Libido Increased,Lip Infection,Lip Pain,Lipase Increased,Lipohypertrophy,Localized Edema,Lordosis,Lower Gastrointestinal Hemorrhage,Lung Infection,Lymph Gland Infection,Lymph Leakage,Lymph Node Pain,Lymphedema,Lymphocele,Lymphocyte Count Decreased,Lymphocyte Count Increased,Malabsorption,Malaise,Mania,Mediastinal Hemorrhage,Mediastinal Infection,Memory Impairment,Meningismus,Meningitis,Menopause,Menorrhagia,Metabolism and Nutrition Disorders Other,Middle Ear Inflammation,Mitral Valve Disease,Mobitz (Type) II Atrioventricular Block,Mobitz Type I,Movements Involuntary,Mucosal Infection,Mucositis Oral,Multi-Organ Failure,Muscle Weakness Left-Sided,Muscle Weakness Lower Limb,Muscle Weakness Right-Sided,Muscle Weakness Trunk,Muscle Weakness Upper Limb,Musculoskeletal and Connective Tissue Disorders Other,Musculoskeletal Deformity,Myalgia,Myelitis,Myelodysplastic Syndrome,Myocardial Infarction,Myocarditis,Myositis,Nail Discoloration,Nail Infection,Nail Loss,Nail Ridging,Nasal Congestion,Nausea,Neck Edema,Neck Pain,Neck Soft Tissue Necrosis,Neoplasms Benign, Malignant and Unspecified (Incl Cysts and Polyps) Other,Nervous System Disorders Other,Neuralgia,Neutrophil Count Decreased,Night Blindness,Nipple Deformity,Non-Cardiac Chest Pain,Nystagmus,Obesity,Obstruction Gastric,Oculomotor Nerve Disorder,Olfactory Nerve Disorder,Oligospermia,Optic Nerve Disorder,Oral Cavity Fistula,Oral Dysesthesia,Oral Hemorrhage,Oral Pain,Osteonecrosis of Jaw,Osteoporosis,Otitis Externa,Otitis Media,Ovarian Hemorrhage,Ovarian Infection,Ovarian Rupture,Ovulation Pain,Pain,Pain in Extremity,Pain of Skin,Palmar-Plantar Erythrodysesthesia Syndrome,Palpitations,Pancreas Infection,Pancreatic Anastomotic Leak,Pancreatic Duct Stenosis,Pancreatic Enzymes Decreased,Pancreatic Fistula,Pancreatic Hemorrhage,Pancreatic Necrosis,Pancreatitis,Papilledema,Papulopustular Rash,Paresthesia,Paronychia,Paroxysmal Atrial Tachycardia,Pelvic Floor Muscle Weakness,Pelvic Infection,Pelvic Pain,Pelvic Soft Tissue Necrosis,Penile Infection,Penile Pain,Perforation Bile Duct,Pericardial Effusion,Pericardial Tamponade,Pericarditis,Perineal Pain,Periodontal Disease,Periorbital Edema,Periorbital Infection,Peripheral Ischemia,Peripheral Motor Neuropathy,Peripheral Nerve Infection,Peripheral Sensory Neuropathy,Peritoneal Infection,Peritoneal Necrosis,Personality Change,Phantom Pain,Pharyngeal Anastomotic Leak,Pharyngeal Fistula,Pharyngeal Hemorrhage,Pharyngeal Mucositis,Pharyngeal Necrosis,Pharyngeal Stenosis,Pharyngitis,Pharyngolaryngeal Pain,Phlebitis,Phlebitis Infective,Photophobia,Photosensitivity,Platelet Count Decreased,Pleural Effusion,Pleural Hemorrhage,Pleural Infection,Pleuritic Pain,Pneumonitis,Pneumothorax,Portal Hypertension,Portal Vein Thrombosis,Postnasal Drip,Postoperative Hemorrhage,Postoperative Thoracic Procedure Complication,Precocious Puberty,Pregnancy, Puerperium and Perinatal Conditions Other,Premature Delivery,Premature Menopause,Presyncope,Proctitis,Productive Cough,Prolapse of Intestinal Stoma,Prolapse of Urostomy,Prostate Infection,Prostatic Hemorrhage,Prostatic Obstruction,Prostatic Pain,Proteinuria,Pruritus,Psychiatric Disorders Other,Psychosis,Pulmonary Edema,Pulmonary Fibrosis,Pulmonary Fistula,Pulmonary Hypertension,Pulmonary Valve Disease,Purpura,Pyramidal Tract Syndrome,Radiation Recall Reaction (Dermatologic),Radiculitis,Rash Acneiform,Rash Maculo-Papular,Rash Pustular,Rectal Anastomotic Leak,Rectal Fistula,Rectal Hemorrhage,Rectal Mucositis,Rectal Necrosis,Rectal Obstruction,Rectal Pain,Rectal Perforation,Rectal Stenosis,Rectal Ulcer,Recurrent Laryngeal Nerve Palsy,Renal and Urinary Disorders Other,Renal Calculi,Renal Colic,Renal Hemorrhage,Reproductive System and Breast Disorders Other,Respiratory Failure,Respiratory, Thoracic and Mediastinal Disorders Other,Restlessness,Restrictive Cardiomyopathy,Retinal Detachment,Retinal Tear,Retinal Vascular Disorder,Retinoic Acid Syndrome,Retinopathy,Retroperitoneal Hemorrhage,Reversible Posterior Leukoencephalopathy Syndrome,Rhinitis Infective,Right Ventricular Dysfunction,Salivary Duct Inflammation,Salivary Gland Fistula,Salivary Gland Infection,Scalp Pain,Scleral Disorder,Scoliosis,Scrotal Infection,Scrotal Pain,Seizure,Sepsis,Seroma,Serum Amylase Increased,Serum Sickness,Sick Sinus Syndrome,Sinus Bradycardia,Sinus Disorder,Sinus Pain,Sinus Tachycardia,Sinusitis,Skin and Subcutaneous Tissue Disorders Other,Skin Atrophy,Skin Hyperpigmentation,Skin Hypopigmentation,Skin Induration,Skin Infection,Skin Ulceration,Sleep Apnea,Small Intestinal Anastomotic Leak,Small Intestinal Mucositis,Small Intestinal Obstruction,Small Intestinal Perforation,Small Intestinal Stenosis,Small Intestine Infection,Small Intestine Ulcer,Sneezing,Social Circumstances Other,Soft Tissue Infection,Soft Tissue Necrosis Lower Limb,Soft Tissue Necrosis Upper Limb,Somnolence,Sore Throat,Spasticity,Spermatic Cord Anastomotic Leak,Spermatic Cord Hemorrhage,Spermatic Cord Obstruction,Spinal Fracture,Spleen Disorder,Splenic Infection,Stenosis of Gastrointestinal Stoma,Stevens-Johnson Syndrome,Stoma Site Infection,Stomach Pain,Stomal Ulcer,Stridor,Stroke,Sudden Death NOS,Suicidal Ideation,Suicide Attempt,Superficial Soft Tissue Fibrosis,Superficial Thrombophlebitis,Superior Vena Cava Syndrome,Supraventricular Tachycardia,Surgical and Medical Procedures Other,Syncope,Telangiectasia,Testicular Disorder,Testicular Hemorrhage,Testicular Pain,Thromboembolic Event,Thrombotic Thrombocytopenic Purpura,Tinnitus,Tooth Development Disorder,Tooth Discoloration,Tooth Infection,Toothache,Toxic Epidermal Necrolysis,Tracheal Fistula,Tracheal Hemorrhage,Tracheal Mucositis,Tracheal Obstruction,Tracheal Stenosis,Tracheitis,Tracheostomy Site Bleeding,Transient Ischemic Attacks,Treatment Related Secondary Malignancy,Tremor,Tricuspid Valve Disease,Trigeminal Nerve Disorder,Trismus,Tumor Lysis Syndrome,Tumor Pain,Typhlitis,Unequal Limb Length,Unintended Pregnancy,Upper Gastrointestinal Hemorrhage,Upper Respiratory Infection,Ureteric Anastomotic Leak,Urethral Anastomotic Leak,Urethral Infection,Urinary Fistula,Urinary Frequency,Urinary Incontinence,Urinary Retention,Urinary Tract Infection,Urinary Tract Obstruction,Urinary Tract Pain,Urinary Urgency,Urine Discoloration,Urine Output Decreased,Urostomy Leak,Urostomy Obstruction,Urostomy Site Bleeding,Urostomy Stenosis,Urticaria,Uterine Anastomotic Leak,Uterine Fistula,Uterine Hemorrhage,Uterine Infection,Uterine Obstruction,Uterine Pain,Uterine Perforation,Uveitis,Vaginal Anastomotic Leak,Vaginal Discharge,Vaginal Dryness,Vaginal Fistula,Vaginal Hemorrhage,Vaginal Infection,Vaginal Inflammation,Vaginal Obstruction,Vaginal Pain,Vaginal Perforation,Vaginal Stricture,Vaginismus,Vagus Nerve Disorder,Vas Deferens Anastomotic Leak,Vascular Access Complication,Vascular Disorders Other,Vasculitis,Vasovagal Reaction,Venous Injury,Ventricular Arrhythmia,Ventricular Fibrillation,Ventricular Tachycardia,Vertigo,Vestibular Disorder,Virilization,Visceral Arterial Ischemia,Vital Capacity Abnormal,Vitreous Hemorrhage,Voice Alteration,Vomiting,Vulval Infection,Watering Eyes,Weight Gain,Weight Loss,Wheezing,White Blood Cell Decreased,Wolff-Parkinson-White Syndrome,Wound Complication,Wound Dehiscence,Wound Infection,Wrist Fracture",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3125302&version=1.1, -BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2006410&version=3.0, -Cause of Response,The text term used to describe the suspected cause or reason for the patient disease response.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161025&version=1.0, -Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.","Acute Renal Failure, Adenocarcinoma, Adrenocortical Insufficiency, Adenomatous Polyposis Coli, Allergies, Alpha-1 Antitrypsin, Anemia, Anxiety, Arrhythmia, Arthritis, Asthma, Atrial Fibrillation, Avascular Necrosis, Barrett's Esophagus,Basal Cell Carcinoma, Beckwith-Wiedemann, Behcet's Disease, Biliary Disorder, Blood Clots, Bone Fracture(s), Bronchitis, Calcium Channel Blockers, Cancer, Cataracts, Celiac Disease, Cirrhosis, Unknown Etiology, Cerebrovascular Disease, Cholelithiasis, Chronic Renal Failure, Colon Polyps, Common Variable Immunodeficiency, Congestive Heart Failure (CHF), Connective Tissue Disorder, COPD, Coronary Artery Disease, Crohn's Disease, Cryptogenic Organizing Pneumonia, Deep Vein Thrombosis / Thromboembolism, Denys-Drash Syndrome, Depression, Diabetes, Diabetes, Type II, Diabetic Neuropathy, Diet Controlled Diabetes, Diverticulitis,DVT/PE, Dyslipidemia, Epilepsy, Eczema, Epstein-Barr Virus, Familial Adenomatous Polyposis, Fanconi Anemia, Fibrosis, Gastroesophageal Reflux Disease, GERD, Glaucoma, Glycogen Storage Disease, Gout, Gonadal Dysfunction, Gorlin Syndrome, H. pylori Infection, Hashimoto's Thyroiditis, Headache, Heart Disease, Hemihypertrophy, Hemorrhagic Cystitis, Hepatitis, Hepatitis A Infection, Hepatitis B Infection, Hepatitis C Infection, Chronic Hepatitis, Hereditary Non-polyposis Colon Cancer, Herpes, High Grade Liver Dysplastic Nodule, HIV / AIDS, Human Papillomavirus Infection, HUS/TTP, Hypercholesterolemia, Hypercalcemia, Hyperglycemia, Hyperlipidemia, Hypertension, Hypospadias, Hypothyroidism, Inflammatory Bowel Disease, Insulin Controlled Diabetes, Interstitial Pneumontis or ARDS, Intraductal Papillary Mucinous Neoplasm, Iron Overload, Ischemic Heart Disease, ITP, Joint Replacement, Kidney Disease, Liver Cirrhosis (Liver Disease), Liver Toxicity (Non-Infectious), Li-Fraumeni Syndrome, Low Grade Liver Dysplastic Nodule, Lupus, Lynch Syndrome, MAI, Myasthenia Gravis, Myocardial Infarction, Neuroendocrine Tumor, Nonalcoholic Steatohepatitis, Obesity, Organ transplant (site), Osteoarthritis, Osteoporosis or Osteopenia, Other, Other Cancer Within 5 Years, Other Nonmalignant Systemic Disease, Other Pulmonary Complications, Pancreatitis, Pain (Various), Peptic Ulcer (Ulcer), Peripheral Neuropathy, Peripheral Vascular Disease, Peutz-Jeghers Disease, Pregnancy in Patient or Partner, Primary Sclerosing Cholangitis, Psoriasis, Pulmonary Fibrosis, Pulmonary Hemorrhage, Renal Failure (Requiring Dialysis), Renal Dialysis, Renal Insufficiency, Rheumatologic Disease, Rheumatoid Arthritis, Rubinstein-Taybi Syndrome, Sarcoidosis, Seizure, Sleep apnea, Smoking, Steatosis, Stroke, Transient Ischemic Attack, Tuberculosis, Turcot Syndrome, Tyrosinemia, Ulcerative Colitis, Wagr Syndrome, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2970715&version=1.0, -Comorbidity Method of Diagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,"Histology, Pathology, Radiology, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142386&version=1.0, -Days to Adverse Event,Number of days between the date used for index and the date of the patient's adverse event.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154728&version=1.0, -Days to Comorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154729&version=1.0, -Days to Progression,Number of days between the date used for index and the date the patient's disease progressed.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154730&version=1.0, -Days to Progression Free,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,,,,FALSE,Diagnosis,,, -Days to Recurrence,Number of days between the date used for index and the date the patient's disease recurred.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154731&version=1.0, -Diabetes Treatment Type,Text term used to describe the types of treatment used to manage diabetes.,"Alpha-Glucosidase Inhibitor, Biguanide, Diet, Injected Insulin, Insulin, Oral Hypoglycemic, Sulfonylurea, Thiazolidinedione, Other, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3587247&version=1.0, -Disease Response,Code assigned to describe the patient's response or outcome to the disease.,"AJ-Adjuvant Therapy, BED-Biochemical Evidence of Disease, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PDM-Persistent Distant Metastasis, PLD-Persistent Locoregional Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, TF-Tumor Free, VGPR-Very Good Partial Response, WT-With Tumor, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5750671&version=1.0, -DLCO Ref Predictive Percent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2180255&version=1.0, -ECOG Performance Status,The ECOG functional performance status of the patient/participant.,"""0"", ""1"", ""2"", ""3"", ""4"", ""5"", Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=88&version=5.1, -FEV1 FVC Post Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302956&version=1.0, -FEV 1 FVC Pre Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302955&version=1.0, -FEV1 Ref Post Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,,,,FALSE,Follow Up,,"https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302948&version=1.0""", -FEV1 Ref Pre Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302947&version=1.0, -Height,The height of the patient in centimeters.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=649&version=4.1, -Hepatitis Sustained Virological Response,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6423783&version=1.0, -HPV Positive Type,Text classification to represent the strain or type of human papillomavirus identified in an individual.,"""16"", ""18"", ""26"", ""31"", ""33"", ""35"", ""39"", ""45"", ""51"", ""52"", ""53"", ""56"", ""58"", ""59"", ""63"", ""66"", ""68"", ""70"", ""73"", ""82"", Other, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2922649&version=1.0, -Karnofsky Performance Status,Text term used to describe the classification used of the functional capabilities of a person.,"""0"", ""10"", ""20"", ""30"", ""40"", ""50"", ""60"", ""70"", ""80"", ""90"", ""100"", Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003853&version=4.2, -Menopause Status,Text term used to describe the patient's menopause status.,"Premenopausal, Perimenopausal, Postmenopausal, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2434914&version=1.1, -Progression or Recurrence,Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, Unknown, Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3121376&version=1.0, -Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,,, -Progression or Recurrence Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, -Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, -Treatment Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, -Progression or Recurrence Type,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,"Biochemical, Distant, Local, Regional, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142385&version=1.0, -Reflux Treatment Type,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,"Antacids, H2 Blockers, Medically Treated, No Treatment, Not Applicable, Not Reported, Proton Pump Inhibitors, Surgically Treated, Unknown",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440206&version=1.0, -Risk Factor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,"Alcohol Consumption,Alcoholic Liver Disease,Allergy Animal NOS,Allergy Ant,Allergy Bee,Allergy Cat,Allergy Dairy or Lactose,Allergy Dog,Allergy Eggs,Allergy Food NOS,Allergy Fruit,Allergy Meat,Allergy Mold or Dust,Allergy Nuts,Allergy Processed Foods,Allergy Seafood,Allergy Wasp,Alpha-1 Antitrypsin Deficiency,Autoimmune Atrophic Chronic Gastritis,Barrett's Esophagus,Beckwith-Wiedemann,Behcet's Disease,Cancer,Cholelithiasis,Chronic Hepatitis,Cirrhosis,Colon Polyps,Common variable immune deficiency (CVID),Denys-Drash Syndrome,Diabetes NOS,Diabetes Type I,Diabetes Type II,Diet,Diverticulitis,Endometriosis,Endosalpingiosis,Eczema,Epstein-Barr Virus,Familial Adenomatous Polyposis,Fanconi Anemia,Fibrosis,Gastric Polyp(s),Gilbert's Syndrome,Gorlin Syndrome,Hashimoto's Thyroiditis,Hay Fever,Headache,Helicobacter Pylori-Associated Gastritis,Hematologic Disorder NOS,Hemihypertrophy,Hemochromatosis,Hepatic Encephalopathy,Hepatitis B Infection,Hepatitis C Infection,Hepatitis NOS,High Grade Dysplasia,HIV,Human Papillomavirus Infection,Hypospadias,Intestinal Metaplasia,Iron Overload,Li-Fraumeni Syndrome,Low Grade Dysplasia,Lymphocytic Thyroiditis,Lynch Syndrome,Myasthenia Gravis,Nonalcoholic Fatty Liver Disease,Nonalcoholic Steatohepatitis,Obesity,Oral Contraceptives,Pancreatitis,Parasitic Disease of Biliary Tract,Primary Sclerosing Cholangitis,Recurrent Pyogenic Cholangitis,Reflux Disease,Rheumatoid Arthritis,Rubinstein-Taybi Syndrome,Sarcoidosis,Seizure,Sensory Changes,Serous tubal intraepithelial carcinoma (STIC),Steatosis,Tattoo,Thyroid Nodular Hyperplasia,Tobacco NOS,Tobacco Smokeless,Tobacco Smoking,Turcot Syndrome,Undescended Testis,Vision Changes,Wagr Syndrome,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142389&version=1.0, -Risk Factor Treatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514356&version=1.0, -Viral Hepatitis Serologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,"HBV Core Antibody, HBV DNA, HBV Genotype, HBV Surface Antibody, HCV Genotype, Hepatitis B Surface Antigen, Hepatitis C Antibody, Hepatitis C Virus RNA, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4395982&version=1.0, -Weight,The weight of the patient measured in kilograms.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=651&version=4.0, -Days to Treatment End,Number of days between the date used for index and the date the treatment ended.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154725&version=1.0, -Days to Treatment Start,Number of days between the date used for index and the date the treatment started.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154726&version=1.0, -Initial Disease Status,The text term used to describe the status of the patient's malignancy when the treatment began.,"Initial Diagnosis, Progressive Disease, Recurrent Disease, Residual Disease, Unknown, Not Reported",,,FALSE,Therapy,,, -Regimen or Line of Therapy,The text term used to describe the regimen or line of therapy.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161024&version=1.0, -Therapeutic Agents,Text identification of the individual agent(s) used as part of a treatment regimen.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2975232&version=1.0, -Treatment Effect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,"Complete Necrosis (No Viable Tumor), Incomplete Necrosis (Viable Tumor Present), No Necrosis, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514354&version=1.0, -Treatment Intent Type,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],"Adjuvant, Cancer Control, Cure, Neoadjuvant, Palliative, Prevention, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2793511&version=1.0, -Treatment or Therapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,"yes, no, unknown, not reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4231463&version=1.0, -Treatment Outcome,Text term that describes the patient's final outcome after the treatment was administered.,"Complete Response, Mixed Response, No Measurable Disease, No Response, Partial Response, Persistent Disease, Progressive Disease, Stable Disease, Treatment Ongoing, Treatment Stopped Due to Toxicity, Very Good Partial Response, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102383&version=1.0, -Treatment Type,Text term that describes the kind of treatment administered.,"Ablation Cryo,Ablation Ethanol Injection,Ablation Microwave,Ablation NOS,Ablation Radiofrequency,Ablation Radiosurgical,Ancillary Treatment,Antiseizure Treatment,Bisphosphonate Therapy,Blinded Study Treatment Unknown,Brachytherapy High Dose,Brachytherapy Low Dose,Brachytherapy NOS,Chemoembolization,Chemoprotectant,Chemotherapy,Concurrent Chemoradiation,Cryoablation,Embolization,Ethanol Injection Ablation,External Beam Radiation,Hormone Therapy,I-131 Radiation Therapy,Internal Radiation,Immunotherapy (Including Vaccines),Isolated Limb Perfusion (ILP),Organ Transplantation,Other,Pharmaceutical Therapy NOS,Pleurodesis,Radiation 2D Conventional,Radiation 3D Conformal,Radiation Combination,Radiation Cyberknife,Radiation External Beam,Radiation Implants,Radiation Intensity-Modulated Radiotherapy,Radiation Internal,Radiation Proton Beam,Radiation Radioisotope,Radiation Stereotactic/Gamma Knife/SRS,Radiation Systemic,Radiation Therapy NOS,Radioactive Iodine Therapy,Radioembolization,Radiosensitizing Agent,Stem Cell Treatment,Stem Cell Transplantation Autologous,Stem Cell Transplantation Double Autologous,Stem Cell Transplantation Allogeneic,Stem Cell Transplantation Non-Myeloablative,Stem Cell Transplantation Syngenic,Stem Cell Transplantation Haploidentical,Stem Cell Transplantation NOS,Stereotactic Radiosurgery,Steroid Therapy,Surgery,Targeted Molecular Therapy,Unknown,Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102381&version=1.0, -Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3225640&version=2.0, -Days to Last Follow up,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0, -Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0, -Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, Unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2759550&version=1.0, -Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of 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Reported, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0, -Primary Diagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS,Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,Unknown",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0, -Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3382736&version=2.0, -Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,, -Site of Resection or Biopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161034&version=1.0, -Tissue or Organ of Origin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161035&version=1.0, -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Low Grade, Unknown, Not Reported, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2785839&version=2.0, +Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules +Assay,"A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]",,,,FALSE,,,http://purl.obolibrary.org/obo/OBI_0000070, +Device,"A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment""",,,,FALSE,Assay,,https://w3id.org/biolink/vocab/Device, +Sequencing,Module for next generation sequencing assays,,,,FALSE,Assay,,http://example.org/htan/Sequencing, +Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",,,,TRUE,,,https://w3id.org/biolink/vocab/category, +Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test",http://example.org/htan/Patient, +File,A type of Information Content Entity specific to OS,,,"Filename, File Format",FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, +Filename,Name of a file ,,,,TRUE,,,http://example.org/htan/filename, +File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe ",,,TRUE,,,http://example.org/htan/fileFormat, +Checksum,MD5 checksum of the fasta file,,,,TRUE,Information Content Entity,,, +HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, +HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, +HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, +HTAN Parent ID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, +HTAN Parent Biospecimen ID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,,,,TRUE,Biospecimen,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing, +HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,,, +Clinical Data Tier 2,Cancer related clinical data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Precancerous Condition Type, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection",,FALSE,Patient,Patient,, +Lung Cancer Tier 3,Lung cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Lung Cancer Detection Method Type, Lung Cancer Participant Procedure History, Lung Adjacent Histology Type, Lung Tumor Location Anatomic Site, Lung Tumor Lobe Bronchial Location, Current Lung Cancer Symptoms, Lung Topography, Lung Cancer Harboring Genomic Aberrations",,FALSE,Patient,Patient,, +Colorectal Cancer Tier 3,Colorectal cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Colorectal Cancer Detection Method Type, History of Prior Colon Polyps, Family Colon Cancer History Indicator, Family Medical History Colorectal Polyp Diagnosis, Immediate Family History Endometrial Cancer, Immediate Family History Ovarian Cancer, Patient Inflammatory Bowel Disease Personal Medica History, Patient Colonoscopy Performed Indicator, Colorectal Cancer Tumor Border Configuration, MLH1 Promoter Methylation Status, Colorectal Cancer KRAS Indicator, Colon Polyp Occurence Indicator, Family History Colorectal Polyp, Colorectal Polyp New Indicator, Colorectal Polyp Shape, Size of Polyp Removed, Colorectal Polyp Count, Colorectal Polyp Type, Colorectal Polyp Adenoma Type",,FALSE,Patient,Patient,, +Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category",,FALSE,Patient,Patient,, +Brain Cancer Tier 3,Brain cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,CNS Tumor Primary Anatomic Site, Glioma Specific Metastasis Sites, Glioma Specific Radiation Field, Supra Tentorial Ependymoma Molecular Subgroup, Infra Tentorial Ependymoma Molecular Subgroup, Neuroblastoma MYCN Gene Amplification Status",,FALSE,Patient,Patient,, +Acute Lymphoblastic Leukemia Tier 3,Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Specimen Blast Count Percentage Value, NCI ALL Risk Group, MRD ALL Diagnostic Sensitivity, CNS Leukemia Status",,FALSE,Patient,Patient,, +Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status",,FALSE,Patient,Patient,, +Prostate Cancer Tier 3,Prostate cancer specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Location Extent Extraprostatic Extension, Location Nature Positive Margins, Seminal Vesicle Invasion, Prostate Carcinoma Histologic Type, Prostate Cancer Local Extent, Additonal Findings Uninvolved Prostate, Prostate Cancer Cytologic Morphologic Subtypes",,FALSE,Patient,Patient,, +Sarcoma Tier 3,Sarcoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Sarcoma Subtype, Sarcoma Diagnosis Classification Category, Sarcoma Tumor Extension Type",,FALSE,Patient,Patient,, +Pancreatic Cancer Tier 3,Pancreatic cancer specific attributes in Clinical Tier Data 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Pancreas Precancer Histopathologic Grade, Pancreatic IPMN Pathology Epithelial Subtype, Pancreatic Duct Final Pathology Type",,FALSE,Patient,Patient,, +Melanoma Tier 3,Melanoma specific attributes in Clinical Data Tier 3,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Cutaneous Melanoma Tumor Infiltrating Lymphocytes, Cutaneous Melanoma Tumor Regression Range, Melanoma Specimen Clark Level Value, Cutaneous Melanoma Surgical Margins, Melanoma Lesion Size, History of Atypical Nevi, Fitzpatrick Skin Tone, History of Chronic UV Exposure, History of Blistering Sunburn, History of Tanning Bed Use, Immediate Family History Melanoma, Melanoma Biopsy Resection Sites, Cutaneous Melanoma Ulceration, Cutaneous Melanoma Additional Findings",,FALSE,Patient,Patient,, +Demographics,Individual biomedical demographics attributes,,"Component, HTAN Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth, Occupation Duration Years, Premature At Birth, Weeks Gestation at Birth",,FALSE,Patient,,, +Family History,Individual's family cancer history,,"Component, HTAN Participant ID, Relative with Cancer History",,FALSE,Patient,,, +Exposure,Individual's exposure to carcenogens,,"Component, HTAN Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica Exposure",,FALSE,Patient,,, +Follow Up,Individual's follow up exams,,"Component, HTAN Participant ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year, Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight, Adverse Event Grade, AIDS Risk Factors, Body Surface Area, CD4 Count, CDC HIV Risk Factors, Days to Imaging, Evidence of Recurrence Type, HAART Treatment Indicator, HIV Viral Load, Hormonal Contraceptive Use, Hysterectomy Margins Involved, Hysterectomy Type, Imaging Result, Imaging Type, Immunosuppressive Treatment Type, Nadir CD4 Count, Pregnancy Outcome, Recist Targeted Regions Number, Recist Targeted Regions Sum, Scan Tracer Used",,FALSE,Patient,,, +Therapy,Individual's first line of therapy or treatment,,"Component, HTAN Participant ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type, Chemo Concurrent to Radiation, Number of Cycles, Reason Treatment Ended, Treatment Arm, Treatment Dose, Treatment Dose Units, Treatment Effect Indicator, Treatment Frequency",,FALSE,Patient,,, +Diagnosis,Individual's diagnosis,,"Component, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status, Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, Tumor Grade, WHO CNS Grade, WHO NTE Grade",,FALSE,Patient,,, +Molecular Test,Individual's clinical molecular test data,,"Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity",,FALSE,Patient,,, +Biospecimen,"HTAN biological entity; this can be tissue, blood, analyte and subsamples of those",,"Component, HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen IDs, Biospecimen Type, Acquisition Method Type, Fixative Type, Site of Resection or Biopsy, Storage Method, Processing Days from Index, Protocol Link, Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method, Preinvasive Morphology, Lysis Buffer, Method of Nucleic Acid Isolation",,FALSE,Biosample,Patient,http://example.org/htan/Biospecimen, +Other Assay,Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay Type",,FALSE,Assay,Biospecimen,, +Assay Type,"The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)",,,,TRUE,Assay,,, +scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913, +scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Sequencing,scRNA-seq Level 1,, +scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version, Workflow Start Datetime, Workflow End Datetime",,FALSE,Sequencing,scRNA-seq Level 2,, +scRNA-seq Level 4,"Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)",,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow Link, Workflow Start Datetime, Workflow End Datetime",,FALSE,Sequencing,scRNA-seq Level 3,, +Bulk RNA-seq Level 1,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Read Indicator, Nucleic Acid Source, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Days from Index, Spike In, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow, Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Transcript Integrity Number, RIN, DV200, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link ",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0003738, +Bulk RNA-seq Level 2,Bulk RNA-seq alignment protocol description,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, HTAN Parent Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion, Targets No Coverage, Proportion Base Mismatch, Short Reads",,FALSE,Sequencing,Bulk RNA-seq Level 1,, +Bulk RNA-seq Level 3,Bulk RNA-seq gene expression matrices,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Pseudo Alignment Used, Data Category, Expression Units, Matrix Type, Fusion Gene Detected, Fusion Gene Identity",,FALSE,Sequencing,Bulk RNA-seq Level 2,, +Bulk WES Level 1,Bulk Whole Exome Sequencing raw files,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Read Indicator, Library Selection Method, Read Length, Target Capture Kit, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Sequencing Platform, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Multiplex Barcode, Library Preparation Days from Index, Size Selection Range, Target Depth, To Trim Adapter Sequence",,FALSE,Sequencing,Biospecimen,, +Bulk WES Level 2,Bulk Whole Exome Sequencing aligned files and QC,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Adapter Content, Basic Statistics, Encoding, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, QC Workflow Type, QC Workflow Version, QC Workflow Link, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X",,FALSE,Sequencing,Bulk WES Level 1,, +Bulk WES Level 3,Bulk Whole Exome Sequencing called variants,,"Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Genomic Reference, Genomic Reference URL, Germline Variants Workflow URL, Germline Variants Workflow Type, Germline Variants Workflow Type, Somatic Variants Workflow URL, Somatic Variants Workflow Type, Somatic Variants Sample Type, Structural Variant Workflow URL, Structural Variant Workflow Type",,FALSE,Sequencing,Bulk WES Level 2,, +scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Sequencing,Biospecimen,, +Imaging Level 2,Raw and pre-processed image data,,"Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Workflow Start Datetime, Workflow End Datetime, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance,WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType",,FALSE,Assay,"Biospecimen, Imaging Level 2 Channels",, +Imaging Level 2 Channels,Channel-level Metadata Attributes,,"Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub Cycle Number, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope Element, Metal Isotope Mass, Oligo Barcode Upper Strand, Oligo Barcode Lower Strand, Dilution, Concentration",,FALSE,Imaging Level 2,,, +Channel ID,"This must match the corresponding field in the OME-XML / TIFF header. (eg ""Channel:0:1"")",,,,TRUE,Imaging Level 2 Channels,,, +Channel Name,This must match the corresponding field in the OME-XML / TIFF header. (eg “Blue” or “CD45” or “E-cadherin”),,,,TRUE,Imaging Level 2 Channels,,, +Channel Passed QC,Identify stains that did not pass QC but are included in the dataset.,"Yes, No",,,TRUE,Imaging Level 2 Channels,,, +Cycle Number,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),,,,FALSE,Imaging Level 2 Channels,,, +Sub Cycle Number,Sub cycle number,,,,FALSE,Imaging Level 2 Channels,,, +Target Name,Short descriptive name (abbreviation) for this target (antigen),,,,FALSE,Imaging Level 2 Channels,,, +Antibody Name,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",,,,FALSE,Imaging Level 2 Channels,,, +RRID identifier,Research Resource Identifier (eg “RRID: AB_394606”),,,,FALSE,Imaging Level 2 Channels,,https://scicrunch.org/resources, +Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),,,,FALSE,Imaging Level 2 Channels,,http://purl.obolibrary.org/obo/MI_0857, +Clone,Clone,,,,FALSE,Imaging Level 2 Channels,,, +Lot,Lot number from vendor,,,,FALSE,Imaging Level 2 Channels,,, +Vendor,Vendor,,,,FALSE,Imaging Level 2 Channels,,, +Catalog Number,Catalog Number,,,,FALSE,Imaging Level 2 Channels,,, +Excitation Wavelength,Center/peak of the excitation spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, +Emission Wavelength,Center/peak of the emission spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, +Excitation Bandwidth,Nominal width of excitation spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, +Emission Bandwidth,Nominal width of emission spectrum (nm),,,,FALSE,Imaging Level 2 Channels,,, +Metal Isotope Element,Element abbreviation. eg “La” or “Nd”,,,,FALSE,Imaging Level 2 Channels,,, +Metal Isotope Mass,Element mass number,,,,FALSE,Imaging Level 2 Channels,,, +Oligo Barcode Upper Strand,Oligo Barcode - Upper Strand,,,,FALSE,Imaging Level 2 Channels,,, +Oligo Barcode Lower Strand,Oligo Barcode - Lower Strand,,,,FALSE,Imaging Level 2 Channels,,, +Dilution,Dilution (eg 1:1000),,,,FALSE,Imaging Level 2 Channels,,, +Concentration,Concentration (eg 10ug/mL),,,,FALSE,Imaging Level 2 Channels,,, +Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH",,,TRUE,Imaging Level 2,,, +Channel Metadata Filename,Full path of uploaded companion CSV file containing channel-level metadata details,,,,TRUE,Imaging Level 2,,, +Image Acquisition Date,Date of image acquisition,,,,FALSE,Imaging Level 2,,, +Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",,,,TRUE,Imaging Level 2,,http://purl.obolibrary.org/obo/OBI_0400169, +Objective,Objective,,,,FALSE,Imaging Level 2,,, +NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),,,,TRUE,Imaging Level 2,,, +LensNA,The numerical aperture of the lens. Floating point value > 0.,,,,FALSE,Imaging Level 2,,, +WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",,WorkingDistanceUnit,,FALSE,Imaging Level 2,,, +WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, +Immersion,Immersion medium,"Air, Oil, Other",,,FALSE,Imaging Level 2,,, +Pyramid,Does data file contain pyramid of images,"Yes, No",,,TRUE,Imaging Level 2,,, +Zstack,Does data file contain a Z-stack of images,"Yes, No",,,TRUE,Imaging Level 2,,, +Tseries,Does data file contain a time-series of images,"Yes, No",,,TRUE,Imaging Level 2,,, +Passed QC,Did all channels pass QC (if not add free text Comment),"Yes, No - Channels QC",,,TRUE,Imaging Level 2,,, +No - Channels QC,Not all channels passed QC,,Comment,,FALSE,Imaging Level 2,,, +Comment,Free text field (generally for QC comment),,,,FALSE,Imaging Level 2,,, +FOV number,Index of FOV (as it pertains to its sequence order). Integer >= 1,,,,FALSE,Imaging Level 2,,, +FOVX,Field of view X dimension. Floating point,,FOVXUnit,,FALSE,Imaging Level 2,,, +FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging Level 2,,, +FOVY,Field of view Y dimension. Floating point value,,FOVYUnit,,FALSE,Imaging Level 2,,, +FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,FALSE,Imaging Level 2,,, +Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",,,,FALSE,Imaging Level 2,,, +Image ID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",,,,TRUE,Imaging Level 2,,, +DimensionOrder,The order in which the individual planes of data are interleaved.,"XYZCT, XYZTC, XYCTZ, XYCZT, XYTZC",,,TRUE,Imaging Level 2,,, +PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,,PhysicalSizeXUnit,,TRUE,Imaging Level 2,,, +PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, +PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,,PhysicalSizeYUnit,,TRUE,Imaging Level 2,,, +PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, +PhysicalSizeYUnit,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,,PhysicalSizeZUnit,,TRUE,Imaging Level 2,,, +PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å",,,TRUE,Imaging Level 2,,, +Pixels BigEndian,Boolean (True/False),"True, False",,,TRUE,Imaging Level 2,,, +PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",,,,TRUE,Imaging Level 2,,, +SizeC,Number of channels. Integer >= 1,,,,TRUE,Imaging Level 2,,, +SizeT,Number of time points. Integer >= 1,,,,TRUE,Imaging Level 2,,, +SizeX,Size of image: X dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, +SizeY,Size of image: Y dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, +SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,,,,TRUE,Imaging Level 2,,, +PixelType,"Data type for each pixel value. E.g. ""uint16""","int8, int16, int32, uint8, uint16, uint32, float, double, bit",,,TRUE,Imaging Level 2,,, +Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,http://example.org/htan/NucleicAcidSource, +Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x, Nuclei Isolation",,,TRUE,scRNA-seq Level 1,,, +Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion, Not Applicable",,,TRUE,scRNA-seq Level 1,,, +Library Layout,Sequencing read type,"Paired End, Single Read",,,TRUE,Sequencing,,, +Nucleus Identifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,Nuclei Barcode,,,TRUE,scATAC-seq Level 1,,, +Nuclei Barcode,Nuclei Barcode,"Nuclei Barcode Read, Nuclei Barcode Length",,,FALSE,scATAC-seq Level 1,,, +scATACseq Library Layout,Sequencing read type,scATACseq Paired End,,,TRUE,scATAC-seq Level 1,,, +Nuclei Barcode Read,Nuclei Barcode Read,,,,TRUE,scATAC-seq Level 1,,, +Nuclei Barcode Length,Nuclei Barcode Length,,,,TRUE,scATAC-seq Level 1,,, +scATACseq Paired End,A library layout type,"scATACseq Read1, scATACseq Read2",,,FALSE,scATAC-seq Level 1,,, +scATACseq Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert",,,TRUE,scATAC-seq Level 1,,, +scATACseq Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert",,,TRUE,scATAC-seq Level 1,,, +Threshold for Minimum Passing Reads,Threshold for calling cells,,,,TRUE,scATAC-seq Level 1,,, +Total Number of Passing Nuclei,Number of nuclei sequenced,,,,TRUE,scATAC-seq Level 1,,, +Median Fraction of Reads in Peaks,Median fraction of reads in peaks (FRIP),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, +Median Fraction of Reads in Annotated cis DNA Elements,Median fraction of reads in annotated cis-DNA elements (FRIADE),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, +Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,, +Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,, +Peaks Calling Software,Generic name of peaks calling tool,,,,TRUE,scATAC-seq Level 1,,, +Read Indicator,Indicate if this is Read 1 (R1) or Read 2 (R2),"R1, R2",,,TRUE,Sequencing,,, +Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,, +Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Level 1,,, +cDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",,"cDNA Offset, cDNA Length",,FALSE,Sequencing,,, +cDNA Offset,Offset in sequence for cDNA read (in bp): number,,,,TRUE,Sequencing,,, +cDNA Length,Length of cDNA read (in bp): number,,,,TRUE,Sequencing,,, +Cell Barcode and UMI,Cell and transcript identifiers,,"UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number",,FALSE,scRNA-seq Level 1,,, +Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, +Cell Barcode Length,Length of cell barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, +Valid Barcodes Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,, +UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",,,,TRUE,scRNA-seq Level 1,,https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html, +UMI Barcode Length,Length of UMI barcode read (in bp): number,,,,TRUE,scRNA-seq Level 1,,, +Median UMIs per Cell Number,Number,,,,TRUE,scRNA-seq Level 1,,, +Cell Median Number Reads,Median number of reads per cell. Number,,,,TRUE,scRNA-seq Level 3,,, +Cell Median Number Genes,Median number of genes detected per cell. Number,,,,TRUE,scRNA-seq Level 3,,, +Cell Total,Number of sequenced cells. Applies to raw counts matrix only.,,,,TRUE,scRNA-seq Level 3,,, +Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711, +Library Selection Method,How the molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Other",,,TRUE,Sequencing,,, +Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,scRNA-seq Level 1,,, +CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,,"Empty Well Barcode, Well Index",,FALSE,scRNA-seq Level 1,,, +Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,,,,TRUE,scRNA-seq Level 1,,, +Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,"Yes, No",,,FALSE,scRNA-seq Level 1,,, +Library Preparation Days from Index,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number],,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Single Cell Dissociation Days from Index,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number],,,,TRUE,scRNA-seq Level 1,,, +Sequencing Library Construction Days from Index,Number of days between sample for assay was received in lab and day of sequencing library construction [number],,,,TRUE,Sequencing,,, +Nucleic Acid Capture Days from Index,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number],,,,TRUE,Sequencing,,, +Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,scRNA-seq Level 1,,, +End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript",,,TRUE,scRNA-seq Level 1,,, +Reverse Transcription Primer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA","Oligo-dT, Poly-dT, Feature barcoding, Random",,,TRUE,scRNA-seq Level 1,,http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer, +Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],,Feature Reference Id,,FALSE,scRNA-seq Level 1,,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc, +Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",,,,TRUE,scRNA-seq Level 1,,, +Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX",,,TRUE,scRNA-seq Level 1,,, +ERCC,The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization,,"Spike In Concentration, Spike In Mix 1, Spike In Mix 2, Both Spike in Mixes",,FALSE,Spike In,,, +Spike In Concentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],,,,TRUE,ERCC,,https://www.ncbi.nlm.nih.gov/pubmed/21816910, +Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4 AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,,, +Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Sequencing,,, +Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,, +Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni",,,TRUE,scATAC-seq Level 1,,, +Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, In-House",,,TRUE,scATAC-seq Level 1,,, +Read Length,"The length of the sequencing reads. Can be integer, null",,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Target Capture Kit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.","Not Applicable, Custom Targets File Provided, Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes, Custom GENIE-DFCI OncoPanel - 275 Genes, Custom GENIE-DFCI Oncopanel - 300 Genes, Custom GENIE-DFCI Oncopanel - 447 Genes, Custom HaloPlex DLBCL Panel - 370 Genes, Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes, Custom Large Construct Capture TARGET-OS Panel - 8 Genes, Custom MSK IMPACT Panel - 341 Genes, Custom MSK IMPACT Panel - 410 Genes, Custom MSK IMPACT Panel - 468 Genes, Custom Myeloid GENIE-VICC Panel - 37 Genes, Custom Personalis ACEcp VAREPOP-APOLLO Panel v2, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes, Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1, Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2, Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb, Custom Solid Tumor GENIE-VICC Panel - 34 Genes, Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb, Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb, Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb, Custom SureSelect GENIE-UHN Panel - 555 Genes, Custom SureSelect Human All Exon v1.1 Plus 3 Boosters, Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb, Custom Twist Broad Exome v1.0 - 35.0 Mb, Custom Twist Broad PanCancer Panel - 396 Genes, Foundation Medicine T5a Panel - 322 Genes, Foundation Medicine T7 Panel - 429 Genes, Ion AmpliSeq Cancer Hotspot Panel v2, Ion AmpliSeq Comprehensive Cancer Panel, Nextera DNA Exome, Nextera Rapid Capture Exome v1.2, SeqCap EZ HGSC VCRome v2.1, SeqCap EZ Human Exome v2.0, SeqCap EZ Human Exome v3.0, SureSelect Human All Exon v3, SureSelect Human All Exon v4, SureSelect Human All Exon v5, SureSelect Human All Exon v5 + UTR, TruSeq Amplicon Cancer Panel, TruSeq Exome Enrichment - 62 Mb, TruSeq RNA Exome, TruSight Myeloid Sequencing Panel, xGen Exome Research Panel v1.0, unknown",,,TRUE,Sequencing,,, +Library Selection Method,How RNA molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Poly-T Enrichment, Random, rRNA Depletion, miRNA Size Fractionation, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Adapter Name,Name of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Adapter Sequence,Base sequence of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Base Caller Name,Name of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Base Caller Version,Version of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Flow Cell Barcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Fragment Maximum Length,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Fragment Mean Length,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Fragment Minimum Length,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Fragment Standard Deviation Length,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Lane Number,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Library Strand,Library stranded-ness.,"Unstranded, First Stranded, Second Stranded, Not Applicable",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Multiplex Barcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Size Selection Range,Range of size selection. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Target Depth,The targeted read depth prior to sequencing. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +To Trim Adapter Sequence,Does the user suggest adapter trimming?,"Yes - Trim Adapter Sequence, No",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, +Yes - Trim Adapter Sequence,Trim adapter sequence,"Adapter Trimmer Name, Adapter Trimmer Version, Adapter Trimmer Options",,,FALSE,Sequencing,,, +Adapter Trimmer Name,Name of adapter trimmer,,,,FALSE,Sequencing,,, +Adapter Trimmer Version,Version of the adapter trimmer,,,,FALSE,Sequencing,,, +Adapter Trimmer Options,Options used by adapter trimmer,,,,FALSE,Sequencing,,, +Transcript Integrity Number,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Adapter Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Basic Statistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Encoding,Version of ASCII encoding of quality values found in the file. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Kmer Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Overrepresented Sequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Base N Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Base Sequence Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Base Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Sequence GC Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Sequence Quality Score,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Per Tile Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Percent GC Content,The overall %GC of all bases in all sequences. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Sequence Duplication Levels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Sequence Length Distribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Total Reads,Total number of reads per sample. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Whitelist Cell Barcode File Link,Link to file listing all possible cell barcodes. URL,,,,TRUE,Sequencing,,, +Cell Barcode Tag,SAM tag for cell barcode field; please provide a valid cell barcode tag,,,,TRUE,Sequencing,,, +UMI Tag,"SAM tag for UMI field; please provide a valid UB, UMI",,,,TRUE,Sequencing,,, +Applied Hard Trimming,"Yes - Applied Hard Trimming, No",,,,TRUE,Sequencing,,, +Yes - Applied Hard Trimming,,,Aligned Read Length,,FALSE,Sequencing,,, +Aligned Read Length,Read length used for alignment if hard trimming was applied,,,,TRUE,Sequencing,,, +scRNAseq Workflow Type,Generic name for the workflow used to analyze a data set.,"CellRanger, STARsolo, HCA Optimus, dropEST, SEQC, Cufflinks, DEXSeq, HTSeq - FPKM, Cell annotation, Differentiation trajectory analysis, Other",,,TRUE,Sequencing,,, +Workflow Type,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,, +Workflow Version,Major version of the workflow (e.g. Cell Ranger v3.1),,,,TRUE,Sequencing,,, +scRNAseq Workflow Parameters Description,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",,,,TRUE,Sequencing,,, +Workflow Parameters Description,Parameters used to run the workflow.,,,,TRUE,Sequencing,,, +Workflow Link,Link to workflow or command. DockStore.org recommended. URL,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow, +Workflow Start Datetime,A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm],,,,FALSE,Sequencing,,, +Workflow End Datetime,A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm],,,,FALSE,Sequencing,,, +QC Workflow Type,Generic name for the workflow used to analyze a data set. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +QC Workflow Version,Major version for a workflow. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +QC Workflow Link,Link to workflow used. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, +Germline Variants Workflow URL,"Link to workflow document, e.g. Github, DockStore.org recommended",,,,TRUE,Sequencing,,, +Germline Variants Workflow Type,Generic name for the workflow used to analyze a data set,"GATK4, Other",,,TRUE,Sequencing,,, +Somatic Variants Workflow URL,Generic name for the workflow used to analyze a data set.,,,,TRUE,Sequencing,,, +Somatic Variants Workflow Type,Generic name for the workflow used to analyze a data set.,"CaVEMan, GATK4, MuTect2, MuSE, MuTect2, Pindel, SomaticSniper, VarScan2",,,TRUE,Sequencing,,, +Somatic Variants Sample Type,Is the sample case or control in somatic variant analysis,"Case Sample, Control Sample",,,TRUE,Sequencing,,, +Structural Variant Workflow URL,Link to workflow document. DockStore.org recommended. URL,,,,TRUE,Sequencing,,, +Structural Variant Workflow Type,Generic name for the workflow used to analyze a data set.,"BRASS, GATK4, CNV, CNVkit",,,TRUE,Sequencing,,, +Alignment Workflow Url,Link to workflow used for read alignment. DockStore.org recommended. String,,,,TRUE,Sequencing,,, +Alignment Workflow Type,Generic name for the workflow used to analyze a data set.,"BWA, BWA with BQSR, BWA-aln, BWA-mem, BWA with Mark Duplicates and BQSR, STAR 2-Pass, STAR 2-Pass Chimeric, STAR 2-Pass Genome, STAR 2-Pass Transcriptome",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, +MSI Workflow Link,Link to method workflow (or command) used in estimating the MSI. URL,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +MSI Score,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,,,,FALSE,Sequencing,,, +MSI Status,MSIsensor determination of either microsatellite stability or instability.,"MSI, MSI-low, MSI-high, MSS",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). URL,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow, +Genomic Reference URL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),,,,TRUE,Sequencing,,, +Genome Annotation URL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),,,,TRUE,Sequencing,,, +Index File Name,The name (or part of a name) of a file (of any type). String,,,,TRUE,Sequencing,,, +Average Base Quality,Average base quality collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads_index, +Average Insert Size,Average insert size collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Average Read Length,Average read length collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Contamination Error,Estimation error of cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Mean Coverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Pairs On Diff CHR,Pairs on different chromosomes collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Total Uniquely Mapped,Number of reads that map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Total Unmapped reads,Number of reads that did not map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Proportion Reads Duplicated,Proportion of duplicated reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Proportion Reads Mapped,Proportion of mapped reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Proportion Targets No Coverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Proportion Base Mismatch,Proportion of mismatched bases collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Proportion Coverage 10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",,,,FALSE,Sequencing,,, +Proportion Coverage 30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",,,,FALSE,Sequencing,,, +Short Reads,Number of reads that were too short. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads, +Pseudo Alignment Used,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,"Yes - Pseudo Alignment Used, No",,,TRUE,Sequencing,,, +Software and Version,Name of software used to generate expression values. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow, +Yes - Pseudo Alignment Used,Pseudo aligner was used,,"Workflow Link, Software and Version, Genomic Reference, Genomic Reference URL",,FALSE,Sequencing,,, +Genomic Reference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/),,,,TRUE,Sequencing,,, +Genomic Reference URL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL],,,,TRUE,Sequencing,,, +Data Category,Specific content type of the data file.,"Gene Expression, Transcript Expression, Exon Expression Quantification, Gene Expression Quantification, Isoform Expression Quantification, Splice Junction Quantification, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=gene_expression, +Expression Units,How quantities are corrected for gene length,"TPM, RPKM, FPKM, Counts, Other, NA",,,TRUE,Sequencing,,, +Fusion Gene Detected,Was a fusion gene identified?,"Yes - Fusion Gene Detected, No, unknown",,,FALSE,Sequencing,,, +Yes - Fusion Gene Detected,A fusion gene was detected,,Fusion Gene Identity,,FALSE,Sequencing,,, +Fusion Gene Identity,The gene symbols of fused genes.,"EWS-FLI, EWS-ERG, SYT-SSX1, SYT-SSX2, EWS-WT1, Other Fusion Gene",,,FALSE,Sequencing,,,list +Other Fusion Gene,Other fusion gene detected.,,Specify Other Fusion Gene,,FALSE,Sequencing,,, +Specify Other Fusion Gene,"Specify fusion gene detected, if not in list",,,,FALSE,Sequencing,,, +Matrix Type,Type of data stored in matrix.,"Raw Counts, Normalized Counts, Scaled Counts, Batch Corrected Counts",,,TRUE,Sequencing,,, +Linked Matrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,,,,FALSE,Sequencing,,, +Biospecimen Type,Biospecimen Type,"Tissue Biospecimen Type, Blood Biospecimen Type, Analyte Biospecimen Type, Mouth Rinse Biospecimen Type, Stool Biospecimen Type, Urine Biospecimen Type, Ascites Biospecimen Type, Sputum Biospecimen Type, Fluids Biospecimen Type, Bone Marrow Biospecimen Type, Cells Biospecimen Type",,,TRUE,Biospecimen,,, +Analyte Biospecimen Type,A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,,"Analyte Type, Fixation Duration, Slide Charge Type, Section Thickness Value, Sectioning Days from Index, Shipping Condition Type, Ischemic Time, Ischemic Temperature",,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0, +Tissue Biospecimen Type,Tissue biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, +Bone Marrow Biospecimen Type,Bone Marrow biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, +Urine Biospecimen Type,Urine biospecimen,,"Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method",,FALSE,Biospecimen,,, +Blood Biospecimen Type,Blood biospecimen,,Shipping Condition Type,,FALSE,Biospecimen,,, +Timepoint Label,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",,,,TRUE,Biospecimen,,, +Collection Days from Index,Number of days from the research participant's index date that the biospecimen was obtained.,,,,TRUE,Biospecimen,,, +Protocol Link,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",,,,TRUE,Information Content Entity,,, +Adjacent Biospecimen IDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",,,,FALSE,Biospecimen,,, +Mounting Medium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media","Aqueous water based, Non-Aqueous Solvent based, Xylene,Toluene,Antifade with DAPI,Antifade without DAPI,PBS,unknown,Not Reported",,,FALSE,Biospecimen,,, +Analyte Type,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0, +Acquisition Method Type,Records the method of acquisition or source for the specimen under consideration.,"Autopsy, Biopsy, Fine Needle Aspirate, Surgical Resection, Punch Biopsy, Shave Biopsy, Excision, Re-excision, Sentinel Node Biopsy, Lymphadenectomy - Regional Nodes, Other Acquisition Method, Not specified",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6626651&version=1.0, +Other Acquisition Method,A custom acquisition method,,Acquisition Method Other Specify,,FALSE,Biospecimen,,, +Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],,,,TRUE,Biospecimen,,, +Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported",,,TRUE,Biospecimen,,, +Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Other, None, unknown",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=65078&version=3.0, +Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5230144&version=1.0, +Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",,,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, +Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20 Deg C Dry Ice, Liquid Nitrogen",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, +Collection Media,Material Specimen is collected into post procedure,"DMEM, DMEM+Serum, RPMI, RPMI+Serum, PBS, PBS+Serum",,,FALSE,Biospecimen,,, +Specimen Laterality,"For tumors in paired organs, designates the side on which the specimen was obtained.","Bilateral, Left, Right, unknown, Not Reported, Not Applicable",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=1.0, +Portion Weight,"Numeric value that represents the sample portion weight, measured in milligrams.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432593&version=1.0, +Total Volume,"Numeric value for the total amount of sample or specimen, measured in milliliters (mL).",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3005019&version=1.0, +Tumor Tissue Type,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0, +Histologic Morphology Code,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0, +Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other",,,FALSE,Biospecimen,,, +Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5227611&version=1.0, +Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3024951&version=1.0, +Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection,,,,TRUE,Biospecimen,,, +Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Raraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, unknown",,,TRUE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method, +Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed,,,,TRUE,Biospecimen,,, +Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped",,,TRUE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5495533&version=1.0, +Site Data Source,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",,,,FALSE,Biospecimen,,, +Processing Location,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",,,,FALSE,Biospecimen,,, +Histology Assessment By,Text term describing who (in what role) made the histological assessments of the sample,"Pathologist, Research Scientist, Other, unknown",,,FALSE,Biospecimen,,, +Histology Assessment Medium,The method of assessment used to characterize histology,"Digital, Microscopy, Other, unknown",,,FALSE,Biospecimen,,, +Tumor Infiltrating Lymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],,,,FALSE,Biospecimen,,, +Degree of Dysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,"Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, unknown",,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5543188&version=1.0, +Dysplasia Fraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2390593&version=1.0, +Number Proliferating Cells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432636&version=1.0, +Percent Eosinophil Infiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897700&version=2.0, +Percent Granulocyte Infiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897705&version=2.0, +Percent Inflam Infiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897695&version=1.0, +Percent Lymphocyte Infiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897710&version=2.0, +Percent Monocyte Infiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5455535&version=1.0, +Percent Necrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841237&version=1.0, +Percent Neutrophil Infiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0, +Percent Normal Cells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0, +Percent Stromal Cells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841241&version=1.0, +Percent Tumor Cells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432686&version=1.0, +Percent Tumor Nuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841225&version=1.0, +Fiducial Marker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,"Nuclear Stain - DAPI, Fluorescent Beads, Grid Slides - Hemocytometer, Adhesive Markers, Other, unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi, +Slicing Method,Imaging specific: the method by which the tissue was sliced.,"Vibratome, Cryosectioning, Tissue molds, Sliding microtome, Sectioning, Other, unknown, Not Reported",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi, +Antigen Retrieval ,"Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ",,,,FALSE,Biospecimen,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64676&version=3.0, +Biospecimen Slide Location,Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable,,,,FALSE,Biospecimen,,, +Staining Markers,Imaging specific: text to identify proteins/ antibodies selected for staining,,,,FALSE,Biospecimen,,, +Lysis Buffer,scRNA-seq specific: Type of lysis buffer used,,,,FALSE,Biospecimen,,, +Method of Nucleic Acid Isolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",,,,FALSE,Biospecimen,,, +Start Days from Index,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",,,,TRUE,Patient,,, +Stop Days from Index,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",,,,FALSE,Patient,,, +Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, unknown, Not Reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0, +Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, Not Reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0, +Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, unknown, Not Reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0, +Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, unknown, Not Reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5&version=5.0, +Dead,This indicates the participant is dead and defines further required metadata,,"Year of Death, Cause of Death, Cause of Death Source, Days to Death",,FALSE,Demographics,,, +Days to Birth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154723&version=1.0, +Year of Death,Numeric value to represent the year of the death of an individual.,,,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897030&version=1.0, +Country of Residence,Country of Residence at enrollment,"Afghanistan,Albania,Algeria,Andorra,Angola,Anguilla,Antigua and Barbuda,Argentina,Armenia,Aruba,Australia,Austria,Azerbaijan,Bahamas,Bahrain,Bangladesh,Barbados,Belarus,Belgium,Belize,Benin,Bermuda,Bhutan,Bolivia,Bosnia and Herzegovina,Botswana,Brazil,Brunei,Bulgaria,Burkina Faso,Burundi,Cambodia,Cameroon,Canada,Cape Verde,Cayman Islands,Central African Republic,Chad,Chile,China,Colombia,Comoros,Congo,Cook Islands,Costa Rica,Cote d'Ivoire,Croatia,Cuba,Curacao,Cyprus,Czech Republic (Czechia),Democratic Republic of the Congo,Denmark,Djibouti,Dominica,Dominican Republic,Ecuador,Egypt,El Salvador,Equatorial Guinea,Eritrea,Estonia,Eswatini,Ethiopia,Falkland Islands (Malvinas),Faroe Islands,Federated States of Micronesia,Fiji,Finland,France,French Guiana,French Polynesia,Gabon,Gambia,Georgia,Germany,Ghana,Gibraltar,Greece,Greenland,Grenada,Guadeloupe,Guam,Guatemala,Guernsey,Guinea,Guinea-Bissau,Guyana,Haiti,Holy See,Honduras,Hong Kong,Hungary,Iceland,India,Indonesia,Iran,Iraq,Ireland,Isle of Man,Israel,Italy,Jamaica,Japan,Jersey,Jordan,Kazakhstan,Kenya,Kiribati,Kosovo,Kuwait,Kyrgyzstan,Laos,Latvia,Lebanon,Lesotho,Liberia,Libya,Liechtenstein,Lithuania,Luxembourg,Macau,Madagascar,Malawi,Malaysia,Maldives,Mali,Malta,Marshall Islands,Martinique,Mauritania,Mauritius,Mayotte,Mexico,Moldova,Monaco,Mongolia,Montenegro,Montserrat,Morocco,Mozambique,Myanmar,Namibia,Nauru,Nepal,Netherlands,New Caledonia,New Zealand,Nicaragua,Niger,Nigeria,Niue,North Korea,North Macedonia,Northern Mariana Islands,Norway,Oman,Pakistan,Palau,Panama,Papua New Guinea,Paraguay,Peru,Philippines,Poland,Portugal,Puerto Rico,Qatar,Reunion,Romania,Russia,Rwanda,Saint Helena Ascension and Tristan da Cunha,Saint Kitts and Nevis,Saint Lucia,Saint Pierre and Miquelon,Saint Vincent and the Grenadines,Samoa,San Marino,Sao Tome and Principe,Saudi Arabia,Senegal,Serbia,Seychelles,Sierra Leone,Singapore,Slovakia,Slovenia,Solomon Islands,Somalia,South Africa,South Korea,South Sudan,Spain,Sri Lanka,State of Palestine,Sudan,Suriname,Svalbard & Jan Mayen Islands,Sweden,Switzerland,Syria,Taiwan,Tajikistan,Tanzania,Thailand,Timor-Leste,Togo,Tokelau,Tonga,Trinidad and Tobago,Tunisia,Turkey,Turkmenistan,Tuvalu,Uganda,Ukraine,United Arab Emirates,United Kingdom,United States,Uruguay,Uzbekistan,Vanuatu,Venezuela,Vietnam,Virgin Islands British,Virgin Islands U.S.,Wallis and Futuna,Western Sahara,Yemen,Zambia,Zimbabwe",,,FALSE,Demographics,,, +Age at Index,For GDC submission only - this is going to be always 0 since HTAN's index is the date of birth,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6028530&version=1.0, +Age Is Obfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,"true, false",,,FALSE,Demographics,,, +Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896954&version=1.0, +Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, unknown, Not Applicable",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2554674&version=3.0, +Cause of Death Source,The text term used to describe the source used to determine the patient's cause of death.,"Autopsy, Death Certificate, Medical Record, Social Security Death Index, unknown, Not Reported",,,FALSE,Demographics,,, +Days to Death,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154724&version=1.0, +Occupation Duration Years,The number of years a patient worked in a specific occupation.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2435424&version=1.0, +Premature At Birth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,"Yes, No, unknown, Not Reported",,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6010765&version=1.0, +Weeks Gestation at Birth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2737369&version=1.0, +Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161021&version=1.0, +Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,,,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5300571&version=1.0, +Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161022&version=1.0, +Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son, Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister, Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2690165&version=2.0, +Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161023&version=1.0, +Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,,,,FALSE,Family History,,, +Yes - Cancer History Relative,Individual has a relative with cancer history,,"Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis",,FALSE,Family History,,, +Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported",,,TRUE,Exposure,,, +Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,,"Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Type of Smoke Exposure, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used, Secondhand Smoke as Child, Smoke Exposure Duration, Tobacco Use per Day, Smokeless Tobacco Quit Age",,FALSE,Exposure,,, +Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2955385&version=1.0, +Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3137957&version=1.0, +Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported",,,TRUE,Exposure,,, +Yes - Alcohol Exposure,,,"Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity, Alcohol Type",,FALSE,Exposure,,, +Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3114013&version=1.0, +Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3124961&version=1.0, +Alcohol History,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2201918&version=1.0, +Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3457767&version=1.0, +Alcohol Type,Type of alcohol use,"Beer, Liquor, Other, Wine, unknown, Not Reported",,,FALSE,Exposure,,, +Asbestos Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=1253&version=3.0, +Cigarettes per Day,The average number of cigarettes smoked per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2001716&version=4.0, +Coal Dust Exposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,"Yes, No, unknown",,,FALSE,Exposure,,, +Environmental Tobacco Smoke Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.","Yes, No, unknown",,,FALSE,Exposure,,, +Radon Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2816352&version=1.0, +Respirable Crystalline Silica Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.","Yes, No, unknown",,,FALSE,Exposure,,, +Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, unknown",,,FALSE,Exposure,,, +Secondhand Smoke as Child,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,"Yes, No, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6841888&version=1.0, +Smoke Exposure Duration,Text term used to describe the length of time the patient was exposed to an environmental factor.,"Six Weeks or More, unknown,Not Reported",,,FALSE,Exposure,,, +Type of Smoke Exposure,The text term used to describe the patient's specific type of smoke exposure.,"Accidental building fire smoke,Accidental grass fire smoke, Accidental fire smoke NOS,Accidental forest fire smoke,Accidental vehicle fire smoke,Aircraft smoke,Burning tree smoke,Coal smoke NOS, Cooking related smoke NOS,Electronic cigarette smoke NOS,Electrical fire smoke,Environmental tobacco smoke,Factory smokestack smoke,Field burning smoke,Fire smoke NOS,Furnace or boiler smoke,Gas burning smoke propane,Grease fire smoke,Grilling smoke,Hashish smoke,Indoor coal burning stove or fireplace smoke,Indoor stove or fireplace smoke NOS,Indoor wood burning stove or fireplace smoke,Machine smoke,Marijuana smoke,No Smoke Exposure,Oil burning smoke Kerosene,Oil burning smoke NOS,Recreational fire smoke,Smoke exposure NOS,Smokehouse smoke,Tobacco smoke cigar,Tobacco smoke cigarettes,Tobacco smoke pipe,unknown,Volcanic smoke,Waste burning smoke,Wood burning smoke factory,Wood burning smoke NOS, Workrelated smoke artificial smoke machines, Workrelated smoke fire fighting,Workrelated smoke foundry,Workrelated smoke generators,Workrelated smoke military,Workrelated smoke NOS,Workrelated smoke paint baking,Workrelated smoke plastics factory,Workrelated smoke plumbing,Workrelated smoke soldering/welding",,,FALSE,Exposure,,, +Marijuana smoke,Marijuana smoke exposure,,Marijuana Use Per Week,,FALSE,Exposure,,, +Marijuana Use Per Week,Numeric value that represents the number of times the patient uses marijuana each day.,,,,FALSE,Exposure,,, +Tobacco Use per Day,Numeric value that represents the number of times the patient uses tobacco each day.,,,,FALSE,Exposure,,, +Smokeless Tobacco Quit Age,Smokeless tobacco quit age,,,,FALSE,Exposure,,, +Time Between Waking and First Smoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,"Within 5 Minutes, 6-30 Minutes, 31-60 Minutes, After 60 Minutes, unknown",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3279220&version=1.0, +Tobacco Smoking Onset Year,The year in which the participant began smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228604&version=1.0, +Tobacco Smoking Quit Year,The year in which the participant quit smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228610&version=1.0, +Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2181650&version=1.0, +Type of Tobacco Used,The text term used to describe the specific type of tobacco used by the patient.,"Cigarettes, Cigar, Electronic Cigarette, Other, Pipe, Smokeless Tobacco, Marijuana",,,FALSE,Exposure,,, +Days to Follow Up,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154727&version=1.0, +Adverse Event,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,"Abdominal Distension, Abdominal Infection,Abdominal Pain,Abdominal Soft Tissue Necrosis,Abducens Nerve Disorder,Accessory Nerve Disorder,Acidosis,Acoustic Nerve Disorder NOS,Activated Partial Thromboplastin Time Prolonged,Acute Coronary Syndrome,Acute Kidney Injury,Adrenal Insufficiency,Adult Respiratory Distress Syndrome, Agitation, Akathisia, Alanine Aminotransferase Increased,Alcohol Intolerance,Alkaline Phosphatase Increased,Alkalosis,Allergic Reaction,Allergic Rhinitis, Alopecia, Amnesia,Anal Fistula,Anal Hemorrhage,Anal Mucositis, Anal Necrosis,Anal Pain,Anal Stenosis,Anal Ulcer,Anaphylaxis,Anemia,Ankle Fracture,Anorectal Infection,Anorexia,Anorgasmia,Anxiety,Aortic Injury,Aortic Valve Disease,Aphonia,Apnea,Appendicitis,Appendicitis Perforated,Arachnoiditis,Arterial Injury,Arteritis Infective,Arthralgia,Arthritis,Ascites,Aspartate Aminotransferase Increased,Aspiration,Asystole,Ataxia,Atelectasis,Atrial Fibrillation,Atrial Flutter,Atrioventricular Block Complete,Atrioventricular Block First Degree,Autoimmune Disorder,Avascular Necrosis,Azoospermia,Back Pain,Bile Duct Stenosis,Biliary Anastomotic Leak,Biliary Fistula,Biliary Tract Infection,Bladder Anastomotic Leak,Bladder Infection,Bladder Perforation,Bladder Spasm,Bloating,Blood and Lymphatic System Disorders Other,Blood Antidiuretic Hormone Abnormal,Blood Bilirubin Increased,Blood Corticotrophin Decreased,Blood Gonadotrophin Abnormal,Blood Prolactin Abnormal,Blurred Vision,Body Odor,Bone Infection,Bone Marrow Hypocellular,Bone Pain,Brachial Plexopathy,Breast Atrophy,Breast Infection,Breast Pain,Bronchial Fistula,Bronchial Infection,Bronchial Obstruction,Bronchial Stricture,Bronchopleural Fistula,Bronchopulmonary Hemorrhage,Bronchospasm,Bruising,Bullous Dermatitis,Burn,Buttock Pain,Capillary Leak Syndrome,Carbon Monoxide Diffusing Capacity Decreased,Cardiac Arrest,Cardiac Disorders Other,Cardiac Troponin I Increased,Cardiac Troponin T Increased,Cataract,Catheter Related Infection,CD4 Lymphocytes Decreased,Cecal Hemorrhage,Cecal Infection,Central Nervous System Necrosis,Cerebrospinal Fluid Leakage,Cervicitis Infection,Cheilitis,Chest Pain Cardiac,Chest Wall Pain,Chills,Cholecystitis,Cholesterol High,Chronic Kidney Disease,Chylothorax,Cognitive Disturbance,Colitis,Colonic Fistula,Colonic Hemorrhage,Colonic Obstruction,Colonic Perforation,Colonic Stenosis,Colonic Ulcer,Concentration Impairment,Conduction Disorder,Confusion,Congenital, Familial and Genetic Disorders Other,Conjunctivitis,Conjunctivitis Infective,Constipation,Constrictive Pericarditis,Corneal Infection,Corneal Ulcer,Cough,CPK Increased,Cranial Nerve Infection,Creatinine Increased,Cushingoid,Cystitis Noninfective,Cytokine Release Syndrome,Death Neonatal,Death NOS,Dehydration,Delayed Orgasm,Delayed Puberty,Delirium,Delusions,Dental Caries,Depressed Level of Consciousness,Depression,Dermatitis Radiation,Device Related Infection,Diarrhea,Disseminated Intravascular Coagulation,Dizziness,Dry Eye,Dry Mouth,Dry Skin,Duodenal Fistula,Duodenal Hemorrhage,Duodenal Infection,Duodenal Obstruction,Duodenal Perforation,Duodenal Stenosis,Duodenal Ulcer,Dysarthria,Dysesthesia,Dysgeusia,Dysmenorrhea,Dyspareunia,Dyspepsia,Dysphagia,Dysphasia,Dyspnea,Ear and Labyrinth Disorders Other,Ear Pain,Edema Cerebral,Edema Face,Edema Limbs,Edema Trunk,Ejaculation Disorder,Ejection Fraction Decreased,Electrocardiogram QT Corrected Interval Prolonged,Encephalitis Infection,Encephalomyelitis Infection,Encephalopathy,Endocarditis Infective,Endocrine Disorders Other,Endophthalmitis,Enterocolitis,Enterocolitis Infectious,Enterovesical Fistula,Epistaxis,Erectile Dysfunction,Erythema Multiforme,Erythroderma,Esophageal Anastomotic Leak,Esophageal Fistula,Esophageal Hemorrhage,Esophageal Infection,Esophageal Necrosis,Esophageal Obstruction,Esophageal Pain,Esophageal Perforation,Esophageal Stenosis,Esophageal Ulcer,Esophageal Varices Hemorrhage,Esophagitis,Euphoria,Exostosis,External Ear Inflammation,External Ear Pain,Extraocular Muscle Paresis,Extrapyramidal Disorder,Eye Disorders Other,Eye Infection,Eye Pain,Eyelid Function Disorder,Facial Muscle Weakness,Facial Nerve Disorder,Facial Pain,Fall,Fallopian Tube Anastomotic Leak,Fallopian Tube Obstruction,Fallopian Tube Perforation,Fallopian Tube Stenosis,Fat Atrophy,Fatigue,Febrile Neutropenia,Fecal Incontinence,Female Genital Tract Fistula,Feminization Acquired,Fetal Death,Fetal Growth Retardation,Fever,Fibrinogen Decreased,Fibrosis Deep Connective Tissue,Flank Pain,Flashing Lights,Flatulence,Floaters,Flu Like Symptoms,Flushing,Forced Expiratory Volume Decreased,Fracture,Gait Disturbance,Gallbladder Fistula,Gallbladder Infection,Gallbladder Necrosis,Gallbladder Obstruction,Gallbladder Pain,Gallbladder Perforation,Gastric Anastomotic Leak,Gastric Fistula,Gastric Hemorrhage,Gastric Necrosis,Gastric Perforation,Gastric Stenosis,Gastric Ulcer,Gastritis,Gastroesophageal Reflux Disease,Gastrointestinal Anastomotic Leak,Gastrointestinal Disorders Other,Gastrointestinal Fistula,Gastrointestinal Pain,Gastrointestinal Stoma Necrosis,Gastroparesis,General Disorders and Administration Site Conditions Other,Generalized Muscle Weakness,Genital Edema,GGT Increased,Gingival Pain,Glaucoma,Glossopharyngeal Nerve Disorder,Glucose Intolerance,Growth Accelerated,Growth Hormone Abnormal,Growth Suppression,Gum Infection,Gynecomastia,Hallucinations,Haptoglobin Decreased,Head Soft Tissue Necrosis,Headache,Hearing Impaired,Heart Failure,Hematoma,Hematosalpinx,Hematuria,Hemoglobin Increased,Hemoglobinuria,Hemolysis,Hemolytic Uremic Syndrome,Hemorrhoidal Hemorrhage,Hemorrhoids,Hepatic Failure,Hepatic Hemorrhage,Hepatic Infection,Hepatic Necrosis,Hepatic Pain,Hepatitis Viral,Hepatobiliary Disorders Other,Hiccups,Hip Fracture,Hirsutism,Hoarseness,Hot Flashes,Hydrocephalus,Hypercalcemia,Hyperglycemia,Hyperhidrosis,Hyperkalemia,Hypermagnesemia,Hypernatremia,Hyperparathyroidism,Hypersomnia,Hypertension,Hyperthyroidism,Hypertrichosis,Hypertriglyceridemia,Hyperuricemia,Hypoalbuminemia,Hypocalcemia,Hypoglossal Nerve Disorder,Hypoglycemia,Hypohidrosis,Hypokalemia,Hypomagnesemia,Hyponatremia,Hypoparathyroidism,Hypophosphatemia,Hypotension,Hypothermia,Hypothyroidism,Hypoxia,Ileal Fistula,Ileal Hemorrhage,Ileal Obstruction,Ileal Perforation,Ileal Stenosis,Ileal Ulcer,Ileus,Immune System Disorders Other,Infections and Infestations Other,Infective Myositis,Infusion Related Reaction,Infusion Site Extravasation,Injection Site Reaction,Injury to Carotid Artery,Injury to Inferior Vena Cava,Injury to Jugular Vein,Injury to Superior Vena Cava,Injury, Poisoning and Procedural Complications Other,INR Increased,Insomnia,Intestinal Stoma Leak,Intestinal Stoma Obstruction,Intestinal Stoma Site Bleeding,Intra-Abdominal Hemorrhage,Intracranial Hemorrhage,Intraoperative Arterial Injury,Intraoperative Breast Injury,Intraoperative Cardiac Injury,Intraoperative Ear Injury,Intraoperative Endocrine Injury,Intraoperative Gastrointestinal Injury,Intraoperative Head and Neck Injury,Intraoperative Hemorrhage,Intraoperative Hepatobiliary Injury,Intraoperative Musculoskeletal Injury,Intraoperative Neurological Injury,Intraoperative Ocular Injury,Intraoperative Renal Injury,Intraoperative Reproductive Tract Injury,Intraoperative Respiratory Injury,Intraoperative Skin Injury,Intraoperative Splenic Injury,Intraoperative Urinary Injury,Intraoperative Venous Injury,Investigations Other,Iron Overload,Irregular Menstruation,Irritability,Ischemia Cerebrovascular,IVth Nerve Disorder,Jejunal Fistula,Jejunal Hemorrhage,Jejunal Obstruction,Jejunal Perforation,Jejunal Stenosis,Jejunal Ulcer,Joint Effusion,Joint Infection,Joint Range of Motion Decreased,Joint Range of Motion Decreased Cervical Spine,Joint Range of Motion Decreased Lumbar Spine,Keratitis,Kidney Anastomotic Leak,Kidney Infection,Kyphosis,Lactation Disorder,Large Intestinal Anastomotic Leak,Laryngeal Edema,Laryngeal Fistula,Laryngeal Hemorrhage,Laryngeal Inflammation,Laryngeal Mucositis,Laryngeal Obstruction,Laryngeal Stenosis,Laryngitis,Laryngopharyngeal Dysesthesia,Laryngospasm,Left Ventricular Systolic Dysfunction,Lethargy,Leukemia Secondary to Oncology Chemotherapy,Leukocytosis,Leukoencephalopathy,Libido Decreased,Libido Increased,Lip Infection,Lip Pain,Lipase Increased,Lipohypertrophy,Localized Edema,Lordosis,Lower Gastrointestinal Hemorrhage,Lung Infection,Lymph Gland Infection,Lymph Leakage,Lymph Node Pain,Lymphedema,Lymphocele,Lymphocyte Count Decreased,Lymphocyte Count Increased,Malabsorption,Malaise,Mania,Mediastinal Hemorrhage,Mediastinal Infection,Memory Impairment,Meningismus,Meningitis,Menopause,Menorrhagia,Metabolism and Nutrition Disorders Other,Middle Ear Inflammation,Mitral Valve Disease,Mobitz (Type) II Atrioventricular Block,Mobitz Type I,Movements Involuntary,Mucosal Infection,Mucositis Oral,Multi-Organ Failure,Muscle Weakness Left-Sided,Muscle Weakness Lower Limb,Muscle Weakness Right-Sided,Muscle Weakness Trunk,Muscle Weakness Upper Limb,Musculoskeletal and Connective Tissue Disorders Other,Musculoskeletal Deformity,Myalgia,Myelitis,Myelodysplastic Syndrome,Myocardial Infarction,Myocarditis,Myositis,Nail Discoloration,Nail Infection,Nail Loss,Nail Ridging,Nasal Congestion,Nausea,Neck Edema,Neck Pain,Neck Soft Tissue Necrosis,Neoplasms Benign, Malignant and Unspecified (Incl Cysts and Polyps) Other,Nervous System Disorders Other,Neuralgia,Neutrophil Count Decreased,Night Blindness,Nipple Deformity,Non-Cardiac Chest Pain,Nystagmus,Obesity,Obstruction Gastric,Oculomotor Nerve Disorder,Olfactory Nerve Disorder,Oligospermia,Optic Nerve Disorder,Oral Cavity Fistula,Oral Dysesthesia,Oral Hemorrhage,Oral Pain,Osteonecrosis of Jaw,Osteoporosis,Otitis Externa,Otitis Media,Ovarian Hemorrhage,Ovarian Infection,Ovarian Rupture,Ovulation Pain,Pain,Pain in Extremity,Pain of Skin,Palmar-Plantar Erythrodysesthesia Syndrome,Palpitations,Pancreas Infection,Pancreatic Anastomotic Leak,Pancreatic Duct Stenosis,Pancreatic Enzymes Decreased,Pancreatic Fistula,Pancreatic Hemorrhage,Pancreatic Necrosis,Pancreatitis,Papilledema,Papulopustular Rash,Paresthesia,Paronychia,Paroxysmal Atrial Tachycardia,Pelvic Floor Muscle Weakness,Pelvic Infection,Pelvic Pain,Pelvic Soft Tissue Necrosis,Penile Infection,Penile Pain,Perforation Bile Duct,Pericardial Effusion,Pericardial Tamponade,Pericarditis,Perineal Pain,Periodontal Disease,Periorbital Edema,Periorbital Infection,Peripheral Ischemia,Peripheral Motor Neuropathy,Peripheral Nerve Infection,Peripheral Sensory Neuropathy,Peritoneal Infection,Peritoneal Necrosis,Personality Change,Phantom Pain,Pharyngeal Anastomotic Leak,Pharyngeal Fistula,Pharyngeal Hemorrhage,Pharyngeal Mucositis,Pharyngeal Necrosis,Pharyngeal Stenosis,Pharyngitis,Pharyngolaryngeal Pain,Phlebitis,Phlebitis Infective,Photophobia,Photosensitivity,Platelet Count Decreased,Pleural Effusion,Pleural Hemorrhage,Pleural Infection,Pleuritic Pain,Pneumonitis,Pneumothorax,Portal Hypertension,Portal Vein Thrombosis,Postnasal Drip,Postoperative Hemorrhage,Postoperative Thoracic Procedure Complication,Precocious Puberty,Pregnancy, Puerperium and Perinatal Conditions Other,Premature Delivery,Premature Menopause,Presyncope,Proctitis,Productive Cough,Prolapse of Intestinal Stoma,Prolapse of Urostomy,Prostate Infection,Prostatic Hemorrhage,Prostatic Obstruction,Prostatic Pain,Proteinuria,Pruritus,Psychiatric Disorders Other,Psychosis,Pulmonary Edema,Pulmonary Fibrosis,Pulmonary Fistula,Pulmonary Hypertension,Pulmonary Valve Disease,Purpura,Pyramidal Tract Syndrome,Radiation Recall Reaction (Dermatologic),Radiculitis,Rash Acneiform,Rash Maculo-Papular,Rash Pustular,Rectal Anastomotic Leak,Rectal Fistula,Rectal Hemorrhage,Rectal Mucositis,Rectal Necrosis,Rectal Obstruction,Rectal Pain,Rectal Perforation,Rectal Stenosis,Rectal Ulcer,Recurrent Laryngeal Nerve Palsy,Renal and Urinary Disorders Other,Renal Calculi,Renal Colic,Renal Hemorrhage,Reproductive System and Breast Disorders Other,Respiratory Failure,Respiratory, Thoracic and Mediastinal Disorders Other,Restlessness,Restrictive Cardiomyopathy,Retinal Detachment,Retinal Tear,Retinal Vascular Disorder,Retinoic Acid Syndrome,Retinopathy,Retroperitoneal Hemorrhage,Reversible Posterior Leukoencephalopathy Syndrome,Rhinitis Infective,Right Ventricular Dysfunction,Salivary Duct Inflammation,Salivary Gland Fistula,Salivary Gland Infection,Scalp Pain,Scleral Disorder,Scoliosis,Scrotal Infection,Scrotal Pain,Seizure,Sepsis,Seroma,Serum Amylase Increased,Serum Sickness,Sick Sinus Syndrome,Sinus Bradycardia,Sinus Disorder,Sinus Pain,Sinus Tachycardia,Sinusitis,Skin and Subcutaneous Tissue Disorders Other,Skin Atrophy,Skin Hyperpigmentation,Skin Hypopigmentation,Skin Induration,Skin Infection,Skin Ulceration,Sleep Apnea,Small Intestinal Anastomotic Leak,Small Intestinal Mucositis,Small Intestinal Obstruction,Small Intestinal Perforation,Small Intestinal Stenosis,Small Intestine Infection,Small Intestine Ulcer,Sneezing,Social Circumstances Other,Soft Tissue Infection,Soft Tissue Necrosis Lower Limb,Soft Tissue Necrosis Upper Limb,Somnolence,Sore Throat,Spasticity,Spermatic Cord Anastomotic Leak,Spermatic Cord Hemorrhage,Spermatic Cord Obstruction,Spinal Fracture,Spleen Disorder,Splenic Infection,Stenosis of Gastrointestinal Stoma,Stevens-Johnson Syndrome,Stoma Site Infection,Stomach Pain,Stomal Ulcer,Stridor,Stroke,Sudden Death NOS,Suicidal Ideation,Suicide Attempt,Superficial Soft Tissue Fibrosis,Superficial Thrombophlebitis,Superior Vena Cava Syndrome,Supraventricular Tachycardia,Surgical and Medical Procedures Other,Syncope,Telangiectasia,Testicular Disorder,Testicular Hemorrhage,Testicular Pain,Thromboembolic Event,Thrombotic Thrombocytopenic Purpura,Tinnitus,Tooth Development Disorder,Tooth Discoloration,Tooth Infection,Toothache,Toxic Epidermal Necrolysis,Tracheal Fistula,Tracheal Hemorrhage,Tracheal Mucositis,Tracheal Obstruction,Tracheal Stenosis,Tracheitis,Tracheostomy Site Bleeding,Transient Ischemic Attacks,Treatment Related Secondary Malignancy,Tremor,Tricuspid Valve Disease,Trigeminal Nerve Disorder,Trismus,Tumor Lysis Syndrome,Tumor Pain,Typhlitis,Unequal Limb Length,Unintended Pregnancy,Upper Gastrointestinal Hemorrhage,Upper Respiratory Infection,Ureteric Anastomotic Leak,Urethral Anastomotic Leak,Urethral Infection,Urinary Fistula,Urinary Frequency,Urinary Incontinence,Urinary Retention,Urinary Tract Infection,Urinary Tract Obstruction,Urinary Tract Pain,Urinary Urgency,Urine Discoloration,Urine Output Decreased,Urostomy Leak,Urostomy Obstruction,Urostomy Site Bleeding,Urostomy Stenosis,Urticaria,Uterine Anastomotic Leak,Uterine Fistula,Uterine Hemorrhage,Uterine Infection,Uterine Obstruction,Uterine Pain,Uterine Perforation,Uveitis,Vaginal Anastomotic Leak,Vaginal Discharge,Vaginal Dryness,Vaginal Fistula,Vaginal Hemorrhage,Vaginal Infection,Vaginal Inflammation,Vaginal Obstruction,Vaginal Pain,Vaginal Perforation,Vaginal Stricture,Vaginismus,Vagus Nerve Disorder,Vas Deferens Anastomotic Leak,Vascular Access Complication,Vascular Disorders Other,Vasculitis,Vasovagal Reaction,Venous Injury,Ventricular Arrhythmia,Ventricular Fibrillation,Ventricular Tachycardia,Vertigo,Vestibular Disorder,Virilization,Visceral Arterial Ischemia,Vital Capacity Abnormal,Vitreous Hemorrhage,Voice Alteration,Vomiting,Vulval Infection,Watering Eyes,Weight Gain,Weight Loss,Wheezing,White Blood Cell Decreased,Wolff-Parkinson-White Syndrome,Wound Complication,Wound Dehiscence,Wound Infection,Wrist Fracture",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3125302&version=1.1, +BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2006410&version=3.0, +Cause of Response,The text term used to describe the suspected cause or reason for the patient disease response.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161025&version=1.0, +Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.","Acute Renal Failure, Adenocarcinoma, Adrenocortical Insufficiency, Adenomatous Polyposis Coli, Allergies, Alpha-1 Antitrypsin, Anemia, Anxiety, Arrhythmia, Arthritis, Asthma, Atrial Fibrillation, Avascular Necrosis, Barrett's Esophagus,Basal Cell Carcinoma, Beckwith-Wiedemann, Behcet's Disease, Biliary Disorder, Blood Clots, Bone Fracture(s), Bronchitis, Calcium Channel Blockers, Cancer, Cataracts, Celiac Disease, Cirrhosis, unknown Etiology, Cerebrovascular Disease, Cholelithiasis, Chronic Renal Failure, Colon Polyps, Common Variable Immunodeficiency, Congestive Heart Failure (CHF), Connective Tissue Disorder, COPD, Coronary Artery Disease, Crohn's Disease, Cryptogenic Organizing Pneumonia, Deep Vein Thrombosis / Thromboembolism, Denys-Drash Syndrome, Depression, Diabetes, Diabetes, Type II, Diabetic Neuropathy, Diet Controlled Diabetes, Diverticulitis,DVT/PE, Dyslipidemia, Epilepsy, Eczema, Epstein-Barr Virus, Familial Adenomatous Polyposis, Fanconi Anemia, Fibrosis, Gastroesophageal Reflux Disease, GERD, Glaucoma, Glycogen Storage Disease, Gout, Gonadal Dysfunction, Gorlin Syndrome, H. pylori Infection, Hashimoto's Thyroiditis, Headache, Heart Disease, Hemihypertrophy, Hemorrhagic Cystitis, Hepatitis, Hepatitis A Infection, Hepatitis B Infection, Hepatitis C Infection, Chronic Hepatitis, Hereditary Non-polyposis Colon Cancer, Herpes, High Grade Liver Dysplastic Nodule, HIV / AIDS, Human Papillomavirus Infection, HUS/TTP, Hypercholesterolemia, Hypercalcemia, Hyperglycemia, Hyperlipidemia, Hypertension, Hypospadias, Hypothyroidism, Inflammatory Bowel Disease, Insulin Controlled Diabetes, Interstitial Pneumontis or ARDS, Intraductal Papillary Mucinous Neoplasm, Iron Overload, Ischemic Heart Disease, ITP, Joint Replacement, Kidney Disease, Liver Cirrhosis (Liver Disease), Liver Toxicity (Non-Infectious), Li-Fraumeni Syndrome, Low Grade Liver Dysplastic Nodule, Lupus, Lynch Syndrome, MAI, Myasthenia Gravis, Myocardial Infarction, Neuroendocrine Tumor, Nonalcoholic Steatohepatitis, Obesity, Organ transplant (site), Osteoarthritis, Osteoporosis or Osteopenia, Other, Other Cancer Within 5 Years, Other Nonmalignant Systemic Disease, Other Pulmonary Complications, Pancreatitis, Pain (Various), Peptic Ulcer (Ulcer), Peripheral Neuropathy, Peripheral Vascular Disease, Peutz-Jeghers Disease, Pregnancy in Patient or Partner, Primary Sclerosing Cholangitis, Psoriasis, Pulmonary Fibrosis, Pulmonary Hemorrhage, Renal Failure (Requiring Dialysis), Renal Dialysis, Renal Insufficiency, Rheumatologic Disease, Rheumatoid Arthritis, Rubinstein-Taybi Syndrome, Sarcoidosis, Seizure, Sleep apnea, Smoking, Steatosis, Stroke, Transient Ischemic Attack, Tuberculosis, Turcot Syndrome, Tyrosinemia, Ulcerative Colitis, Wagr Syndrome, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2970715&version=1.0, +Comorbidity Method of Diagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,"Histology, Pathology, Radiology, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142386&version=1.0, +Days to Adverse Event,Number of days between the date used for index and the date of the patient's adverse event.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154728&version=1.0, +Days to Comorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154729&version=1.0, +Days to Progression,Number of days between the date used for index and the date the patient's disease progressed.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154730&version=1.0, +Days to Progression Free,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,,,,FALSE,Diagnosis,,, +Days to Recurrence,Number of days between the date used for index and the date the patient's disease recurred.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154731&version=1.0, +Diabetes Treatment Type,Text term used to describe the types of treatment used to manage diabetes.,"Alpha-Glucosidase Inhibitor, Biguanide, Diet, Injected Insulin, Insulin, Oral Hypoglycemic, Sulfonylurea, Thiazolidinedione, Other, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3587247&version=1.0, +Disease Response,Code assigned to describe the patient's response or outcome to the disease.,"AJ-Adjuvant Therapy, BED-Biochemical Evidence of Disease, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PDM-Persistent Distant Metastasis, PLD-Persistent Locoregional Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, TF-Tumor Free, VGPR-Very Good Partial Response, WT-With Tumor, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5750671&version=1.0, +DLCO Ref Predictive Percent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2180255&version=1.0, +ECOG Performance Status,The ECOG functional performance status of the patient/participant.,"""0"", ""1"", ""2"", ""3"", ""4"", ""5"", unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=88&version=5.1, +FEV1 FVC Post Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302956&version=1.0, +FEV 1 FVC Pre Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302955&version=1.0, +FEV1 Ref Post Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,,,,FALSE,Follow Up,,"https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302948&version=1.0""", +FEV1 Ref Pre Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302947&version=1.0, +Height,The height of the patient in centimeters.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=649&version=4.1, +Hepatitis Sustained Virological Response,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6423783&version=1.0, +HPV Positive Type,Text classification to represent the strain or type of human papillomavirus identified in an individual.,"""16"", ""18"", ""26"", ""31"", ""33"", ""35"", ""39"", ""45"", ""51"", ""52"", ""53"", ""56"", ""58"", ""59"", ""63"", ""66"", ""68"", ""70"", ""73"", ""82"", Other, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2922649&version=1.0, +Karnofsky Performance Status,Text term used to describe the classification used of the functional capabilities of a person.,"""0"", ""10"", ""20"", ""30"", ""40"", ""50"", ""60"", ""70"", ""80"", ""90"", ""100"", unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003853&version=4.2, +Menopause Status,Text term used to describe the patient's menopause status.,"Premenopausal, Perimenopausal, Postmenopausal, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2434914&version=1.1, +Adverse Event Grade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","Grade 1, Grade 2, Grade 3, Grade 4, Grade 5",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2944515&version=1.0, +AIDS Risk Factors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,"Candidiasis,Coccidioidomycosis,Cryptococcosis,Cytomegalovirus,Encephalopathy,Herpes Simplex Virus,Histoplasmosis,Isosporiasis,Mycobacterium avium Complex,Mycobacterium tuberculosis,Mycobacterium, NOS,Nocardiosis,Pneumocystis Pneumonia,Pneumonia, NOS,Progressive Multifocal Leukoencephalopathy,Salmonella Septicemia,Toxoplasmosis,Wasting Syndrome",,,FALSE,Follow Up,,, +Body Surface Area,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=653&version=6.0, +CD4 Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4182751&version=1.0, +CDC HIV Risk Factors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.","Hemophiliac,Heterosexual Contact,Homosexual Contact,Intravenous Drug User,None,Transfusion Recipient,unknown,Not Reported",,,FALSE,Follow Up,,, +Days to Imaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient.,,,,FALSE,Follow Up,,, +Evidence of Recurrence Type,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,"Biopsy with Histologic Confirmation, Convincing Image Source, Positive Biomarkers",,,FALSE,Follow Up,,, +HAART Treatment Indicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,, +HIV Viral Load,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2649682&version=1.0, +Hormonal Contraceptive Use,The text term used to indicate whether the patient used hormonal contraceptives.,"Current User, Former User, Never Used, unknown, Not Reported",,,FALSE,Follow Up,,, +Hysterectomy Margins Involved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,"Bladder,Macroscopic Parametrium,Microscopic Parametrium,None,Vagina,unknown,Not Reported",,,FALSE,Follow Up,,, +Hysterectomy Type,The text term used to describe the type of hysterectomy the patient had.,"Hysterectomy NOS, Not performed, Radical Hysterectomy, Simple Hysterectomy, unknown, Not Reported",,,FALSE,Follow Up,,, +Imaging Result,The text term used to describe the result of the imaging or scan performed on the patient.,"Positive, Indeterminate, Negative, Not Performed, unknown, Not Reported",,,FALSE,Follow Up,,, +Imaging Type,The text term used to describe the type of imaging or scan performed on the patient.,"99mTc Bone Scintigraphy, CT Scan, MRI, PET",,,FALSE,Follow Up,,, +Immunosuppressive Treatment Type,The text term used to describe the type of immunosuppresive treatment the patient received.,"Anti-TNFTherapy,Azathioprine,Cyclophosphamide,Methotrexate,None,Other,unknown,Not Reported",,,FALSE,Follow Up,,, +Nadir CD4 Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,,,,FALSE,Follow Up,,, +Pregnancy Outcome,The text term used to describe the type of pregnancy the patient had,"Ectopic Pregnancy,Induced Abortion,Live Birth,Miscarriage,Stillbirth,unknown,Not Reported",,,FALSE,Follow Up,,, +Recist Targeted Regions Number,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",,,,FALSE,Follow Up,,, +Recist Targeted Regions Sum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",,,,FALSE,Follow Up,,, +Scan Tracer Used,The text term used to describe the type of tracer used during the imaging or scan of the patient.,"Acetate, Axumin, Choline, PSMA, Sodium Fluoride",,,FALSE,Follow Up,,, +Progression or Recurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, unknown, Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3121376&version=1.0, +Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,,, +Progression or Recurrence Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, +Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, +Treatment Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0, +Progression or Recurrence Type,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,"Biochemical, Distant, Local, Regional, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142385&version=1.0, +Reflux Treatment Type,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,"Antacids, H2 Blockers, Medically Treated, No Treatment, Not Applicable, Not Reported, Proton Pump Inhibitors, Surgically Treated, unknown",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440206&version=1.0, +Risk Factor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,"Alcohol Consumption,Alcoholic Liver Disease,Allergy Animal NOS,Allergy Ant,Allergy Bee,Allergy Cat,Allergy Dairy or Lactose,Allergy Dog,Allergy Eggs,Allergy Food NOS,Allergy Fruit,Allergy Meat,Allergy Mold or Dust,Allergy Nuts,Allergy Processed Foods,Allergy Seafood,Allergy Wasp,Alpha-1 Antitrypsin Deficiency,Autoimmune Atrophic Chronic Gastritis,Barrett's Esophagus,Beckwith-Wiedemann,Behcet's Disease,Cancer,Cholelithiasis,Chronic Hepatitis,Cirrhosis,Colon Polyps,Common variable immune deficiency (CVID),Denys-Drash Syndrome,Diabetes NOS,Diabetes Type I,Diabetes Type II,Diet,Diverticulitis,Endometriosis,Endosalpingiosis,Eczema,Epstein-Barr Virus,Familial Adenomatous Polyposis,Fanconi Anemia,Fibrosis,Gastric Polyp(s),Gilbert's Syndrome,Gorlin Syndrome,Hashimoto's Thyroiditis,Hay Fever,Headache,Helicobacter Pylori-Associated Gastritis,Hematologic Disorder NOS,Hemihypertrophy,Hemochromatosis,Hepatic Encephalopathy,Hepatitis B Infection,Hepatitis C Infection,Hepatitis NOS,High Grade Dysplasia,HIV,Human Papillomavirus Infection,Hypospadias,Intestinal Metaplasia,Iron Overload,Li-Fraumeni Syndrome,Low Grade Dysplasia,Lymphocytic Thyroiditis,Lynch Syndrome,Myasthenia Gravis,Nonalcoholic Fatty Liver Disease,Nonalcoholic Steatohepatitis,Obesity,Oral Contraceptives,Pancreatitis,Parasitic Disease of Biliary Tract,Primary Sclerosing Cholangitis,Recurrent Pyogenic Cholangitis,Reflux Disease,Rheumatoid Arthritis,Rubinstein-Taybi Syndrome,Sarcoidosis,Seizure,Sensory Changes,Serous tubal intraepithelial carcinoma (STIC),Steatosis,Tattoo,Thyroid Nodular Hyperplasia,Tobacco NOS,Tobacco Smokeless,Tobacco Smoking,Turcot Syndrome,Undescended Testis,Vision Changes,Wagr Syndrome,unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142389&version=1.0, +Risk Factor Treatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514356&version=1.0, +Viral Hepatitis Serologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,"HBV Core Antibody, HBV DNA, HBV Genotype, HBV Surface Antibody, HCV Genotype, Hepatitis B Surface Antigen, Hepatitis C Antibody, Hepatitis C Virus RNA, unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4395982&version=1.0, +Weight,The weight of the patient measured in kilograms.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=651&version=4.0, +Days to Treatment End,Number of days between the date used for index and the date the treatment ended.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154725&version=1.0, +Days to Treatment Start,Number of days between the date used for index and the date the treatment started.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154726&version=1.0, +Initial Disease Status,The text term used to describe the status of the patient's malignancy when the treatment began.,"Initial Diagnosis, Progressive Disease, Recurrent Disease, Residual Disease, unknown, Not Reported",,,FALSE,Therapy,,, +Regimen or Line of Therapy,The text term used to describe the regimen or line of therapy.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161024&version=1.0, +Therapeutic Agents,Text identification of the individual agent(s) used as part of a treatment regimen.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2975232&version=1.0, +Treatment Effect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,"Complete Necrosis (No Viable Tumor), Incomplete Necrosis (Viable Tumor Present), No Necrosis, unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514354&version=1.0, +Treatment Intent Type,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],"Adjuvant, Cancer Control, Cure, Neoadjuvant, Palliative, Prevention, unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2793511&version=1.0, +Treatment or Therapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,"yes, no, unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4231463&version=1.0, +Treatment Outcome,Text term that describes the patient's final outcome after the treatment was administered.,"Complete Response, Mixed Response, No Measurable Disease, No Response, Partial Response, Persistent Disease, Progressive Disease, Stable Disease, Treatment Ongoing, Treatment Stopped Due to Toxicity, Very Good Partial Response, unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102383&version=1.0, +Treatment Type,Text term that describes the kind of treatment administered.,"Ablation Cryo,Ablation Ethanol Injection,Ablation Microwave,Ablation NOS,Ablation Radiofrequency,Ablation Radiosurgical,Ancillary Treatment,Antiseizure Treatment,Bisphosphonate Therapy,Blinded Study Treatment unknown,Brachytherapy High Dose,Brachytherapy Low Dose,Brachytherapy NOS,Chemoembolization,Chemoprotectant,Chemotherapy,Concurrent Chemoradiation,Cryoablation,Embolization,Ethanol Injection Ablation,External Beam Radiation,Hormone Therapy,I-131 Radiation Therapy,Internal Radiation,Immunotherapy (Including Vaccines),Isolated Limb Perfusion (ILP),Organ Transplantation,Other,Pharmaceutical Therapy NOS,Pleurodesis,Radiation 2D Conventional,Radiation 3D Conformal,Radiation Combination,Radiation Cyberknife,Radiation External Beam,Radiation Implants,Radiation Intensity-Modulated Radiotherapy,Radiation Internal,Radiation Proton Beam,Radiation Radioisotope,Radiation Stereotactic/Gamma Knife/SRS,Radiation Systemic,Radiation Therapy NOS,Radioactive Iodine Therapy,Radioembolization,Radiosensitizing Agent,Stem Cell Treatment,Stem Cell Transplantation Autologous,Stem Cell Transplantation Double Autologous,Stem Cell Transplantation Allogeneic,Stem Cell Transplantation Non-Myeloablative,Stem Cell Transplantation Syngenic,Stem Cell Transplantation Haploidentical,Stem Cell Transplantation NOS,Stereotactic Radiosurgery,Steroid Therapy,Surgery,Targeted Molecular Therapy,unknown,Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102381&version=1.0, +Chemo Concurrent to Radiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,"Yes, No, unknown, Not Reported",,,FALSE,Therapy,,, +Number of Cycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,,,,FALSE,Therapy,,, +Reason Treatment Ended,The text term used to describe the reason a specific treatment or regimen ended.,"Adverse Therapy Event, Course of Therapy Completed, Death, Disease Progression, Other, Withdrawal by Subject",,,FALSE,Therapy,,, +Treatment Arm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,"A081105, E4512, EA5142",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=7068995&version=1.0, +Treatment Dose,The numeric value used to describe the dose of an agent the patient received.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2182728&version=3.0, +Treatment Dose Units,The text term used to describe the dose units of an agent the patient received.,"cGy, Gy",,,FALSE,Therapy,,, +Treatment Effect Indicator,The text term used to indicate whether the treatment had an effect on the patient.,"Yes, No, Not Reported, unknown",,,FALSE,Therapy,,, +Treatment Frequency,The text term used to describe the frequency the patient received an agent or regimen.,"Every Hour,Five Times Daily,Four Times Daily,Three Times Daily,Twice Daily,Every 24 Hours,Every Other Day,Twice Weekly,Once Weekly,unknown,Not Reported",,,FALSE,Therapy,,, +Sentinel Lymph Node Count,Numeric count of sentinel lymph nodes.,,,,FALSE,Diagnosis,,, +Sentinel Node Positive Assessment Count,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,,,,FALSE,Diagnosis,,, +Tumor Extranodal Extension Indicator,The indicator to determine extranodal involvement or extent of the disease.,"Absent,Indeterminate,NO, YES, No source documentation,Not applicable,Not sampled or dissected,Present,Present - extensive,Present - minimal,UNKNOWN,Unspecified",,,FALSE,Diagnosis,,, +Satellite Metastasis Present Indicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,"Yes, No, unknown",,,FALSE,Diagnosis,,, +Other Biopsy Resection Site,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1),,,,FALSE,Diagnosis,,, +Extent of Tumor Resection,"The degree to which the lesion has been cut out, or resected.","Gross Total Resection, Open Biopsy, Subtotal Resection, Extensive Subtotal, Minor, Optimal debulking, Other, Partial debulking, Segmental, Suboptimal, Suboptimal debulking, NTR, unknown, Not Reported, Not Applicable ",,,FALSE,Diagnosis,,, +Precancerous Condition Type,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS,No diagnosis possible",,,FALSE,Diagnosis,,, +Prior Sites of Radiation,The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.,"Abdomen total,Abdominal Wall,Acetabulum,Adenoid,Adipose,Adrenal,Alveolar Ridge,Amniotic Fluid,Ampulla of Vater,Anal Sphincter,Ankle,Anorectum,Antecubital Fossa,Antrum,Anus,Aorta,Aortic Body,Appendix,Aqueous Fluid,Arm,Artery,Ascending Colon,Ascending Colon Hepatic Flexure,Ascites,Auditory Canal,Autonomic Nervous System,Axilla,Back,Bile Duct,Bladder,Blood,Blood Vessel,Body total,Bone,Bone Marrow,Bone non-spine,Bowel,Brain,Brain Stem,Breast,Broad Ligament,Bronchiole,Bronchus,Brow,Buccal Cavity,Buccal Mucosa,Buttock,Calf,Capillary,Cardia,Carina,Carotid Artery,Carotid Body,Cartilage,Cecum,Cell-Line,Central Nervous System,Cerebellum,Cerebral Cortex,Cerebrospinal Fluid,Cerebrum,Cervical Spine,Cervix,Chest,Chest Wall,Chin,Clavicle,Clitoris,Colon,Colon Mucosa Only,Common Duct,Conjunctiva,Connective Tissue,Dermal,Descending Colon,Diaphragm,Distant Site,Duodenum,Ear,Ear Canal,Ear Pinna (External),Elbow,Endocrine Gland,Epididymis,Epidural Space,Epitrochlear,Esophagogastric Junction,Esophagus,Esophagus Mucosa Only,Eye,Fallopian Tube,Femoral Artery,Femoral Vein,Femur,Fibroblasts,Fibula,Finger,Floor of Mouth,Fluid,Foot,Forearm,Forehead,Foreskin,Frontal Cortex,Frontal Lobe,Fundus of Stomach,Gallbladder,Ganglia,Gastroesophageal Junction,Gastrointestinal Tract,Gastrointestinal Intestine,Genitourinary NOS,Groin,Gum,Hand,Hard Palate,Head Face Or Neck Nos,Head and Neck,Heart,Hepatic,Hepatic Duct,Hepatic Vein,Hilar,Hip,Hippocampus,Humerus,Hypopharynx,Ileocecal Valve,Ileum,Ilium,Index Finger,Ischium,Islet Cells,Jaw,Jejunum,Joint,Kidney,Knee,Lacrimal Gland,Large Bowel,Laryngopharynx,Larynx,Leg,Leptomeninges,Ligament,Lip,Liver,Lumbar Spine,Lung,Lymph Node,Lymph Node(s) Axilla,Lymph Node(s) Cervical,Lymph Node(s) Distant,Lymph Node(s) Epitrochlear,Lymph Node(s) Femoral,Lymph Node(s) Hilar,Lymph Node(s) Iliac-Common,Lymph Node(s) Iliac-External,Lymph Node(s) Inguinal,Lymph Node(s) Internal Mammary,Lymph Node(s) Mammary,Lymph Node(s) Mediastinal,Lymph Node(s) Mesenteric,Lymph Node(s) Occipital,Lymph Node(s) Paraaortic,Lymph Node(s) Parotid,Lymph Node(s) Pelvic,Lymph Node(s) Popliteal,Lymph Node(s) Regional,Lymph Node(s) Retroperitoneal,Lymph Node(s) Scalene,Lymph Node(s) Splenic,Lymph Node(s) Subclavicular,Lymph Node(s) Submandibular,Lymph Node(s) Supraclavicular,Mandible,Mantle,Maxilla,Mediastinal Soft Tissue,Mediastinum,Mesentery,Mesothelium,Middle Finger,Mitochondria,Muscle,Nails,Nasal Cavity,Nasal Soft Tissue,Nasopharynx,Neck,Nerve,Nerve(s) Cranial,Occipital Cortex,Ocular Orbits,Omentum,Oral Cavity,Oral Cavity Mucosa Only,Oropharynx,Other,Ovary,Palate,Pancreas,Parametrium,Paraspinal Ganglion,Parathyroid,Parotid Gland,Patella,Pelvis,Penis,Pericardium,Periorbital Soft Tissue,Peritoneal Cavity,Peritoneum,Pharynx,Pineal,Pineal Gland,Pituitary Gland,Placenta,Pleura,Popliteal Fossa,Pouch,Primary Tumor Field,Primary tumor site,Prostate,Prostate Bed,Prostate Seminal Vesicles and Lymph Nodes,Pylorus,Rectosigmoid Junction,Rectum,Regional Site,Retina,Retro-Orbital Region,Retroperitoneum,Rib,Ring Finger,Round Ligament,Sacrum,Salivary Gland,Scalp,Scapula,Sciatic Nerve,Scrotum,Seminal Vesicle,Shoulder,Sigmoid Colon,Sinus,Sinus(es) Maxillary,Skeletal Muscle,Skin,Skin lower extremity local,Skin total,Skin trunk local,Skin upper extremity local,Skull,Small Bowel,Small Bowel Mucosa Only,Small Finger,Soft Tissue,Spinal Column,Spinal Cord,Spine,Spleen,Splenic Flexure,Sternum,Stomach,Stomach Mucosa Only,Subcutaneous Tissue,Synovium,Temporal Cortex,Tendon,Testis,Thigh,Thoracic Spine,Thorax,Throat,Thumb,Thymus,Thyroid,Tibia,Tongue,Tonsil,Tonsil (Pharyngeal),Trachea / Major Bronchi,Transverse Colon,Trunk,Umbilical Cord,unknown,Ureter,Urethra,Urinary Tract,Uterus,Uvula,Vagina,Vas Deferens,Vein,Venous,Vertebra,Vulva,White Blood Cells,Wrist,Not Reported",,,FALSE,Therapy,,, +Immunosuppression,The indicator that describes whether or not immunosuppressive therapy was administered.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Therapy,,, +Concomitant Medication Received Type,An enumerated list of the type of concomitant medication received by the patient.,"Anticoagulant agents,Anticonvulsant,Antifungal,Antiplatelet agents,Antidepressants-Moderate CYP2D6 inhibitors,Antidepressants-Strong CYP2D6 inhibitors,Antidepressants-weak CYP2D2 inhibitors or non-inhibitors,Anxiolytics or sedatives,Aspirin,Bisphosphonates for treatment/prevention of bone loss,Corticosteroid,COX-2 inhibitor,Decadron,Diabetes-Insulin,Diabetes-Metformin containing agents,Growth factor,Intravaginal estrogen preparations,Lipid-lowering drugs,Non-prescription supplements for memory,Non-prescription supplements for relief of hot flashes,Non-steroidal anti-inflammatory agents,Opioids,Other,Prescription medications for memory,Prescription medications for relief of hot flashes,Prophylactic antiplatelet therapy,Tricyclic antidepressants,Not Applicable,unknown,Not Reported",,,FALSE,Therapy,,, +Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported",,,FALSE,Family History,,, +COVID19 Occurrence Indicator,The indicator that describes whether or not a COVID-19 infectious disorder occurred.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,, +COVID19 Current Status,The patient's current COVID-19 status of sign or symptom events or interventions,"Patient currently has symptoms, Patient had symptoms but now is fully recovered, Patient never had any symptoms of COVID-19, Status unknown due to general COVID-19 related travel restrictions, Status unknown due to lack of disease/tumor assessment due to COVID-19 diagnosis, Status unknown due to other reasons",,,FALSE,Exposure,,, +COVID19 Positive Lab Test Indicator,The indicator that describes whether or not there was a COVID-19 positive test result.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,, +COVID19 Antibody Testing,Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.,"SARS-CoV-2 IgM antibody positive, SARS-CoV-2 IgG antibody positive, SARS-CoV-2 IgG/IgM antibody positive, SARS-CoV-2 IgM antibody negative, SARS-CoV-2 IgG antibody negative, SARS-CoV-2 IgG/IgM antibody negative, unknown, Not Applicable, Not Done",,,FALSE,Exposure,,, +COVID19 Complications Severity,Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.,"Cardiac complications, Pulmonary complications, Systemic complications, Other, Not Applicable, unknown",,,FALSE,Exposure,,, +COVID19 Cancer Treatment Followup,Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder,"Yes, No, unknown, Not Applicable",,,FALSE,Exposure,,, +Ecig vape use,"Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)","Current, Former, Never, unknown",,,FALSE,Exposure,,, +Ecig vape 30 day use num,Number of days e-cigarettes or vaping device was used in the last 30 days,,,,FALSE,Exposure,,, +Ecig vape times per day,e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes),,,,FALSE,Exposure,,, +Type of smoke exposure cumulative years,The number of cumulative years of the patient's specific type of smoke exposure,,,,FALSE,Exposure,,, +Chewing tobacco daily use count,"The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.",,,,FALSE,Exposure,,, +Second hand smoke exposure years,The number of cumulative years of the patient's exposure to second-hand cigarette smoke,,,,FALSE,Exposure,,, +Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown",,,FALSE,Family History,,, +Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome",,,FALSE,Family History,,, +Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation",,,FALSE,Family History,,, +Mutational Signatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ","UV light induced mutations,Alkylating Agents (Temozolomide) induced mutations,Tobacco use associated mutations,age of cancer diagnosis,transcriptional strand bias,microsatellite instability (additions and deletions),methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine) ,Activation Induced Deaminases (AID) associated mutations,APOBEC enzymes associated mutations,altered activity of the error-prone polymerase POLε (POLE) ,localized substitution hypermutation (kataegis),DNA MMR Deficiency,Ig gene hypermutation,Signature 1A,Signature 1B,Signature 2,Signature 3,Signature 4,Signature 5,Signature 6,Signature 7,Signature 8,Signature 9,Signature 10,Signature 11,Signature 12,Signature 13,Signature 14,Signature 15,Signature 16,Signature 17,Signature 18,Signature 19,Signature 20,Signature 21,Other,Data not available,Not Applicable,Not Reported,unknown",,,FALSE,Molecular Test,,, +Mismatch Repair System Status,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,"Mismatch repair deficiency MMRD, Mismatch repair proficiency MMPP, Microsatellite instability high MSIH, Microsatellite stable MSS, unknown or other",,,FALSE,Molecular Test,,, +Lab Tests for MMR Status,Laboratory tests used to evaluate the status of mismatch repair pathways,"IHC staining for mismatch repair proteins, PCR to evaluate microsatellite instability, MLH1 promoter methylation analysis, BRAF sequencing, Other, Not Applicable, unknown",,,FALSE,Molecular Test,,, +Mode of Cancer Detection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection","Standard of Care Screening, Clinical Examination of unrelated cancer symptoms, Incidentaloma, Interval Cancer, Data not available",,,FALSE,Diagnosis,,, +Gene Symbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",,,,TRUE,Molecular Test,,, +Molecular Analysis Method,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Comparative Genomic Hybridization,Cytogenetics NOS,FISH,Flow Cytometry,IHC,ISH,Karyotype,Microarray,Microsatellite Analysis,Nuclear Staining,Other,RNA Sequencing,RT-PCR,Sequencing NOS,Southern Blotting,Targeted Sequencing,WGS,WXS,unknown,Not Reported,Not Applicable",,,TRUE,Molecular Test,,, +Test Result,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Abnormal NOS,Copy Number Reported,Equivocal,High,Intermediate,Loss of Expression,Low,Negative,Normal,Overexpressed,Positive,Test Value Reported,unknown,Not Reported,Not Applicable",,,TRUE,Molecular Test,,, +AA Change,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,,,,FALSE,Molecular Test,,, +Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"BCL6, CA-125, CA19-9, CCND1, CD10, CD117, CD138, CD14, CD15, CD19, CD20, CD22, CD23, CD25, CD3, CD30, CD33, CD34, CD45, CD5, CD56, CD7, CD79A, CEA, HLA-DR, Mesothelin, NSE, Squamous Cell Carcinoma Antigen, unknown, Not Reported",,,FALSE,Molecular Test,,, +Clinical Biospecimen Type,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","Blood, Bone Marrow, Buccal Mucosa, Buffy Coat, Cerebrospinal Fluid, Connective Tissue, Embryonic Fluid, Embryonic Tissue, Feces, Granulocyte, Muscle Tissue, Nerve Tissue, Peritoneal Fluid, Plasma, Pleural Fluid, Saliva, Serum, Skin, Soft Tissue, Tissue NOS, Uninvolved Tissue NOS, Urine, unknown, Not Reported",,,FALSE,Molecular Test,,, +Blood Test Normal Range Upper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,,,,FALSE,Molecular Test,,, +Blood Test Normal Range Lower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,,,,FALSE,Molecular Test,,, +Cell Count,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,,,,FALSE,Molecular Test,,, +Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chrM,chrX,chrY,unknown,Not Reported",,,FALSE,Molecular Test,,, +Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Clonal, Non-clonal",,,FALSE,Molecular Test,,, +Copy Number,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",,,,FALSE,Molecular Test,,, +Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",,,,FALSE,Molecular Test,,, +Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",,,,FALSE,Molecular Test,,, +Histone Family,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.","H1, H2A, H2B, H3, H4, unknown, Not Reported",,,FALSE,Molecular Test,,, +Histone Variant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","CENP-A, H2A-Bbd, H2A.X, H2A.Z,H2A.Z.1, H2A.Z.2, H2A.Z.2.2, H3.1, H3.2, H3.3, H3.5, H3.X, H3.Y, H3t (H3.4), mH2A, mH2A.1, mH2A.2, unknown, Not Reported",,,FALSE,Molecular Test,,, +Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",,,,FALSE,Molecular Test,,, +Laboratory Test,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.","Absolute Neutrophil,Albumin,Alpha Fetoprotein,B-cell genotyping,Basophil,Beta 2 Microglobulin,Blood Urea Nitrogen,C-Reactive Protein,Calcium,Cellularity,Circulating Tumor Cells,Creatinine,Eosinophil,Epstein-Barr Virus,Glucose,Hematocrit,Hemoglobin,HPV-E6/E7,Human Chorionic Gonadotropin,Human Papillomavirus,Immunoglobulin A,Immunoglobulin G,Immunoglobulin M,Lactate Dehydrogenase,Leukocytes,Luteinizing Hormone,Lymphoblasts,Lymphocytes,M Protein,Metamyelocytes,Myeloblasts,Myelocytes,Neutrophil Bands,Platelets,Prolymphocytes,Promonocytes,Promyelocytes,Segmented Neutrophil,Serum Free Immunoglobulin Light Chain, Kappa,Serum Free Immunoglobulin Light Chain, Lambda,Serum Free Immunoglobulin Light Chain, NOS,Testosterone,Total Bilirubin,Total Protein,unknown,Not Reported",,,FALSE,Molecular Test,,, +Loci Abnormal Count,Numeric value used to describe the number of loci determined to be abnormal.,,,,FALSE,Molecular Test,,, +Loci Count,Numeric value used to describe the number of loci tested.,,,,FALSE,Molecular Test,,, +Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,,,,FALSE,Molecular Test,,, +Mismatch Repair Mutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Yes, No, unknown, Not Reported",,,FALSE,Molecular Test,,, +Molecular Consequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"3 Prime UTR Variant, 5 Prime UTR Variant, Coding Sequence Variant, Downstream Gene Variant, Feature Elongation, Feature Truncation, Frameshift Variant, Incomplete Terminal Codon Variant, Inframe Deletion, Inframe Insertion, Intergenic Variant, Intron Variant, Mature miRNA Variant, Missense Variant, NMD Transcript Variant, Non-coding Transcript Exon Variant, Non-coding Transcript Variant, Protein Altering Variant, Regulatory Region Ablation, Regulatory Region Amplification, Regulatory Region Variant, Splice Acceptor Variant, Splice Donor Variant, Splice Region Variant, Start Lost, Stop Gain, Stop Lost, Stop Retained Variant, Synonymous Variant, TF Binding Site Variant, TFBS Ablation, TFBS Amplification, Transcript Ablation, Transcript Amplification, Upstream Gene Variant",,,FALSE,Molecular Test,,, +Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,"Benign, Likely Benign, Likely Pathogenic, Pathogenic, Uncertain Significance",,,FALSE,Molecular Test,,, +Ploidy,Text term used to describe the number of sets of homologous chromosomes.,"Aneuploid, Diploid, Hyperdiploid, Hypodiploid, Near Diploid, Tetraploid, unknown, Not Reported",,,FALSE,Molecular Test,,, +Second Exon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",,,,FALSE,Molecular Test,,, +Second Gene Symbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",,,,FALSE,Molecular Test,,, +Specialized Molecular Test,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,,,,FALSE,Molecular Test,,, +Test Analyte Type,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"DNA, mRNA, miRNA, Protein Analyte, Total RNA, unknown, Not Reported",,,FALSE,Molecular Test,,, +Test Units,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,,,,FALSE,Molecular Test,,, +Test Value,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,,,,FALSE,Molecular Test,,, +Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,,,,FALSE,Molecular Test,,, +Variant Origin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Germline, Somatic, unknown",,,FALSE,Molecular Test,,, +Variant Type,The text term used to describe the type of genetic variation.,"Alleles, Amplification, Chrimerism, Conversion, Deletion, Deletion-Insertion, Duplication, Extension, Gain, Hypermethylation, Insertion, Inversion, Loss, Methylation, Mosaicism, Other, Partial Methylation, Rearrangement, Repeated Sequences, Splice, Substitution, Translocation, unknown, Not Reported",,,FALSE,Molecular Test,,, +Zygosity,The text term used to describe the zygosity of a specific genetic variant.,"Heterozygous, Hemizygous, Homozygous, Nullizygous, unknown, Not Reported",,,FALSE,Molecular Test,,, +Cog Neuroblastoma Risk Group,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,"High Risk, Intermediate Risk, Low Risk, unknown, Not Reported",,,FALSE,Diagnosis,,, +Cog Rhabdomyosarcoma Risk Group,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).","High Risk, Intermediate Risk, Low Risk, unknown, Not Reported",,,FALSE,Diagnosis,,, +Gleason Grade Group,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Group 1, Group 2, Group 3, Group 4, Group 5",,,FALSE,Diagnosis,,, +Gleason Grade Tertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,"Pattern 4, Pattern 5",,,FALSE,Diagnosis,,, +Gleason Patterns Percent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",,,,FALSE,Diagnosis,,, +Greatest Tumor Dimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,,,,FALSE,Diagnosis,,, +IGCCCG Stage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.","Good Prognosis, Intermediate Prognosis, Poor Prognosis, unknown, Not Reported",,,FALSE,Diagnosis,,, +INPC Grade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).","Differentiating, Poorly Differentiated, Undifferentiated,unknown, Not Reported",,,FALSE,Diagnosis,,, +INPC Histologic Group,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.","Favorable, Unfavorable, unknown, Not Reported",,,FALSE,Diagnosis,,, +INRG Stage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).","L1, L2, M, Ms, unknown, Not Reported",,,FALSE,Diagnosis,,, +INSS Stage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).","Stage 1, Stage 2A, Stage 2B, Stage 3, Stage 4, Stage 4S, unknown, Not Reported",,,FALSE,Diagnosis,,, +International Prognostic Index,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.","Low Risk, Low-Intermediate Risk, High-Intermediate Risk, High Risk",,,FALSE,Diagnosis,,, +IRS Group,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).","Group I,Group Ia,Group Ib,Group II, Group IIa,Group IIc,Group III,Group IIIa,Group IIIb,Group IV,unknown,Not Reported",,,FALSE,Diagnosis,,, +IRS Stage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).","1,2,3,4,unknown,Not Reported",,,FALSE,Diagnosis,,, +ISS Stage,The multiple myeloma disease stage at diagnosis.,"I,II,III, Not Reported, unknown",,,FALSE,Diagnosis,,, +Lymph Node Involved Site,The text term used to describe the anatomic site of lymph node involvement.,"Axillary,Cervical,Epitrochlear,Femoral,Hilar,Iliac-common,Iliac-external,Iliac, NOS,Inguinal,Mediastinal,Mesenteric,None,Occipital,Paraaortic,Parotid,Popliteal,Retroperitoneal,Splenic,Submandibular,Supraclavicular,unknown,Not Reported",,,FALSE,Diagnosis,,, +Margin Distance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,,,,FALSE,Diagnosis,,, +Margins Involved Site,The text term used to describe the anatomic sites that were involved in the survival margins.,"Gerota Fascia, Parenchyma, Perinephric Fat, Renal, Renal Capsule, Renal Sinus, Renal Vein, Ureter",,,FALSE,Diagnosis,,, +Medulloblastoma Molecular Classification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,"Not Determined, Non-WNT/non-SHH Activated, SHH-Activated, WNT-Activated, unknown, Not Reported",,,FALSE,Diagnosis,,, +Micropapillary Features,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,"Absent, Present, unknown, Not Reported",,,FALSE,Diagnosis,,, +Mitosis Karyorrhexis Index,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,"High, Intermediate, Low, unknown, Not Reported",,,FALSE,Diagnosis,,, +Non Nodal Regional Disease,The text term used to describe whether the patient had non-nodal regional disease.,"Absent, Indeterminate, Present, unknown, Not Reported",,,FALSE,Diagnosis,,, +Non Nodal Tumor Deposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,, +Ovarian Specimen Status,The text term used to describe the physical condition of the involved ovary.,"Ovarian Capsule Intact, Ovarian Capsule Ruptured, Ovarian Capsule Fragmented, unknown, Not Reported",,,FALSE,Diagnosis,,, +Ovarian Surface Involvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,"Absent, Present, Indeterminate, unknown, Not Reported",,,FALSE,Diagnosis,,, +Pregnant at Diagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,, +Primary Gleason Grade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5",,,FALSE,Diagnosis,,, +Secondary Gleason Grade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5",,,FALSE,Diagnosis,,, +Supratentorial Localization,Text term to specify the location of the supratentorial tumor.,"Cerebral Cortex, Deep Gray, Spinal Cord, White Matter, unknown, Not Reported",,,FALSE,Diagnosis,,, +Tumor Depth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",,,,FALSE,Diagnosis,,, +Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Intermediate Grade, Low Grade, unknown, Not Reported",,,FALSE,Diagnosis,,, +WHO CNS Grade,WHO CNS Grade,"Grade I, Grade II, Grade III, Grade IV, Grade Not Assigned, unknown, Not Reported",,,FALSE,Diagnosis,,, +WHO NTE Grade,WHO NTE Grade,"G1, G2, G3, GX, unknown, Not Reported",,,FALSE,Diagnosis,,, +Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3225640&version=2.0, +Days to Last Follow up,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0, +Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0, +Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2759550&version=1.0, +Primary Diagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS,Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,unknown",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0, +Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3382736&version=2.0, +Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,, +Site of Resection or Biopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161034&version=1.0, +Tissue or Organ of Origin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161035&version=1.0, +Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Low Grade, unknown, Not Reported, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2785839&version=2.0, AJCC Clinical M,"Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment.","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440331&version=1.0, + assessment parameters determined prior to treatment.","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440331&version=1.0, AJCC Clinical N,"Extent of the regional lymph node involvement for the cancer based on evidence obtained from - clinical assessment parameters determined prior to treatment.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440330&version=1.0, + clinical assessment parameters determined prior to treatment.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440330&version=1.0, AJCC Clinical Stage,"Stage group determined from clinical information on the tumor (T), regional node (N) and - metastases (M) and by grouping cases with similar prognosis for cancer.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440332&version=1.0, + metastases (M) and by grouping cases with similar prognosis for cancer.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440332&version=1.0, AJCC Clinical T,"Extent of the primary cancer based on evidence obtained from clinical assessment parameters - determined prior to treatment.","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440328&version=1.0, + determined prior to treatment.","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440328&version=1.0, AJCC Pathologic M,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using - criteria established by the American Joint Committee on Cancer (AJCC).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045439&version=1.0, + criteria established by the American Joint Committee on Cancer (AJCC).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045439&version=1.0, AJCC Pathologic N,"The codes that represent the stage of cancer based on the nodes present (N stage) according - to criteria based on multiple editions of the AJCC's Cancer Staging Manual.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203106&version=1.0, + to criteria based on multiple editions of the AJCC's Cancer Staging Manual.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203106&version=1.0, AJCC Pathologic Stage,"The extent of a cancer, especially whether the disease has spread from the original site to - other parts of the body based on AJCC staging criteria.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203222&version=1.0, + other parts of the body based on AJCC staging criteria.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203222&version=1.0, AJCC Pathologic T,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer - (AJCC).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045435&version=1.0, + (AJCC).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045435&version=1.0, AJCC Staging System Edition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with - other accepted classifications.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2722309&version=1.0, -Anaplasia Present,"Yes/no/unknown/not reported indicator used to describe whether anaplasia was present at the -time of diagnosis.","Yes - Anaplasia Present, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6059599&version=1.0, -Yes - Anaplasia Present,Indicates anaplasia is present,,Anaplasia Present Type,,FALSE,Diagnosis,,, -Anaplasia Present Type,"The text term used to describe the morphologic findings indicating the presence of a malignant - cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and - high mitotic activity in a tissue sample.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925534&version=1.0, -Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003324&version=4.0, -Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis -and the deepest point of tumor penetration.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64809&version=3.0, -Classification of Tumor,"Text that describes the kind of disease present in the tumor specimen as related to a specific - timepoint.","Primary, Metastasis, Recurrence, Other, Unknown, Not reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0, -Days to Diagnosis,"Number of days between the date used for index and the date the patient was diagnosed with the - malignant disease.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154733&version=1.0, -First Symptom Prior to Diagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,"Altered Mental Status, Headaches, Motor or Movement Changes, Seizures, Sensory Changes, Visual Changes, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133605&version=1.0, -Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133606&version=1.0, -Laterality,"For tumors in paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=827&version=3.0, -Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=89&version=3.0, -Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3&version=3.0, -Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64171&version=3.0, -Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133614&version=1.0, -Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver, Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum, Omentum, Ovary, Pelvis, Peritoneal Cavity, Peritoneum, Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3029815&version=1.0, -Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Imaging,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,Unknown,Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161031&version=1.0, -Mitotic Count,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",,,,FALSE,Diagnosis,,, -Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,,,,FALSE,Diagnosis,,, -Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6690681&version=1.0, -Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64181&version=3.0, -Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2608702&version=1.0, -Synchronous Malignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.","Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142390&version=1.0, -Tumor Confined to Organ of Origin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,"Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925494&version=1.0, -Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3174022&version=1.0, -Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64215&version=3.0, -Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64358&version=3.0, -Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,,Vascular Invasion Type,,FALSE,Diagnosis,,, -Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3168001&version=1.0, -Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896960&version=1.0, \ No newline at end of file + other accepted classifications.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2722309&version=1.0, +Anaplasia Present,"Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the +time of diagnosis.","Yes - Anaplasia Present, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6059599&version=1.0, +Yes - Anaplasia Present,Indicates anaplasia is present,,Anaplasia Present Type,,FALSE,Diagnosis,,, +Anaplasia Present Type,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925534&version=1.0, +Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003324&version=4.0, +Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64809&version=3.0, +Classification of Tumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Primary, Metastasis, Recurrence, Other, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0, +Days to Diagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154733&version=1.0, +First Symptom Prior to Diagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,"Altered Mental Status, Headaches, Motor or Movement Changes, Seizures, Sensory Changes, Visual Changes, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133605&version=1.0, +Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133606&version=1.0, +Laterality,"For tumors in paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=827&version=3.0, +Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=89&version=3.0, +Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3&version=3.0, +Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64171&version=3.0, +Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133614&version=1.0, +Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver, Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum, Omentum, Ovary, Pelvis, Peritoneal Cavity, Peritoneum, Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3029815&version=1.0, +Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Imaging,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,unknown,Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161031&version=1.0, +Mitotic Count,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",,,,FALSE,Diagnosis,,, +Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,,,,FALSE,Diagnosis,,, +Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6690681&version=1.0, +Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64181&version=3.0, +Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2608702&version=1.0, +Synchronous Malignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.","Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142390&version=1.0, +Tumor Confined to Organ of Origin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,"Yes, No, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925494&version=1.0, +Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3174022&version=1.0, +Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64215&version=3.0, +Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64358&version=3.0, +Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,,Vascular Invasion Type,,FALSE,Diagnosis,,, +Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3168001&version=1.0, +Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896960&version=1.0, +Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0, +Lung Cancer Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer","Low Dose Computed Tomography (LDCT), Chest X-ray, Chest CT, unknown, Data not available, Other",,,FALSE,Lung Cancer Tier 3,,, +Lung Cancer Participant Procedure History,Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.,"Lobectomy Bilateral, Lobectomy Left, Lobectomy Right, Lung Wedge Resection Bilateral, Lung Wedge Resection Left, Lung Wedge Resection Multiple, Lung Wedge Resection Right, Pneumonectomy Left, Pneumonectomy Right, Endobronchial biopsy, Mediastinoscopy, VATS Sclerosis, Brain resection, Segmentectomy, unknown, Other, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Lung Adjacent Histology Type,The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth,"Lung adenocarcinoma, Adenosquamous carcinoma, Carcinoid tumor and lung atypical carcinoid tumor, Lung adenocarcinoma in situ, Large cell lung carcinoma, Large cell neuroendocrine carcinoma, Lung lymphoepithelioma-like carcinoma, Bronchioalveolar carcinoma, Thoracic NUT carcinoma, Sarcomatoid carcinoma, Small cell lung carcinoma, Squamous cell lung carcinoma, Lung squamous cell carcinoma in situ, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Lung Tumor Location Anatomic Site,Anatomic location of the tumor inside the lung,"Main carina, Left, Right, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Lung Tumor Lobe Bronchial Location,Anatomic lobe and bronchial location of the tumor inside the lung,"Upper lobe, Middle lobe, Lower lobe, Stump, Bronchus, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Current Lung Cancer Symptoms,Reported lung cancer related symptoms person is currently experiencing,"asbestosis, productive cough, non-productive cough, wheezing, rhonci, crackles, hemoptysis, dyspnea, unexplained weight loss, unexplained loss of energy/fatigue, chest pain or discomfort, dysphagia, pneumonia, hoarseness/laryngitis/vocal cord inflammation, air entry decreased/fair/poor/diminished, fair/poor aeration, shallow inspiration, breath sounds coarse/diminished, dullness to percussion, abnormal breath sounds, clear lungs to auscultation or percussion, unlabored/normal breathing, cold symptoms/flu/sinus/nasal congestion, sinus pain/infection, finger clubbing, no evidence of lung cancer recurrence, patient is NED, oxygen supplemental-portable O2 at night or continuous, prolonged expiration-long/forced expiratory phase, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Lung Topography,Lung PCA specific topography (not covered in previous tiers),"MC-Carina between right and left lungs (main carina), TR -Trachea (airway wall between tracheo-esophageal bifurcation and main carina), Carina NOS (Carina not otherwise specified), LUDB-Carina between the lingula and upper division left upper lobe, Carina between LUDB orifice and lingula orifice, LUDB-orifice airway wall between LUDB and LB3(LB1+2 carinae), Lingula orifice airway wall between LUDB and LB4/5 carinae, RMB-Right mainstem bronchus(airway wall between MC & RUL carina), LMB-Left mainstem bronchus(airway wall between MC & LUL carina), RL NOS (Right lung not otherwise specified), RB1/2 - Carina between apical and posterior segments right upper lobe (Carina between RB1 orifice and RB2 orifice), RB6A/B - Carina between apical and lateral subsegments superior segment RLL, RB6A/C - Carina between apical and medial subsegments superior segment RLL, RB6B/C - Carina between medial and lateral subsegments superior segment RLL, RB7A/B - Carina between medial and lateral subsegments medial basal segment RLL, RB8/9 - Carina between anterior and lateral segments RLL (Carina between RB8 orifice and RB9 orifice), RB8A/B - Carina between medial and lateral subsegments anterior segment RLL, RB9/10 - Carina between lateral and posterior segments RLL, RB9A/B - Carina between medial and lateral subsegments lateral segment RLL, RB10A/B - Carina between medial and lateral subsegments posterior segment RLL, RB10A/C - Carina between medial and apical subsegments posterior segment RLL, RB1A/B - Carina between medial and lateral subsegments apical segment RUL, RB10B/C - Carina between medial and lateral subsegments posterior segment RLL, RB6 - Carina of superior segment RLL (Carina between RB6 orifice and lower portion of RLL orifice), RB6 orifice Airway wall between RB6 and RB6A/B/C carinae, Bronchus Intermedius Bronchus (airway wall) between right upper and right middle lobes, RB1/3 - Carina between apical and anterior segments RUL (Carina between RB1 orifice and RB3 orifice), RB2/3 - Carina between anterior and posterior segments RUL (Carina between RB2 orifice and RB3 orifice), RB2A/B - Carina between the medial and lateral subsegments of the posterior segment (RUL), RB3A/B - Carina between the medial and lateral subsegments of the anterior segment RUL, RB4/5 - Carina between the lateral and medial segments right middle lobe (Carina between RB4 orifice and RB5 orifice), RB4A/B - Carina between the medial and lateral subsegments of the lateral segment of the right middle lobe, RB5A/B - Carina between the medial and lateral subsegments of the medial segment of the right middle lobe, RUL Carinae between RUL orifice and bronchus intermedius, RUL orifice Airway wall between RUL and RB1/RB2/RB3, RB1 orifice Apical segment - right upper lobe(airway wall between RB1 and RB1A/B carinae), RB2 orifice Posterior segment - right upper lobe(airway wall between RB2 and RB2A/B carinae), RB3 orifice Anterior segment - right upper lobe(airway wall between RB3 and RB3A/B carinae), RML - Carina between RML orifice and RLL orifice, RML orifice Airway wall between RML and RB4/5, RB4 orifice Lateral segment right middle lobe (airway wall between RB4 and RB4A/B carinae), RB5 orifice Medial segment right middle lobe (airway wall between RB5 and RB5A/B carinae), RLL orifice Airway wall between RML and RB6-10 carinae, RB7 Medial basal segment right lower lobe (Carina at RB7 orifice takeoff from RLL orifice), RB7 orifice Airway wall between RB7 and RB7A/B carinae, RB8 orifice Anterior segment right lower lobe(airway wall between RB8 and RB8A/B carinae), RB9 orifice Lateral segment right lower lobe(airway wall between RB9 and RB9A/B carinae), RB10 Posterior segment right lower lobe (Carina at RB10 orifice takeoff from RLL orifice), RB10 orifice Airway wall between RB10 and RB10A/B carinae, LL NOS (Left lung not otherwise specified), LB1/2 Carina between apical and posterior segment left upper lobe (Carina between LB1 orifice and LB2 orifice), LB4/5 Carina between superior and inferior segment lingula (Carina between LB4 orifice and LB5 orifice), LB4A/B Carina between medial and lateral subsegments superior segment lingula, LB5A/B Carina between the medial and lateral subsegments inferior segment lingula, LB6A/B Carina between the superior and lateral subsegments superior segment LLL, LB6A/C Carina between the superior and medial subsegments of superior segment LLL, LB6B/C Carina between the medial and lateral subsegments of the superior segment LLL, LB8/9 Carina between the anterior and lateral segments LLL (Carina between LB8 orifice and LB9 orifice), LB8A/B Carina between the medial and lateral subsegments of the anterior segment LLL, LB9/10 Carina between the lateral and posterior segments LLL (Carina between LB9 orifice and LB10 orifice), LB9A/B Carina between the medial and lateral subsegments of the lateral segment LLL, LB1A/B Carina between the lateral and medial subsegments of the apical segment of the LUL, LB10A/B Carina between the apical and lateral subsegments of the posterior segment of the LLL, LB10A/C Carina between the apical and medial segments of the posterior segment of the LLL, LB10B/C Carina between the medial and lateral subsegments of the posterior segment of the LLL, LB1+2 orifice The apico-posterior segment of the left upper lobe (airway wall between LB1+2/3 carina and LB1 or LB2), LB6 The superior segment of the left lower lobe (Carina between LB6 orifice and lower portion of LLL orifice), LB6 orifice Airway wall between LB6 and LB6A/B carinae, LB1A/C Carina between the apical and lateral subsegments of the apical segment left upper lobe, LB1B/C Carina between the medial and lateral subsegments of the apical segment of the left upper lobe, LB2A/B Carina between the apical and lateral subsegments of the posterior segment of the left upper lobe, LB2A/C Carina between the apical and medial subsegments of the posterior segment of the left upper lobe, LB2B/C Carina between the medial and lateral subsegments of the posterior segment left upper lobe, LB1+2/3 Carina between the apico-posterior and anterior segments of the left upper lobe (Carina between LB1+2 orifice and LB3 orifice), LB3A/B Carina between the apical and lateral subsegments of the anterior segment of the left upper lobe , LUL Carina between the LUL orifice and LLL orifice (airways), LUL orifice Airway wall between LUL and LUDB, LB3 orifice Anterior segment left upper lobe(airway wall between LB3 and LB3A/B carinae), LB4 orifice Superior segment lingula(airway wall between LB4 and LB4A/B carinae), LB5 orifice Inferior segment lingula(airway wall between LB5 and LB5A/B carinae), LLL orifice Airway wall between LUL carina and LB6-10 carinae, LB9 orifice Lateral segment left lower lobe(airway wall between LB9 and LB9A/B carinae), LB8 orifice Anterior segment left lower lobe(airway wall between LB8 and LB8A/B carinae), LB10 orifice Posterior segment left lower lobe(airway wall between LB10 and LB10A/B carinae), Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Lung Cancer Harboring Genomic Aberrations,Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2),"G12A KRAS mutation, G12C KRAS mutation, G12D KRAS mutation, G12R KRAS mutation, G12S KRAS mutation, G12V KRAS mutation, G13D KRAS mutation, G13R KRAS mutation, G13C KRAS mutation, G13A KRAS mutation, G13V KRAS mutation, Q61L KRAS mutation, Q61H KRAS mutation, A146T KRAS mutation, G719X EGFR mutation, T790M EGFR mutation, C797S EGFR mutation, L858R EGFR mutation, L861Q EGFR mutation, Exon 19 deletion, Exon 20 insertion, EML4-ALK translocation-variant 1, EML4-ALK translocation-variant 2, EML4-ALK translocation-variant 3, EML4-ALK translocation-variant 4, EML4-ALK translocation-variant 5, V600E BRAF mutation, V600D BRAF mutation, V600K BRAF mutation, V600R BRAF mutation, K601E BRAF mutation, D963 splice MET mutation, D1010N MET mutation, D1010 splice MET mutation, Intron 13 mutation, Intron 14 mutation, Exon 14 mutation, Exon 14 deletion, Other, unknown, Not Reported",,,FALSE,Lung Cancer Tier 3,,, +Colorectal Cancer Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer","Fecal occult blood test, Sigmoidoscopy, Colonoscopy, Virtual colonoscopy, DNA stool test, Other, unknown, Data not available",,,FALSE,Colorectal Cancer Tier 3,,, +History of Prior Colon Polyps,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,, +Family Colon Cancer History Indicator,The indicator to designate if any first degree relative has a history of colorectal cancer.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,, +Family Medical History Colorectal Polyp Diagnosis,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,, +Immediate Family History Endometrial Cancer,Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Immediate Family History Ovarian Cancer,Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Patient Inflammatory Bowel Disease Personal Medica History,"The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).","Yes - Crohn's disease, Yes - Ulcerative colitis, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Patient Colonoscopy Performed Indicator,The yes/no indicator that records if the subject has undergone a previous colonoscopy.,"Yes, No, Not Applicable, unknown",,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Cancer Tumor Border Configuration,The description of the border configuration of a colorectal tumor at pathologic assessment.,"Indeterminate, Infiltrating, Other, Pushing, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +MLH1 Promoter Methylation Status,Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.,"Absent, Indeterminate, Not Assessed, Present",,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Cancer KRAS Indicator,The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Colon Polyp Occurence Indicator,Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Family History Colorectal Polyp,A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Polyp New Indicator,A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.,"Yes, No, unknown, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Polyp Shape,Shape of polyp identified in the participant,"Pedunculated, Sessile, Flat, Not stated, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Size of Polyp Removed,Size of the polyp removed in cm,,,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Polyp Count,The total number of polyps detected,,,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Polyp Type,Type of polyp found in the participant,"Adenoma, Hyperplastic, Mixed, Papillomatous, Normal, Cancer, Other, unknown",,,FALSE,Colorectal Cancer Tier 3,,, +Colorectal Polyp Adenoma Type,Type of adenoma associated with the polyp,"Tubular, Villous, Tubulovillous, Sessile serrated, Traditional serrated, Serrated not specified, Not stated, Not Applicable",,,FALSE,Colorectal Cancer Tier 3,,, +Breast Carcinoma Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.","Clinical Exam, Data not available, Nipple Discharge, Other, Screening Mammography, Screening MRI, Self exam, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma Histology Category,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,"Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Invasive mammary carcinoma NOS, Invasive mixed ductal and lobular carcinoma, Other",,,FALSE,Breast Cancer Tier 3,,, +Invasive Lobular Breast Carcinoma Histologic Category,The histologic subtype for an infiltrating lobular carcinoma of the breast.,"Alveolar type, Classical type, Data not available, Pleomorphic type, unknown",,,FALSE,Breast Cancer Tier 3,,, +Invasive Ductal Breast Carcinoma Histologic Category,The histologic subtype for the most common type of invasive breast carcinoma.,"Classical type, Invasive carcinoma-type cannot be determined, Invasive cribriform carcinoma, Invasive micropapillary carcinoma, Invasive papillary carcinoma, Invasive tubular carcinoma, Medullary carcinoma, Mucinous carcinoma, Tubulolobular carcinoma, Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Breast Biopsy Procedure Finding Type,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,"Atypical hyperplasia, DCIS, LCIS, Cancer, No cancer, Other",,,FALSE,Breast Cancer Tier 3,,, +Breast Quadrant Site,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,"Upper outer quadrant, Lower outer quadrant, Upper inner quadrant, Lower inner quadrant, Central, Nipple, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Breast Cancer Assessment Tests,Text term to identify assessment tests done in participants during diagnosis,"Estrogen receptor IHC, Progesterone receptor IHC, HER2 IHC, HER2 FISH-CISH, HER2 FISH, Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Breast Cancer Genomic Test Performed,Text term that represents the name of the genomic test performed for breast cancer.,"Oncotype, MammaPrint, Other, Data not available, unknown, Not performed",,,FALSE,Breast Cancer Tier 3,,, +Mammaprint Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,"High risk, Intermediate risk, Low risk, Data not available, unknown",,,FALSE,Breast Cancer Tier 3,,, +Oncotype Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,"High risk, Intermediate risk, Low risk, Data not available, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma Estrogen Receptor Status,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma Progesteroner Receptor Status,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Cancer Allred Estrogen Receptor Score,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.","0, 1, 2, 3, 4, 5, 6, 7, 8, 10, unknown",,,FALSE,Breast Cancer Tier 3,,, +Prior Invasive Breast Disease,Text term to indicate prior invasive breast condition in the participant,"DCIS, LCIS, Invasive breast cancer (unrelated to the current cancer), Other, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma ER Status Percentage Value,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma PR Status Percentage Value,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,, +HER2 Breast Carcinoma Copy Number Total,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.",,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma Centromere 17 Copy Number,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.",,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma HER2 Centromere17 Copynumber Total,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma HER2 Chromosome17 Ratio,HER2 chromosome 17 ratio in participants with breast cancer,,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma Surgical Procedure Name,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,"Lumpectomy, Radical mastectomy, Modified radical mastectomy, Other, Partial mastectomy, Re-excision, Simple mastectomy, Surgery not performed, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma HER2 Ratio Diagnosis,HER2 ratio of the participant at diagnosis,,,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma HER2 Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,"Positive, Negative, Amplified, Non-amplified, Equivocal, Indeterminate, Not Performed, unknown",,,FALSE,Breast Cancer Tier 3,,, +Hormone Therapy Breast Cancer Prevention Indicator,Did the patient receive hormonal therapy for prevention of breast cancer?,"Yes, No, unknown, Not Applicable",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma ER Staining Intensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown",,,FALSE,Breast Cancer Tier 3,,, +Breast Carcinoma PR Staining Intensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown",,,FALSE,Breast Cancer Tier 3,,, +Oncotype Score,OncotypeDX recurrence score,,,,FALSE,Breast Cancer Tier 3,,, +Breast Imaging Performed Type,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).","Mammogram, Ultrasound, MRI, PET/CT, CT, Multiple imaging modalities, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Multifocal Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,"Yes, No, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +Multicentric Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,"Yes, No, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +BIRADS Mammography Breast Density Category,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,"Predominantly fatty, Scattered fibroglandular densities, Heterogeneously dense, Extremely dense, unknown, Data not available",,,FALSE,Breast Cancer Tier 3,,, +CNS Tumor Primary Anatomic Site,Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2,"Thalamus, Ventricles, Intracranial/Leptomeningeal, Suprasellar/Hypothalamic/Pituitary, Cerebellar/Posterior fossa, Brain stem-Medulla, Brain stem-Midbrain/Tectum, Brainstem-Pons, Spinal cord-Cervical, Spinal cord-Thoracic, Spinal cord-Lumbar, Optic pathway, Other locations NOS, Paraspinal ganglion, Basal ganglia, Hippocampus, Meninges/Dura, Other lymph nodes",,,FALSE,Brain Cancer Tier 3,,, +Glioma Specific Metastasis Sites,Evidence of active brain metastasis including leptomeningeal involvement,"CSF, Spine, Bone marrow, Brain, Other, Leptomeningeal, Not Applicable",,,FALSE,Brain Cancer Tier 3,,, +Glioma Specific Radiation Field,A description of the location on or within the CNS where radiation was administered in a partcipant with glioma,"Craniospinal, Focal-tumor bed, unknown, Not Applicable",,,FALSE,Brain Cancer Tier 3,,, +Supra Tentorial Ependymoma Molecular Subgroup,Text term to identify the molecular subgroup in a supra tentorial ependymoma,"ST-EPN-RELA, ST-EPN-YAP1, unknown, Not Applicable",,,FALSE,Brain Cancer Tier 3,,, +Infra Tentorial Ependymoma Molecular Subgroup,Text term to identify the molecular subgroup in a infra tentorial ependymoma,"PF-EPN-A, PF-EPN-B, Myxopapillary ependymoma, unknown, Not Applicable",,,FALSE,Brain Cancer Tier 3,,, +Neuroblastoma MYCN Gene Amplification Status,Neuroblastoma MYCN amplification or over-expression status,"Amplified, Not amplified, Not done, unknown",,,FALSE,Brain Cancer Tier 3,,, +Specimen Blast Count Percentage Value,"The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis",,,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,, +NCI ALL Risk Group,The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.,"NCI High Risk, NCI Standard Risk, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,, +MRD ALL Diagnostic Sensitivity,The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.,"Optimal, Suboptimal, Indeterminate, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,, +CNS Leukemia Status,The status of central nervous system leukemia at the time of diagnosis.,"CNS 1, CNS 2, CNS 3, CNS 2a, CNS 2b, CNS 2c, CNS 3a, CNS 3b, CNS 3c, Not evaluated, unknown",,,FALSE,Acute Lymphoblastic Leukemia Tier 3,,, +Ovarian Cancer Histologic Subtype,Text term to describe the histological subtype of ovarian cancer in the participant,"High-grade serous, Low-grade serous, High-grade endometrioid, Low-grade endometrioid, Clear cell, Mucinous, Sex-cord stromal, Germ cell, Other, unknown, Data not available",,,FALSE,Ovarian Cancer Tier 3,,, +Ovarian Cancer Surgical Outcome,Text term that describes the kind of surgical treatment administered.,"R0 resection,Optimal cytoreduction, Sub-optimal cytoreduction, Other, unknown, Data not available",,,FALSE,Ovarian Cancer Tier 3,,, +Ovarian Cancer Platinum Status,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,"Platinum-refractory, Platinum-sensitive, Platinum-resistant, Data not available, unknown",,,FALSE,Ovarian Cancer Tier 3,,, +Location Extent Extraprostatic Extension,Location and extent of extraprostatic extension,"Left Anterior, Left Lateral, Left Posterolateral, Left Posterior, Left Apex, Left Mid, Left Base, Left Focal, Left Non-focal (established), Right Anterior, Right Lateral, Right Posterolateral, Right Posterior, Right Apex, Right Mid, Right Base, Right Focal, Right Non-focal (established), unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Location Nature Positive Margins,Location and nature of positive margins,"Left Anterior, Left Lateral, Left Posterolateral, Left Posterior, Left Apex, Left Mid, Left Base, Left Focal, Left Extensive, Left Positive in an area of extraprostatic extension (EPE), Left Positive in an area of intraprostatic incision (II), Left Positive where it is difficult to distinguish EPE vs II, Right Anterior, Right Lateral, Right Posterolateral, Right Posterior, Right Apex, Right Mid, Right Base, Right Focal, Right Extensive, Right Positive in an area of extraprostatic extension (EPE), Right Positive in an area of intraprostatic incision (II), Right Positive where it is difficult to distinguish EPE vs II, Bladder neck (block PUM), Vas deferens, Apical margin (block DUM), unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Seminal Vesicle Invasion,An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.,"None, Left, Right, Both sides, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Prostate Carcinoma Histologic Type,The diagnostic subclassification of an invasive prostate carcinoma.,"Prostatic adenocarcinoma (conventional NOS), Prostatic duct adenocarcinoma, Acinar prostate mucinous (colloid) adenocarcinoma, Acinar prostate adenocarcinoma-signet-ring variant, Prostatic adenosquamous carcinoma, Acinar prostate mucinous adenocarcinoma, Prostatic small cell carcinoma, Acinar prostate adenocarcinoma-sarcomatoid variant, Undifferentiated carcinoma NOS, Other",,,FALSE,Prostate Cancer Tier 3,,, +Prostate Cancer Local Extent,The response used to categorize the local extent of disease for prostate cancer.,"Organ Confined, Extraprostatic extension, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Additonal Findings Uninvolved Prostate,"Additional findings, uninvolved prostate","High-grade prostatic intraepithelial neoplasia (PIN), Inflammation, Benign prostatic hyperplasia (BPH), Prostatic Intraductal adenocarcinoma, Other, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Prostate Cancer Cytologic Morphologic Subtypes,Text term that describes various morphological and cytological subtypes in protate tumors.,"prostatic basal cell hyperplasia, prostatic clear cell cribiform hyperplasia, prostatic atypical adenomatous hyperplasia (adenosis or AAH), Low grade prostatic intraepithelial neoplasia (PIN)/(PIN I), High grade prostatic intraepithelial neoplasia (HGPIN)/ (PIN II & PIN III), Other, unknown, Not Reported",,,FALSE,Prostate Cancer Tier 3,,, +Sarcoma Subtype,"The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.","Undifferentiated pleomorphic sarcoma, Leiomyosarcoma (uterine or extra-uterine), Other Synovial Sarcoma Or Malignant Peripheral Nerve Sheath Tumor Sarcoma, Gastrointestinal Stromal Tumor, Liposarcoma, undifferentiated pleomorphic sarcoma or malignant fibrous histiosarcoma, Other, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,, +Sarcoma Diagnosis Classification Category,"High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.","Bone Sarcoma, Musculoskeletal Sarcoma, Soft Tissue Sarcoma, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,, +Sarcoma Tumor Extension Type,The field to indicate the organs and structures to which the tumor has become adherent or has invaded.,"Extraosseous, Intracranial, Lymph nodes, Parameningeal, Thoracic cavity, Other, unknown, Not Reported",,,FALSE,Sarcoma Tier 3,,, +Pancreas Precancer Histopathologic Grade,The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.,"IPMN-Adenoma, IPMN-Borderline, IPMN-Carcinoma in situ, IPMN-Invasive carcinoma, PanIN 1, PanIN 1A, PanIN 1B, PanIN 2, PanIN 3, unknown, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,, +Pancreatic IPMN Pathology Epithelial Subtype,The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen,"Gastric Foveolar, Intestinal, Intraductal Tubopapillary, Pancreatobiliary, Oncocytic, Other, unknown, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,, +Pancreatic Duct Final Pathology Type,The final pathology result of the pancreatic duct communication type.,"Side-Branch, Main Duct, Mixed, Not Specified, None, Not Reported",,,FALSE,Pancreatic Cancer Tier 3,,, +Cutaneous Melanoma Tumor Infiltrating Lymphocytes,Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.,"Absent, Brisk, Nonbrisk, unknown",,,FALSE,Melanoma Tier 3,,, +Cutaneous Melanoma Tumor Regression Range,Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.,"Absent, Present involving 75% or more, Present involving less than 75%, unknown",,,FALSE,Melanoma Tier 3,,, +Melanoma Specimen Clark Level Value,Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.,"I, II, III, IV, V, No Source Documentation, unknown",,,FALSE,Melanoma Tier 3,,, +Cutaneous Melanoma Surgical Margins,Text term to indicate presence of tumor at resection margins,"Positive, Negative, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,, +Melanoma Lesion Size,"Diameter of lesion determined on skin examination (pre-bx), in mm",,,,FALSE,Melanoma Tier 3,,, +History of Atypical Nevi,Patient has a history of atypical nevi,"Yes (more than 50), Yes (less than 50), No, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,, +Fitzpatrick Skin Tone,The Fitzpatrick classification of skin phototype,"I, II, III, IV, V, VI, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,, +History of Chronic UV Exposure,History of chronic UV exposure,"Outdoor occupational, Outdoor recreational, Therapeutic, None, Not Reported",,,FALSE,Melanoma Tier 3,,, +History of Blistering Sunburn,Patient has history of blistering sunburn,"Yes, No, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,, +History of Tanning Bed Use,History of tanning bed use of the patient,"Never, Less than 10 times, 10-50 times, 50-100 times, More than 100 times, Not Reported",,,FALSE,Melanoma Tier 3,,, +Immediate Family History Melanoma,Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.,"Before age 50, Not before age 50, unknown",,,FALSE,Melanoma Tier 3,,, +Melanoma Biopsy Resection Sites,Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2),"skin of scalp, skin of eye lid, skin of nose, skin of lip, skin of ear, skin of neck, skin of other parts of face, skin of chest, skin of back, skin of abdomen, skin of trunk-other, skin of breast, skin of upper limb and shoulder, skin of palm, skin of lower limb and hip, skin of sole, skin of penis, skin of scrotum, skin of vulva, skin other, skin NOS, Not Reported",,,FALSE,Melanoma Tier 3,,, +Cutaneous Melanoma Ulceration,Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.,"Absent, Present, unknown, Not Reported",,,FALSE,Melanoma Tier 3,,, +Cutaneous Melanoma Additional Findings,Significant pathologic finding present in addition to the cutaneous melanoma.,"Actinic Keratosis, Nevus Remnant, Solar Elastosis, Fibrosing Regression, Nesting Melanoma, Pagetoid Spread, Vascular Proliferation, Other, unknown, Not Applicable",,,FALSE,Melanoma Tier 3,,, diff --git a/data/schema_org_schemas/HTAN.csv b/data/schema_org_schemas/HTAN.csv deleted file mode 100644 index 3444a455b..000000000 --- a/data/schema_org_schemas/HTAN.csv +++ /dev/null @@ -1,303 +0,0 @@ -Attribute,Description,Valid Values,Requires,Properties,Required,Parent,Requires Component,Source -Assay,"A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]",,,,FALSE,,,http://purl.obolibrary.org/obo/OBI_0000070 -Device,"A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment""",,,,FALSE,Assay,,https://w3id.org/biolink/vocab/Device -Sequencing,Module for next generation sequencing assays,,,,FALSE,Assay,,http://example.org/htan/Sequencing -Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Assay, etc.); provide the same one for all items/rows.",,,,TRUE,,,https://w3id.org/biolink/vocab/category -File,A type of Information Content Entity specific to OS,,,"Filename, File Format",FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile -Filename,Name of a file ,,,,TRUE,,,http://example.org/htan/filename -File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",,,,TRUE,,,http://example.org/htan/fileFormat -Patient,HTAN patient,,"Component, HTAN Patient ID",,FALSE,Individual Organism,"Demographics, Family History, Exposure, Follow Up, Diagnosis, Therapy",http://example.org/htan/Patient -Biospecimen,"HTAN biological entity; bio entity can be a sample, slide, aliquot, analyte, etc. ",,HTAN Biosample ID,"HTAN Biospecimen ID, Biospecimen Type, Component",FALSE,Biosample,Patient,http://example.org/htan/Biospecimen -Biospecimen Type,Type of biospecimen,"Sample, Slide, Aliquot, Analyte",,,TRUE,Biosample,,http://example.org/htan/biospecimenType -HTAN ID,HTAN ID of this file HTANID SOP,,,,TRUE,Individual Organism,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing -HTAN Data File ID,self-dentifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing -HTAN Parent ID,Parent Identifier for data from which the analysis was obtained.,,,,TRUE,Individual Organism,,https://www.w3.org/ns/prov#wasDerivedFrom -HTAN Patient ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,http://www.w3.org/ns/prov#Entity -HTAN Biospecimen ID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,Biosample,,http://www.w3.org/ns/prov#Entity -HTAN Parent Biospecimen ID,HTAN Biospecimen Identifier indicating the biospecimen(s) from which these files were derived [https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing],,,,TRUE,Biosample,, -HTAN Parent Data File ID,HTAN Data File Identifier indicating the file(s) from which these files were derived,,,,TRUE,File,, -Demographics,Individual biomedical demographics attributes,,"Component, HTAN Patient ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Year of Death, Age at Index, Age Is Obfuscated, Year Of Birth, Cause of Death, Cause of Death Source, Days to Death, Occupation Duration Years, Premature At Birth, Weeks Gestation at Birth",,FALSE,Patient,, -Family History,Individual's family cancer history,,"Component, HTAN Patient ID, Relative with Cancer History",,FALSE,Patient,, -Exposure,Individual's exposure to carcenogens,,"Component, HTAN Patient ID, Smoking Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica Exposure",,FALSE,Patient,, -Follow Up,Individual's follow up exams,,"Component, HTAN Patient ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year, Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight",,FALSE,Patient,, -Therapy,Individual's first line of therapy or treatment,,"Component, HTAN Patient ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type",,FALSE,Patient,, -Diagnosis,Individual's diagnosis,,"Component, HTAN Patient ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status, Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition",,FALSE,Patient,, -scRNA-seq Assay,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Date, Single Cell Dissociation Date, Sequencing Library Construction Date, Nucleic Acid Capture Date, Protocol Link, Technical Replicate Group",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913 -scRNA-seq QC,QC pipelines downstream of scRNA-seq assay,,"Component, Median Number of Reads or UMIs per Cell, Median Number Genes per Cell, Total Number of Cells",,FALSE,Sequencing,scRNA-seq Assay, -Bulk RNA-seq Assay,Bulk RNA-seq [EFO_0003738],,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Nucleic Acid Source, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Date, Spike In, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow, Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Transcript Integrity Number (TIN), RIN, DV200, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow Link ",,FALSE,Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0003738 -Bulk RNA-seq Alignment,Bulk RNA-seq alignment protocol description,,"Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, HTAN Parent Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, MSI Workflow Name/URL, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion, Targets No Coverage, Proportion Base Mismatch, Short Reads",,FALSE,Sequencing,, -Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,http://example.org/htan/NucleicAcidSource -Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS",,,TRUE,scRNA-seq Assay,, -Dissociation Method,The tissue dissociation method used for scRNASeq assays,gentleMACS,,,TRUE,scRNA-seq Assay,, -Library Layout,Sequencing read type,"Paired End, Single Read",,,TRUE,Sequencing,, -Paired End,A library layout type,,,,FALSE,Sequencing,, -Read1,Read 1 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Assay,, -Read2,Read 2 content description,"Cell Barcode and UMI, cDNA",,,TRUE,scRNA-seq Assay,, -cDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",,"cDNA Offset, cDNA Length",,FALSE,Sequencing,, -cDNA Offset,Offset in sequence for cDNA read (in bp): number,,,,TRUE,Sequencing,, -cDNA Length,Length of cDNA read (in bp): number,,,,TRUE,Sequencing,, -Cell Barcode and UMI,Cell and transcript identifiers,,"UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number",,FALSE,scRNA-seq Assay,, -Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,,,,TRUE,scRNA-seq Assay,, -Cell Barcode Length,Length of cell barcode read (in bp): number,,,,TRUE,scRNA-seq Assay,, -Valid Barcodes Cell Number,Number,,,,TRUE,scRNA-seq Assay,, -UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",,,,TRUE,scRNA-seq Assay,,https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html -UMI Barcode Length,Length of UMI barcode read (in bp): number,,,,TRUE,scRNA-seq Assay,, -Median UMIs per Cell Number,Number,,,,TRUE,scRNA-seq Assay,, -Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711 -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,scRNA-seq Assay,, -CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,,"Empty Well Barcode, Well Index",,FALSE,scRNA-seq Assay,, -Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,,,,TRUE,scRNA-seq Assay,, -Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,,,,TRUE,scRNA-seq Assay,, -Library Preparation Date,"The date that the libraries were prepared for sequencing (in number of days since sample received in lab). A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] or ""null""",,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Single Cell Dissociation Date,The date when the sample was dissociated and cells were isolated (date format),,,,TRUE,scRNA-seq Assay,, -Sequencing Library Construction Date,Date of sequencing library construction part of library construction (in number of days since sample received in lab),,,,TRUE,Sequencing,, -Nucleic Acid Capture Date,Date of nucleic acid capture part of library construction (in number of days since sample received in lab),,,,TRUE,Sequencing,, -Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,scRNA-seq Assay,, -End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript",,,TRUE,scRNA-seq Assay,, -Reverse Transcription Primer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA","Oligo-dT, Poly-dT, Feature barcoding, Random",,,TRUE,scRNA-seq Assay,,http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer -Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],,Feature Reference Id,,FALSE,scRNA-seq Assay,,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc -Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",,,,TRUE,scRNA-seq Assay,, -Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX",,,TRUE,scRNA-seq Assay,, -ERCC,The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization,"Spike In Mix 1, Spike In Mix 2, Both Spike in Mixes",Spike In Concentration,,FALSE,Spike In,, -Spike In Concentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],,,,TRUE,ERCC,,https://www.ncbi.nlm.nih.gov/pubmed/21816910 -Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 2500, Illumina NovaSeq 6000, 454 GS FLX Titanium, AB SOLiD 4 AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, Other, Unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,, -Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Sequencing,, -Protocols Link,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.).",,,,TRUE,Assay,, -Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,, -Read Length,"The length of the sequencing reads. Can be integer, null",,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Library Selection Method,How RNA molecules are isolated.,"Hybrid Selection, PCR, Affinity Enrichment, Poly-T Enrichment, Random, rRNA Depletion, miRNA Size Fractionation, Other",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Library Preparation Kit Name,Name of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Library Preparation Kit Vendor,Vendor of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Library Preparation Kit Version,Version of Library Preparation Kit. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Adapter Name,Name of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Adapter Sequence,Base sequence of the sequencing adapter. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Base Caller Name,Name of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Base Caller Version,Version of the base caller. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Flow Cell Barcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Fragment Maximum Length,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Fragment Mean Length,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Fragment Minimum Length,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Fragment Standard Deviation Length,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Lane Number,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Library Strand,Library stranded-ness.,"Unstranded, First Stranded, Second Stranded, Not Applicable",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Multiplex Barcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Size Selection Range,Range of size selection. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Target Depth,The targeted read depth prior to sequencing. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -To Trim Adapter Sequence,Does the user suggest adapter trimming?,"Yes, No",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group -Transcript Integrity Number (TIN),"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Adapter Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Basic Statistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Encoding,Version of ASCII encoding of quality values found in the file. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Kmer Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Overrepresented Sequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Base N Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Base Sequence Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Base Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Sequence GC Content,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Sequence Quality Score,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Per Tile Sequence Quality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Percent GC Content,The overall %GC of all bases in all sequences. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Sequence Duplication Levels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Sequence Length Distribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,"FAIL, PASS, WARN, Unknown, Not Reported",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Total Reads,Total number of reads. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -QC Workflow Type,Generic name for the workflow used to analyze a data set. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -QC Workflow Version,Major version for a GDC workflow. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -QC Workflow Link,Link to workflow used. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc -Alignment Workflow Url,Link to workflow used for read alignment. DockStore.org recommended. String,,,,TRUE,Sequencing,, -Alignment Workflow Type,Generic name for the workflow used to analyze a data set.,"BWA, BWA with BQSR, BWA-aln, BWA-mem, BWA with Mark Duplicates and BQSR, STAR 2-Pass, STAR 2-Pass Chimeric, STAR 2-Pass Genome, STAR 2-Pass Transcriptome",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow -Genomic Reference,The human genome reference used in the alignment of reads. String,,,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=alignment_workflow -Genomic Reference URL,URL refering to specific reference used. String,,,,TRUE,Sequencing,, -Index File Name,The name (or part of a name) of a file (of any type). String,,,,TRUE,Sequencing,, -Average Base Quality,Average base quality collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads_index -Average Insert Size,Average insert size collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Average Read Length,Average read length collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Contamination Error,Estimation error of cross-sample contamination collected from GATK4. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Mean Coverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools. Number",,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -MSI Workflow Name/URL,Method used in estimating the MSI. String,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -MSI Score,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,,,,FALSE,Sequencing,, -MSI Status,MSIsensor determination of either microsatellite stability or instability.,"MSI, MSI-low, MSI-high, MSS",,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Pairs On Diff CHR,Pairs on different chromosomes collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Total Reads,Total number of reads collected from samtools. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Total Uniquely Mapped,Number of reads that map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Total Unmapped reads,Number of reads that did not map to genome. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Proportion Reads Duplicated,Proportion of duplicated reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Proportion Reads Mapped,Proportion of mapped reads collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Proportion Targets No Coverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Proportion Base Mismatch,Proportion of mismatched bases collected from samtools. Number,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Short Reads,Number of reads that were too short. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads -Psuedo Alignment Used,Psuedo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,"Yes, No",,,TRUE,Sequencing,, -Workflow URL or command,Link to workflow document. DockStore.org recommended. String,,Psuedo Alignment Used,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow -Software and version,Name of software used to generate expression values. String,,Psuedo Alignment Used,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=rna_expression_workflow -Genomic Reference,The human genome reference used in the alignment of reads.,GRCh38,Psuedo Alignment Used,,TRUE,Sequencing,, -Genomic Reference URL,URL refering to exact reference used. String,,Psuedo Alignment Used,,TRUE,Sequencing,, -Data Format,Format of the data files.,"CSV, HDF5, TSV, TXT",,,TRUE,File,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=gene_expression -Data Category,Specific content type of the data file.,"Exon Expression Quantification, Gene Expression Quantification, Isoform Expression Quantification, Splice Junction Quantification",,,TRUE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=gene_expression -Expression Units,How quantities are corrected for gene length,"TPM, RPKM, FPKM, Counts, Other, NA",,,TRUE,Sequencing,, -Matrix Type,Type of data stored in matrix.,"Raw Counts, Normalized Counts, Scaled Counts, Batch Corrected Counts",,,TRUE,Sequencing,, -Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories -defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, Unknown, not reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0 -Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification -of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, not reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0 -Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. - ","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, Unknown, not reported, not allowed to collect",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0 -Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, Unknown, Not Reported",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5&version=5.0 -Dead,This indicates the participant is dead and defines further required metadata,,"Year of Death, Cause of Death, Cause of Death Source, Days to Death",,FALSE,Demographics,, -Days to Birth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,,,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154723&version=1.0 -Year of Death,Numeric value to represent the year of the death of an individual.,Not Applicable,,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897030&version=1.0 -Age at Index,The patient's age (in years) on the reference or anchor date used during date obfuscation.,null,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6028530&version=1.0 -Age Is Obfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,"true, false",,,FALSE,Demographics,, -Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,null,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896954&version=1.0 -Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, Unknown",,,TRUE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2554674&version=3.0 -Cause of Death Source,The text term used to describe the source used to determine the patient's cause of death.,"Autopsy, Death Certificate, Medical Record, Social Security Death Index, Unknown, Not Reported",,,FALSE,Demographics,, -Days to Death,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154724&version=1.0 -Occupation Duration Years,The number of years a patient worked in a specific occupation.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2435424&version=1.0 -Premature At Birth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,"Yes, No, Unknown, Not Reported",,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6010765&version=1.0 -Weeks Gestation at Birth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,,,,FALSE,Demographics,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2737369&version=1.0 -Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161021&version=1.0 -Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,,,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5300571&version=1.0 -Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, Unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161022&version=1.0 -Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son, Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister, Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, Unknown, Not Reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2690165&version=2.0 -Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, Unknown, Not reported",,,FALSE,Family History,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161023&version=1.0 -Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,,,,FALSE,Family History,, -Yes - Cancer History Relative,Individual has a relative with cancer history,,"Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis",,FALSE,Family History,, -Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported",,,TRUE,Exposure,, -Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,,"Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used",,FALSE,Exposure,, -Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2955385&version=1.0 -Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,,,,TRUE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3137957&version=1.0 -Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported",,,TRUE,Exposure,, -Yes - Alcohol Exposure,,,"Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity",,FALSE,Exposure,, -Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3114013&version=1.0 -Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3124961&version=1.0 -Alcohol History,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2201918&version=1.0 -Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3457767&version=1.0 -Asbestos Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=1253&version=3.0 -Cigarettes per Day,The average number of cigarettes smoked per day.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2001716&version=4.0 -Coal Dust Exposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,"Yes, No, Unknown",,,FALSE,Exposure,, -Environmental Tobacco Smoke Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.","Yes, No, Unknown",,,FALSE,Exposure,, -Radon Exposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,"Yes, No, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2816352&version=1.0 -Respirable Crystalline Silica Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.","Yes, No, Unknown",,,FALSE,Exposure,, -Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, Unknown",,,FALSE,Exposure,, -Time Between Waking and First Smoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,"Within 5 Minutes, 6-30 Minutes, 31-60 Minutes, After 60 Minutes, Unknown",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3279220&version=1.0 -Tobacco Smoking Onset Year,The year in which the participant began smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228604&version=1.0 -Tobacco Smoking Quit Year,The year in which the participant quit smoking.,,,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2228610&version=1.0 -Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, Unknown, Not Reported",,,FALSE,Exposure,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2181650&version=1.0 -Type of Smoke Exposure,The text term used to describe the patient's specific type of smoke exposure.,"Accidental building fire smoke,Accidental grass fire smoke, Accidental fire smoke NOS,Accidental forest fire smoke,Accidental vehicle fire smoke,Aircraft smoke,Burning tree smoke,Coal smoke NOS, Cooking related smoke NOS,Electronic cigarette smoke NOS,Electrical fire smoke,Environmental tobacco smoke,Factory smokestack smoke,Field burning smoke,Fire smoke NOS,Furnace or boiler smoke,Gas burning smoke propane,Grease fire smoke,Grilling smoke,Hashish smoke,Indoor coal burning stove or fireplace smoke,Indoor stove or fireplace smoke NOS,Indoor wood burning stove or fireplace smoke,Machine smoke,Marijuana smoke,No Smoke Exposure,Oil burning smoke Kerosene,Oil burning smoke NOS,Recreational fire smoke,Smoke exposure NOS,Smokehouse smoke,Tobacco smoke cigar,Tobacco smoke cigarettes,Tobacco smoke pipe,Unknown,Volcanic smoke,Waste burning smoke,Wood burning smoke factory,Wood burning smoke NOS, Workrelated smoke artificial smoke machines, Workrelated smoke fire fighting,Workrelated smoke foundry,Workrelated smoke generators,Workrelated smoke military,Workrelated smoke NOS,Workrelated smoke paint baking,Workrelated smoke plastics factory,Workrelated smoke plumbing,Workrelated smoke soldering/welding",,,FALSE,Exposure,, -Type of Tobacco Used,The text term used to describe the specific type of tobacco used by the patient.,"Cigarettes, Cigar, Electronic Cigarette, Other, Pipe, Smokeless Tobacco",,,FALSE,Exposure,, -Days to Follow Up,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154727&version=1.0 -Adverse Event,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,"Abdominal Distension, Abdominal Infection,Abdominal Pain,Abdominal Soft Tissue Necrosis,Abducens Nerve Disorder,Accessory Nerve Disorder,Acidosis,Acoustic Nerve Disorder NOS,Activated Partial Thromboplastin Time Prolonged,Acute Coronary Syndrome,Acute Kidney Injury,Adrenal Insufficiency,Adult Respiratory Distress Syndrome, Agitation, Akathisia, Alanine Aminotransferase Increased,Alcohol Intolerance,Alkaline Phosphatase Increased,Alkalosis,Allergic Reaction,Allergic Rhinitis, Alopecia, Amnesia,Anal Fistula,Anal Hemorrhage,Anal Mucositis, Anal Necrosis,Anal Pain,Anal Stenosis,Anal Ulcer,Anaphylaxis,Anemia,Ankle Fracture,Anorectal Infection,Anorexia,Anorgasmia,Anxiety,Aortic Injury,Aortic Valve Disease,Aphonia,Apnea,Appendicitis,Appendicitis Perforated,Arachnoiditis,Arterial Injury,Arteritis Infective,Arthralgia,Arthritis,Ascites,Aspartate Aminotransferase Increased,Aspiration,Asystole,Ataxia,Atelectasis,Atrial Fibrillation,Atrial Flutter,Atrioventricular Block Complete,Atrioventricular Block First Degree,Autoimmune Disorder,Avascular Necrosis,Azoospermia,Back Pain,Bile Duct Stenosis,Biliary Anastomotic Leak,Biliary Fistula,Biliary Tract Infection,Bladder Anastomotic Leak,Bladder Infection,Bladder Perforation,Bladder Spasm,Bloating,Blood and Lymphatic System Disorders Other,Blood Antidiuretic Hormone Abnormal,Blood Bilirubin Increased,Blood Corticotrophin Decreased,Blood Gonadotrophin Abnormal,Blood Prolactin Abnormal,Blurred Vision,Body Odor,Bone Infection,Bone Marrow Hypocellular,Bone Pain,Brachial Plexopathy,Breast Atrophy,Breast Infection,Breast Pain,Bronchial Fistula,Bronchial Infection,Bronchial Obstruction,Bronchial Stricture,Bronchopleural Fistula,Bronchopulmonary Hemorrhage,Bronchospasm,Bruising,Bullous Dermatitis,Burn,Buttock Pain,Capillary Leak Syndrome,Carbon Monoxide Diffusing Capacity Decreased,Cardiac Arrest,Cardiac Disorders Other,Cardiac Troponin I Increased,Cardiac Troponin T Increased,Cataract,Catheter Related Infection,CD4 Lymphocytes Decreased,Cecal Hemorrhage,Cecal Infection,Central Nervous System Necrosis,Cerebrospinal Fluid Leakage,Cervicitis Infection,Cheilitis,Chest Pain Cardiac,Chest Wall Pain,Chills,Cholecystitis,Cholesterol High,Chronic Kidney Disease,Chylothorax,Cognitive Disturbance,Colitis,Colonic Fistula,Colonic Hemorrhage,Colonic Obstruction,Colonic Perforation,Colonic Stenosis,Colonic Ulcer,Concentration Impairment,Conduction Disorder,Confusion,Congenital, Familial and Genetic Disorders Other,Conjunctivitis,Conjunctivitis Infective,Constipation,Constrictive Pericarditis,Corneal Infection,Corneal Ulcer,Cough,CPK Increased,Cranial Nerve Infection,Creatinine Increased,Cushingoid,Cystitis Noninfective,Cytokine Release Syndrome,Death Neonatal,Death NOS,Dehydration,Delayed Orgasm,Delayed Puberty,Delirium,Delusions,Dental Caries,Depressed Level of Consciousness,Depression,Dermatitis Radiation,Device Related Infection,Diarrhea,Disseminated Intravascular Coagulation,Dizziness,Dry Eye,Dry Mouth,Dry Skin,Duodenal Fistula,Duodenal Hemorrhage,Duodenal Infection,Duodenal Obstruction,Duodenal Perforation,Duodenal Stenosis,Duodenal Ulcer,Dysarthria,Dysesthesia,Dysgeusia,Dysmenorrhea,Dyspareunia,Dyspepsia,Dysphagia,Dysphasia,Dyspnea,Ear and Labyrinth Disorders Other,Ear Pain,Edema Cerebral,Edema Face,Edema Limbs,Edema Trunk,Ejaculation Disorder,Ejection Fraction Decreased,Electrocardiogram QT Corrected Interval Prolonged,Encephalitis Infection,Encephalomyelitis Infection,Encephalopathy,Endocarditis Infective,Endocrine Disorders Other,Endophthalmitis,Enterocolitis,Enterocolitis Infectious,Enterovesical Fistula,Epistaxis,Erectile Dysfunction,Erythema Multiforme,Erythroderma,Esophageal Anastomotic Leak,Esophageal Fistula,Esophageal Hemorrhage,Esophageal Infection,Esophageal Necrosis,Esophageal Obstruction,Esophageal Pain,Esophageal Perforation,Esophageal Stenosis,Esophageal Ulcer,Esophageal Varices Hemorrhage,Esophagitis,Euphoria,Exostosis,External Ear Inflammation,External Ear Pain,Extraocular Muscle Paresis,Extrapyramidal Disorder,Eye Disorders Other,Eye Infection,Eye Pain,Eyelid Function Disorder,Facial Muscle Weakness,Facial Nerve Disorder,Facial Pain,Fall,Fallopian Tube Anastomotic Leak,Fallopian Tube Obstruction,Fallopian Tube Perforation,Fallopian Tube Stenosis,Fat Atrophy,Fatigue,Febrile Neutropenia,Fecal Incontinence,Female Genital Tract Fistula,Feminization Acquired,Fetal Death,Fetal Growth Retardation,Fever,Fibrinogen Decreased,Fibrosis Deep Connective Tissue,Flank Pain,Flashing Lights,Flatulence,Floaters,Flu Like Symptoms,Flushing,Forced Expiratory Volume Decreased,Fracture,Gait Disturbance,Gallbladder Fistula,Gallbladder Infection,Gallbladder Necrosis,Gallbladder Obstruction,Gallbladder Pain,Gallbladder Perforation,Gastric Anastomotic Leak,Gastric Fistula,Gastric Hemorrhage,Gastric Necrosis,Gastric Perforation,Gastric Stenosis,Gastric Ulcer,Gastritis,Gastroesophageal Reflux Disease,Gastrointestinal Anastomotic Leak,Gastrointestinal Disorders Other,Gastrointestinal Fistula,Gastrointestinal Pain,Gastrointestinal Stoma Necrosis,Gastroparesis,General Disorders and Administration Site Conditions Other,Generalized Muscle Weakness,Genital Edema,GGT Increased,Gingival Pain,Glaucoma,Glossopharyngeal Nerve Disorder,Glucose Intolerance,Growth Accelerated,Growth Hormone Abnormal,Growth Suppression,Gum Infection,Gynecomastia,Hallucinations,Haptoglobin Decreased,Head Soft Tissue Necrosis,Headache,Hearing Impaired,Heart Failure,Hematoma,Hematosalpinx,Hematuria,Hemoglobin Increased,Hemoglobinuria,Hemolysis,Hemolytic Uremic Syndrome,Hemorrhoidal Hemorrhage,Hemorrhoids,Hepatic Failure,Hepatic Hemorrhage,Hepatic Infection,Hepatic Necrosis,Hepatic Pain,Hepatitis Viral,Hepatobiliary Disorders Other,Hiccups,Hip Fracture,Hirsutism,Hoarseness,Hot Flashes,Hydrocephalus,Hypercalcemia,Hyperglycemia,Hyperhidrosis,Hyperkalemia,Hypermagnesemia,Hypernatremia,Hyperparathyroidism,Hypersomnia,Hypertension,Hyperthyroidism,Hypertrichosis,Hypertriglyceridemia,Hyperuricemia,Hypoalbuminemia,Hypocalcemia,Hypoglossal Nerve Disorder,Hypoglycemia,Hypohidrosis,Hypokalemia,Hypomagnesemia,Hyponatremia,Hypoparathyroidism,Hypophosphatemia,Hypotension,Hypothermia,Hypothyroidism,Hypoxia,Ileal Fistula,Ileal Hemorrhage,Ileal Obstruction,Ileal Perforation,Ileal Stenosis,Ileal Ulcer,Ileus,Immune System Disorders Other,Infections and Infestations Other,Infective Myositis,Infusion Related Reaction,Infusion Site Extravasation,Injection Site Reaction,Injury to Carotid Artery,Injury to Inferior Vena Cava,Injury to Jugular Vein,Injury to Superior Vena Cava,Injury, Poisoning and Procedural Complications Other,INR Increased,Insomnia,Intestinal Stoma Leak,Intestinal Stoma Obstruction,Intestinal Stoma Site Bleeding,Intra-Abdominal Hemorrhage,Intracranial Hemorrhage,Intraoperative Arterial Injury,Intraoperative Breast Injury,Intraoperative Cardiac Injury,Intraoperative Ear Injury,Intraoperative Endocrine Injury,Intraoperative Gastrointestinal Injury,Intraoperative Head and Neck Injury,Intraoperative Hemorrhage,Intraoperative Hepatobiliary Injury,Intraoperative Musculoskeletal Injury,Intraoperative Neurological Injury,Intraoperative Ocular Injury,Intraoperative Renal Injury,Intraoperative Reproductive Tract Injury,Intraoperative Respiratory Injury,Intraoperative Skin Injury,Intraoperative Splenic Injury,Intraoperative Urinary Injury,Intraoperative Venous Injury,Investigations Other,Iron Overload,Irregular Menstruation,Irritability,Ischemia Cerebrovascular,IVth Nerve Disorder,Jejunal Fistula,Jejunal Hemorrhage,Jejunal Obstruction,Jejunal Perforation,Jejunal Stenosis,Jejunal Ulcer,Joint Effusion,Joint Infection,Joint Range of Motion Decreased,Joint Range of Motion Decreased Cervical Spine,Joint Range of Motion Decreased Lumbar Spine,Keratitis,Kidney Anastomotic Leak,Kidney Infection,Kyphosis,Lactation Disorder,Large Intestinal Anastomotic Leak,Laryngeal Edema,Laryngeal Fistula,Laryngeal Hemorrhage,Laryngeal Inflammation,Laryngeal Mucositis,Laryngeal Obstruction,Laryngeal Stenosis,Laryngitis,Laryngopharyngeal Dysesthesia,Laryngospasm,Left Ventricular Systolic Dysfunction,Lethargy,Leukemia Secondary to Oncology Chemotherapy,Leukocytosis,Leukoencephalopathy,Libido Decreased,Libido Increased,Lip Infection,Lip Pain,Lipase Increased,Lipohypertrophy,Localized Edema,Lordosis,Lower Gastrointestinal Hemorrhage,Lung Infection,Lymph Gland Infection,Lymph Leakage,Lymph Node Pain,Lymphedema,Lymphocele,Lymphocyte Count Decreased,Lymphocyte Count Increased,Malabsorption,Malaise,Mania,Mediastinal Hemorrhage,Mediastinal Infection,Memory Impairment,Meningismus,Meningitis,Menopause,Menorrhagia,Metabolism and Nutrition Disorders Other,Middle Ear Inflammation,Mitral Valve Disease,Mobitz (Type) II Atrioventricular Block,Mobitz Type I,Movements Involuntary,Mucosal Infection,Mucositis Oral,Multi-Organ Failure,Muscle Weakness Left-Sided,Muscle Weakness Lower Limb,Muscle Weakness Right-Sided,Muscle Weakness Trunk,Muscle Weakness Upper Limb,Musculoskeletal and Connective Tissue Disorders Other,Musculoskeletal Deformity,Myalgia,Myelitis,Myelodysplastic Syndrome,Myocardial Infarction,Myocarditis,Myositis,Nail Discoloration,Nail Infection,Nail Loss,Nail Ridging,Nasal Congestion,Nausea,Neck Edema,Neck Pain,Neck Soft Tissue Necrosis,Neoplasms Benign, Malignant and Unspecified (Incl Cysts and Polyps) Other,Nervous System Disorders Other,Neuralgia,Neutrophil Count Decreased,Night Blindness,Nipple Deformity,Non-Cardiac Chest Pain,Nystagmus,Obesity,Obstruction Gastric,Oculomotor Nerve Disorder,Olfactory Nerve Disorder,Oligospermia,Optic Nerve Disorder,Oral Cavity Fistula,Oral Dysesthesia,Oral Hemorrhage,Oral Pain,Osteonecrosis of Jaw,Osteoporosis,Otitis Externa,Otitis Media,Ovarian Hemorrhage,Ovarian Infection,Ovarian Rupture,Ovulation Pain,Pain,Pain in Extremity,Pain of Skin,Palmar-Plantar Erythrodysesthesia Syndrome,Palpitations,Pancreas Infection,Pancreatic Anastomotic Leak,Pancreatic Duct Stenosis,Pancreatic Enzymes Decreased,Pancreatic Fistula,Pancreatic Hemorrhage,Pancreatic Necrosis,Pancreatitis,Papilledema,Papulopustular Rash,Paresthesia,Paronychia,Paroxysmal Atrial Tachycardia,Pelvic Floor Muscle Weakness,Pelvic Infection,Pelvic Pain,Pelvic Soft Tissue Necrosis,Penile Infection,Penile Pain,Perforation Bile Duct,Pericardial Effusion,Pericardial Tamponade,Pericarditis,Perineal Pain,Periodontal Disease,Periorbital Edema,Periorbital Infection,Peripheral Ischemia,Peripheral Motor Neuropathy,Peripheral Nerve Infection,Peripheral Sensory Neuropathy,Peritoneal Infection,Peritoneal Necrosis,Personality Change,Phantom Pain,Pharyngeal Anastomotic Leak,Pharyngeal Fistula,Pharyngeal Hemorrhage,Pharyngeal Mucositis,Pharyngeal Necrosis,Pharyngeal Stenosis,Pharyngitis,Pharyngolaryngeal Pain,Phlebitis,Phlebitis Infective,Photophobia,Photosensitivity,Platelet Count Decreased,Pleural Effusion,Pleural Hemorrhage,Pleural Infection,Pleuritic Pain,Pneumonitis,Pneumothorax,Portal Hypertension,Portal Vein Thrombosis,Postnasal Drip,Postoperative Hemorrhage,Postoperative Thoracic Procedure Complication,Precocious Puberty,Pregnancy, Puerperium and Perinatal Conditions Other,Premature Delivery,Premature Menopause,Presyncope,Proctitis,Productive Cough,Prolapse of Intestinal Stoma,Prolapse of Urostomy,Prostate Infection,Prostatic Hemorrhage,Prostatic Obstruction,Prostatic Pain,Proteinuria,Pruritus,Psychiatric Disorders Other,Psychosis,Pulmonary Edema,Pulmonary Fibrosis,Pulmonary Fistula,Pulmonary Hypertension,Pulmonary Valve Disease,Purpura,Pyramidal Tract Syndrome,Radiation Recall Reaction (Dermatologic),Radiculitis,Rash Acneiform,Rash Maculo-Papular,Rash Pustular,Rectal Anastomotic Leak,Rectal Fistula,Rectal Hemorrhage,Rectal Mucositis,Rectal Necrosis,Rectal Obstruction,Rectal Pain,Rectal Perforation,Rectal Stenosis,Rectal Ulcer,Recurrent Laryngeal Nerve Palsy,Renal and Urinary Disorders Other,Renal Calculi,Renal Colic,Renal Hemorrhage,Reproductive System and Breast Disorders Other,Respiratory Failure,Respiratory, Thoracic and Mediastinal Disorders Other,Restlessness,Restrictive Cardiomyopathy,Retinal Detachment,Retinal Tear,Retinal Vascular Disorder,Retinoic Acid Syndrome,Retinopathy,Retroperitoneal Hemorrhage,Reversible Posterior Leukoencephalopathy Syndrome,Rhinitis Infective,Right Ventricular Dysfunction,Salivary Duct Inflammation,Salivary Gland Fistula,Salivary Gland Infection,Scalp Pain,Scleral Disorder,Scoliosis,Scrotal Infection,Scrotal Pain,Seizure,Sepsis,Seroma,Serum Amylase Increased,Serum Sickness,Sick Sinus Syndrome,Sinus Bradycardia,Sinus Disorder,Sinus Pain,Sinus Tachycardia,Sinusitis,Skin and Subcutaneous Tissue Disorders Other,Skin Atrophy,Skin Hyperpigmentation,Skin Hypopigmentation,Skin Induration,Skin Infection,Skin Ulceration,Sleep Apnea,Small Intestinal Anastomotic Leak,Small Intestinal Mucositis,Small Intestinal Obstruction,Small Intestinal Perforation,Small Intestinal Stenosis,Small Intestine Infection,Small Intestine Ulcer,Sneezing,Social Circumstances Other,Soft Tissue Infection,Soft Tissue Necrosis Lower Limb,Soft Tissue Necrosis Upper Limb,Somnolence,Sore Throat,Spasticity,Spermatic Cord Anastomotic Leak,Spermatic Cord Hemorrhage,Spermatic Cord Obstruction,Spinal Fracture,Spleen Disorder,Splenic Infection,Stenosis of Gastrointestinal Stoma,Stevens-Johnson Syndrome,Stoma Site Infection,Stomach Pain,Stomal Ulcer,Stridor,Stroke,Sudden Death NOS,Suicidal Ideation,Suicide Attempt,Superficial Soft Tissue Fibrosis,Superficial Thrombophlebitis,Superior Vena Cava Syndrome,Supraventricular Tachycardia,Surgical and Medical Procedures Other,Syncope,Telangiectasia,Testicular Disorder,Testicular Hemorrhage,Testicular Pain,Thromboembolic Event,Thrombotic Thrombocytopenic Purpura,Tinnitus,Tooth Development Disorder,Tooth Discoloration,Tooth Infection,Toothache,Toxic Epidermal Necrolysis,Tracheal Fistula,Tracheal Hemorrhage,Tracheal Mucositis,Tracheal Obstruction,Tracheal Stenosis,Tracheitis,Tracheostomy Site Bleeding,Transient Ischemic Attacks,Treatment Related Secondary Malignancy,Tremor,Tricuspid Valve Disease,Trigeminal Nerve Disorder,Trismus,Tumor Lysis Syndrome,Tumor Pain,Typhlitis,Unequal Limb Length,Unintended Pregnancy,Upper Gastrointestinal Hemorrhage,Upper Respiratory Infection,Ureteric Anastomotic Leak,Urethral Anastomotic Leak,Urethral Infection,Urinary Fistula,Urinary Frequency,Urinary Incontinence,Urinary Retention,Urinary Tract Infection,Urinary Tract Obstruction,Urinary Tract Pain,Urinary Urgency,Urine Discoloration,Urine Output Decreased,Urostomy Leak,Urostomy Obstruction,Urostomy Site Bleeding,Urostomy Stenosis,Urticaria,Uterine Anastomotic Leak,Uterine Fistula,Uterine Hemorrhage,Uterine Infection,Uterine Obstruction,Uterine Pain,Uterine Perforation,Uveitis,Vaginal Anastomotic Leak,Vaginal Discharge,Vaginal Dryness,Vaginal Fistula,Vaginal Hemorrhage,Vaginal Infection,Vaginal Inflammation,Vaginal Obstruction,Vaginal Pain,Vaginal Perforation,Vaginal Stricture,Vaginismus,Vagus Nerve Disorder,Vas Deferens Anastomotic Leak,Vascular Access Complication,Vascular Disorders Other,Vasculitis,Vasovagal Reaction,Venous Injury,Ventricular Arrhythmia,Ventricular Fibrillation,Ventricular Tachycardia,Vertigo,Vestibular Disorder,Virilization,Visceral Arterial Ischemia,Vital Capacity Abnormal,Vitreous Hemorrhage,Voice Alteration,Vomiting,Vulval Infection,Watering Eyes,Weight Gain,Weight Loss,Wheezing,White Blood Cell Decreased,Wolff-Parkinson-White Syndrome,Wound Complication,Wound Dehiscence,Wound Infection,Wrist Fracture",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3125302&version=1.1 -BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2006410&version=3.0 -Cause of Response,The text term used to describe the suspected cause or reason for the patient disease response.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161025&version=1.0 -Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.","Acute Renal Failure, Adenocarcinoma, Adrenocortical Insufficiency, Adenomatous Polyposis Coli, Allergies, Alpha-1 Antitrypsin, Anemia, Anxiety, Arrhythmia, Arthritis, Asthma, Atrial Fibrillation, Avascular Necrosis, Barrett's Esophagus,Basal Cell Carcinoma, Beckwith-Wiedemann, Behcet's Disease, Biliary Disorder, Blood Clots, Bone Fracture(s), Bronchitis, Calcium Channel Blockers, Cancer, Cataracts, Celiac Disease, Cirrhosis, Unknown Etiology, Cerebrovascular Disease, Cholelithiasis, Chronic Renal Failure, Colon Polyps, Common Variable Immunodeficiency, Congestive Heart Failure (CHF), Connective Tissue Disorder, COPD, Coronary Artery Disease, Crohn's Disease, Cryptogenic Organizing Pneumonia, Deep Vein Thrombosis / Thromboembolism, Denys-Drash Syndrome, Depression, Diabetes, Diabetes, Type II, Diabetic Neuropathy, Diet Controlled Diabetes, Diverticulitis,DVT/PE, Dyslipidemia, Epilepsy, Eczema, Epstein-Barr Virus, Familial Adenomatous Polyposis, Fanconi Anemia, Fibrosis, Gastroesophageal Reflux Disease, GERD, Glaucoma, Glycogen Storage Disease, Gout, Gonadal Dysfunction, Gorlin Syndrome, H. pylori Infection, Hashimoto's Thyroiditis, Headache, Heart Disease, Hemihypertrophy, Hemorrhagic Cystitis, Hepatitis, Hepatitis A Infection, Hepatitis B Infection, Hepatitis C Infection, Chronic Hepatitis, Hereditary Non-polyposis Colon Cancer, Herpes, High Grade Liver Dysplastic Nodule, HIV / AIDS, Human Papillomavirus Infection, HUS/TTP, Hypercholesterolemia, Hypercalcemia, Hyperglycemia, Hyperlipidemia, Hypertension, Hypospadias, Hypothyroidism, Inflammatory Bowel Disease, Insulin Controlled Diabetes, Interstitial Pneumontis or ARDS, Intraductal Papillary Mucinous Neoplasm, Iron Overload, Ischemic Heart Disease, ITP, Joint Replacement, Kidney Disease, Liver Cirrhosis (Liver Disease), Liver Toxicity (Non-Infectious), Li-Fraumeni Syndrome, Low Grade Liver Dysplastic Nodule, Lupus, Lynch Syndrome, MAI, Myasthenia Gravis, Myocardial Infarction, Neuroendocrine Tumor, Nonalcoholic Steatohepatitis, Obesity, Organ transplant (site), Osteoarthritis, Osteoporosis or Osteopenia, Other, Other Cancer Within 5 Years, Other Nonmalignant Systemic Disease, Other Pulmonary Complications, Pancreatitis, Pain (Various), Peptic Ulcer (Ulcer), Peripheral Neuropathy, Peripheral Vascular Disease, Peutz-Jeghers Disease, Pregnancy in Patient or Partner, Primary Sclerosing Cholangitis, Psoriasis, Pulmonary Fibrosis, Pulmonary Hemorrhage, Renal Failure (Requiring Dialysis), Renal Dialysis, Renal Insufficiency, Rheumatologic Disease, Rheumatoid Arthritis, Rubinstein-Taybi Syndrome, Sarcoidosis, Seizure, Sleep apnea, Smoking, Steatosis, Stroke, Transient Ischemic Attack, Tuberculosis, Turcot Syndrome, Tyrosinemia, Ulcerative Colitis, Wagr Syndrome, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2970715&version=1.0 -Comorbidity Method of Diagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,"Histology, Pathology, Radiology, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142386&version=1.0 -Days to Adverse Event,Number of days between the date used for index and the date of the patient's adverse event.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154728&version=1.0 -Days to Comorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154729&version=1.0 -Days to Progression,Number of days between the date used for index and the date the patient's disease progressed.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154730&version=1.0 -Days to Progression Free,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,,,,FALSE,Diagnosis,, -Days to Recurrence,Number of days between the date used for index and the date the patient's disease recurred.,,,,TRUE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154731&version=1.0 -Diabetes Treatment Type,Text term used to describe the types of treatment used to manage diabetes.,"Alpha-Glucosidase Inhibitor, Biguanide, Diet, Injected Insulin, Insulin, Oral Hypoglycemic, Sulfonylurea, Thiazolidinedione, Other, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3587247&version=1.0 -Disease Response,Code assigned to describe the patient's response or outcome to the disease.,"AJ-Adjuvant Therapy, BED-Biochemical Evidence of Disease, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PDM-Persistent Distant Metastasis, PLD-Persistent Locoregional Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, TF-Tumor Free, VGPR-Very Good Partial Response, WT-With Tumor, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5750671&version=1.0 -DLCO Ref Predictive Percent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2180255&version=1.0 -ECOG Performance Status,The ECOG functional performance status of the patient/participant.,"""0"", ""1"", ""2"", ""3"", ""4"", ""5"", Unknown, Not Reported",,"""0"", ""1"", ""2"", ""3"", ""4"", ""5""",FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=88&version=5.1 -FEV1 FVC Post Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302956&version=1.0 -FEV 1 FVC Pre Bronch Percent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302955&version=1.0 -FEV1 Ref Post Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,,,,FALSE,Follow Up,,"https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302948&version=1.0""" -FEV1 Ref Pre Bronch Percent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3302947&version=1.0 -Height,The height of the patient in centimeters.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=649&version=4.1 -Hepatitis Sustained Virological Response,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6423783&version=1.0 -HPV Positive Type,Text classification to represent the strain or type of human papillomavirus identified in an individual.," -""16"", ""18"", ""26"", ""31"", ""33"", ""35"", ""39"", ""45"", ""51"", ""52"", ""53"", ""56"", ""58"", ""59"", ""63"", ""66"", ""68"", ""70"", ""73"", ""82"", Other, Unknown, Not Reported",,"""16"", ""18"", ""26"", ""31"", ""33"", ""35"", ""39"", ""45"", ""51"", ""52"", ""53"", ""56"", ""58"", ""59"", ""63"", ""66"", ""68"", ""70"", ""73"", ""82""",FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2922649&version=1.0 -Karnofsky Performance Status,Text term used to describe the classification used of the functional capabilities of a person.,"""0"", ""10"", ""20"", ""30"", ""40"", ""50"", ""60"", ""70"", ""80"", ""90"", ""100"", Unknown, Not Reported",,"""0"", ""10"", ""20"", ""30"", ""40"", ""50"", ""60"", ""70"", ""80"", ""90"", ""100""",FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003853&version=4.2 -Menopause Status,Text term used to describe the patient's menopause status.,"Premenopausal, Perimenopausal, Postmenopausal, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2434914&version=1.1 -Progression or Recurrence,Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, Unknown, Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3121376&version=1.0 -Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,,"Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site",,FALSE,Diagnosis,, -Progression or Recurrence Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0 -Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0 -Treatment Anatomic Site,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,"Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161026&version=1.0 -Progression or Recurrence Type,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,"Biochemical, Distant, Local, Regional, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142385&version=1.0 -Reflux Treatment Type,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,"Antacids, H2 Blockers, Medically Treated, No Treatment, Not Applicable, Not Reported, Proton Pump Inhibitors, Surgically Treated, Unknown",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440206&version=1.0 -Risk Factor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,"Alcohol Consumption,Alcoholic Liver Disease,Allergy Animal NOS,Allergy Ant,Allergy Bee,Allergy Cat,Allergy Dairy or Lactose,Allergy Dog,Allergy Eggs,Allergy Food NOS,Allergy Fruit,Allergy Meat,Allergy Mold or Dust,Allergy Nuts,Allergy Processed Foods,Allergy Seafood,Allergy Wasp,Alpha-1 Antitrypsin Deficiency,Autoimmune Atrophic Chronic Gastritis,Barrett's Esophagus,Beckwith-Wiedemann,Behcet's Disease,Cancer,Cholelithiasis,Chronic Hepatitis,Cirrhosis,Colon Polyps,Common variable immune deficiency (CVID),Denys-Drash Syndrome,Diabetes NOS,Diabetes Type I,Diabetes Type II,Diet,Diverticulitis,Endometriosis,Endosalpingiosis,Eczema,Epstein-Barr Virus,Familial Adenomatous Polyposis,Fanconi Anemia,Fibrosis,Gastric Polyp(s),Gilbert's Syndrome,Gorlin Syndrome,Hashimoto's Thyroiditis,Hay Fever,Headache,Helicobacter Pylori-Associated Gastritis,Hematologic Disorder NOS,Hemihypertrophy,Hemochromatosis,Hepatic Encephalopathy,Hepatitis B Infection,Hepatitis C Infection,Hepatitis NOS,High Grade Dysplasia,HIV,Human Papillomavirus Infection,Hypospadias,Intestinal Metaplasia,Iron Overload,Li-Fraumeni Syndrome,Low Grade Dysplasia,Lymphocytic Thyroiditis,Lynch Syndrome,Myasthenia Gravis,Nonalcoholic Fatty Liver Disease,Nonalcoholic Steatohepatitis,Obesity,Oral Contraceptives,Pancreatitis,Parasitic Disease of Biliary Tract,Primary Sclerosing Cholangitis,Recurrent Pyogenic Cholangitis,Reflux Disease,Rheumatoid Arthritis,Rubinstein-Taybi Syndrome,Sarcoidosis,Seizure,Sensory Changes,Serous tubal intraepithelial carcinoma (STIC),Steatosis,Tattoo,Thyroid Nodular Hyperplasia,Tobacco NOS,Tobacco Smokeless,Tobacco Smoking,Turcot Syndrome,Undescended Testis,Vision Changes,Wagr Syndrome,Unknown,Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142389&version=1.0 -Risk Factor Treatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,"Yes, No, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514356&version=1.0 -Viral Hepatitis Serologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,"HBV Core Antibody, HBV DNA, HBV Genotype, HBV Surface Antibody, HCV Genotype, Hepatitis B Surface Antigen, Hepatitis C Antibody, Hepatitis C Virus RNA, Unknown, Not Reported",,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4395982&version=1.0 -Weight,The weight of the patient measured in kilograms.,,,,FALSE,Follow Up,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=651&version=4.0 -Days to Treatment End,Number of days between the date used for index and the date the treatment ended.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154725&version=1.0 -Days to Treatment Start,Number of days between the date used for index and the date the treatment started.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154726&version=1.0 -Initial Disease Status,The text term used to describe the status of the patient's malignancy when the treatment began.,"Initial Diagnosis, Progressive Disease, Recurrent Disease, Residual Disease, Unknown, Not Reported",,,FALSE,Therapy,, -Regimen or Line of Therapy,The text term used to describe the regimen or line of therapy.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161024&version=1.0 -Therapeutic Agents,Text identification of the individual agent(s) used as part of a treatment regimen.,,,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2975232&version=1.0 -Treatment Effect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,"Complete Necrosis (No Viable Tumor), Incomplete Necrosis (Viable Tumor Present), No Necrosis, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6514354&version=1.0 -Treatment Intent Type,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],"Adjuvant, Cancer Control, Cure, Neoadjuvant, Palliative, Prevention, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2793511&version=1.0 -Treatment or Therapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,"yes, no, unknown, not reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4231463&version=1.0 -Treatment Outcome,Text term that describes the patient's final outcome after the treatment was administered.,"Complete Response, Mixed Response, No Measurable Disease, No Response, Partial Response, Persistent Disease, Progressive Disease, Stable Disease, Treatment Ongoing, Treatment Stopped Due to Toxicity, Very Good Partial Response, Unknown, Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102383&version=1.0 -Treatment Type,Text term that describes the kind of treatment administered.,"Ablation Cryo,Ablation Ethanol Injection,Ablation Microwave,Ablation NOS,Ablation Radiofrequency,Ablation Radiosurgical,Ancillary Treatment,Antiseizure Treatment,Bisphosphonate Therapy,Blinded Study Treatment Unknown,Brachytherapy High Dose,Brachytherapy Low Dose,Brachytherapy NOS,Chemoembolization,Chemoprotectant,Chemotherapy,Concurrent Chemoradiation,Cryoablation,Embolization,Ethanol Injection Ablation,External Beam Radiation,Hormone Therapy,I-131 Radiation Therapy,Internal Radiation,Immunotherapy (Including Vaccines),Isolated Limb Perfusion (ILP),Organ Transplantation,Other,Pharmaceutical Therapy NOS,Pleurodesis,Radiation 2D Conventional,Radiation 3D Conformal,Radiation Combination,Radiation Cyberknife,Radiation External Beam,Radiation Implants,Radiation Intensity-Modulated Radiotherapy,Radiation Internal,Radiation Proton Beam,Radiation Radioisotope,Radiation Stereotactic/Gamma Knife/SRS,Radiation Systemic,Radiation Therapy NOS,Radioactive Iodine Therapy,Radioembolization,Radiosensitizing Agent,Stem Cell Treatment,Stem Cell Transplantation Autologous,Stem Cell Transplantation Double Autologous,Stem Cell Transplantation Allogeneic,Stem Cell Transplantation Non-Myeloablative,Stem Cell Transplantation Syngenic,Stem Cell Transplantation Haploidentical,Stem Cell Transplantation NOS,Stereotactic Radiosurgery,Steroid Therapy,Surgery,Targeted Molecular Therapy,Unknown,Not Reported",,,FALSE,Therapy,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5102381&version=1.0 -Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3225640&version=2.0 -Days to Last Follow up,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0 -Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.",,,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0 -Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, Unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2759550&version=1.0 -Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.","8000/0,8000/1,8000/3,8000/6,8000/9,8001/0,8001/1,8001/3,8002/3,8003/3,8004/3,8005/0,8005/3,8010/0,8010/2,8010/3,8010/6,8010/9,8011/0,8011/3,8012/3,8013/3,8014/3,8015/3,8020/3,8021/3,8022/3,8023/3,8030/3,8031/3,8032/3,8033/3,8034/3,8035/3,8040/0,8040/1,8041/3,8041/34,8042/3,8043/3,8044/3,8045/3,8046/3,8050/0,8050/2,8050/3,8051/0,8051/3,8052/0,8052/2,8052/3,8053/0,8060/0,8070/2,8070/3,8070/33,8070/6,8071/2,8071/3,8072/3,8073/3,8074/3,8075/3,8076/2,8076/3,8077/0,8077/2,8078/3,8080/2,8081/2,8082/3,8083/3,8084/3,8085/3,8086/3,8090/1,8090/3,8091/3,8092/3,8093/3,8094/3,8095/3,8096/0,8097/3,8098/3,8100/0,8101/0,8102/0,8102/3,8103/0,8110/0,8110/3,8120/0,8120/1,8120/2,8120/3,8121/0,8121/1,8121/3,8122/3,8123/3,8124/3,8130/1,8130/2,8130/3,8131/3,8140/0,8140/1,8140/2,8140/3,8140/33,8140/6,8141/3,8142/3,8143/3,8144/3,8145/3,8146/0,8147/0,8147/3,8148/0,8148/2,8149/0,8150/0,8150/1,8150/3,8151/0,8151/3,8152/1,8152/3,8153/1,8153/3,8154/3,8155/1,8155/3,8156/1,8156/3,8158/1,8160/0,8160/3,8161/0,8161/3,8162/3,8163/0,8163/2,8163/3,8170/0,8170/3,8171/3,8172/3,8173/3,8174/3,8175/3,8180/3,8190/0,8190/3,8191/0,8200/0,8200/3,8201/2,8201/3,8202/0,8204/0,8210/0,8210/2,8210/3,8211/0,8211/3,8212/0,8213/0,8213/3,8214/3,8215/3,8220/0,8220/3,8221/0,8221/3,8230/2,8230/3,8231/3,8240/1,8240/3,8241/3,8242/1,8242/3,8243/3,8244/3,8245/1,8245/3,8246/3,8247/3,8248/1,8249/3,8250/1,8250/2,8250/3,8251/0,8251/3,8252/3,8253/3,8254/3,8255/3,8256/3,8257/3,8260/0,8260/3,8261/0,8261/2,8261/3,8262/3,8263/0,8263/2,8263/3,8264/0,8265/3,8270/0,8270/3,8271/0,8272/0,8272/3,8280/0,8280/3,8281/0,8281/3,8290/0,8290/3,8300/0,8300/3,8310/0,8310/3,8311/1,8311/3,8312/3,8313/0,8313/1,8313/3,8314/3,8315/3,8316/3,8317/3,8318/3,8319/3,8320/3,8321/0,8322/0,8322/3,8323/0,8323/3,8324/0,8325/0,8330/0,8330/1,8330/3,8331/3,8332/3,8333/0,8333/3,8334/0,8335/3,8336/0,8337/3,8339/3,8340/3,8341/3,8342/3,8343/2,8343/3,8344/3,8345/3,8346/3,8347/3,8350/3,8360/1,8361/0,8370/0,8370/1,8370/3,8371/0,8372/0,8373/0,8374/0,8375/0,8380/0,8380/1,8380/2,8380/3,8381/0,8381/1,8381/3,8382/3,8383/3,8384/3,8390/0,8390/3,8391/0,8392/0,8400/0,8400/1,8400/3,8401/0,8401/3,8402/0,8402/3,8403/0,8403/3,8404/0,8405/0,8406/0,8407/0,8407/3,8408/0,8408/1,8408/3,8409/0,8409/3,8410/0,8410/3,8413/3,8420/0,8420/3,8430/1,8430/3,8440/0,8440/3,8441/0,8441/2,8441/3,8442/1,8443/0,8444/1,8450/0,8450/3,8451/1,8452/1,8452/3,8453/0,8453/2,8453/3,8454/0,8460/0,8460/2,8460/3,8461/0,8461/3,8462/1,8463/1,8470/0,8470/2,8470/3,8471/0,8471/3,8472/1,8473/1,8474/1,8474/3,8480/0,8480/1,8480/3,8480/6,8481/3,8482/3,8490/3,8490/6,8500/2,8500/3,8501/2,8501/3,8502/3,8503/0,8503/2,8503/3,8504/0,8504/2,8504/3,8505/0,8506/0,8507/2,8507/3,8508/3,8509/2,8509/3,8510/3,8512/3,8513/3,8514/3,8519/2,8520/2,8520/3,8521/1,8521/3,8522/1,8522/2,8522/3,8523/3,8524/3,8525/3,8530/3,8540/3,8541/3,8542/3,8543/3,8550/0,8550/1,8550/3,8551/3,8552/3,8560/0,8560/3,8561/0,8562/3,8570/3,8571/3,8572/3,8573/3,8574/3,8575/3,8576/3,8580/0,8580/1,8580/3,8581/1,8581/3,8582/1,8582/3,8583/1,8583/3,8584/1,8584/3,8585/1,8585/3,8586/3,8587/0,8588/3,8589/3,8590/1,8591/1,8592/1,8593/1,8594/1,8600/0,8600/3,8601/0,8602/0,8610/0,8620/1,8620/3,8621/1,8622/1,8623/1,8630/0,8630/1,8630/3,8631/0,8631/1,8631/3,8632/1,8633/1,8634/1,8634/3,8640/1,8640/3,8641/0,8642/1,8650/0,8650/1,8650/3,8660/0,8670/0,8670/3,8671/0,8680/0,8680/1,8680/3,8681/1,8682/1,8683/0,8690/1,8691/1,8692/1,8693/1,8693/3,8700/0,8700/3,8710/3,8711/0,8711/3,8712/0,8713/0,8714/3,8720/0,8720/2,8720/3,8721/3,8722/0,8722/3,8723/0,8723/3,8725/0,8726/0,8727/0,8728/0,8728/1,8728/3,8730/0,8730/3,8740/0,8740/3,8741/2,8741/3,8742/2,8742/3,8743/3,8744/3,8745/3,8746/3,8750/0,8760/0,8761/0,8761/1,8761/3,8762/1,8770/0,8770/3,8771/0,8771/3,8772/0,8772/3,8773/3,8774/3,8780/0,8780/3,8790/0,8800/0,8800/3,8800/9,8801/3,8802/3,8803/3,8804/3,8805/3,8806/3,8810/0,8810/1,8810/3,8811/0,8811/1,8811/3,8812/0,8812/3,8813/0,8813/3,8814/3,8815/0,8815/1,8815/3,8820/0,8821/1,8822/1,8823/0,8824/0,8824/1,8825/0,8825/1,8825/3,8826/0,8827/1,8830/0,8830/1,8830/3,8831/0,8832/0,8832/3,8833/3,8834/1,8835/1,8836/1,8840/0,8840/3,8841/1,8842/0,8842/3,8850/0,8850/1,8850/3,8851/0,8851/3,8852/0,8852/3,8853/3,8854/0,8854/3,8855/3,8856/0,8857/0,8857/3,8858/3,8860/0,8861/0,8862/0,8870/0,8880/0,8881/0,8890/0,8890/1,8890/3,8891/0,8891/3,8892/0,8893/0,8894/0,8894/3,8895/0,8895/3,8896/3,8897/1,8898/1,8900/0,8900/3,8901/3,8902/3,8903/0,8904/0,8905/0,8910/3,8912/3,8920/3,8921/3,8930/0,8930/3,8931/3,8932/0,8933/3,8934/3,8935/0,8935/1,8935/3,8936/0,8936/1,8936/3,8940/0,8940/3,8941/3,8950/3,8951/3,8959/0,8959/1,8959/3,8960/1,8960/3,8963/3,8964/3,8965/0,8966/0,8967/0,8970/3,8971/3,8972/3,8973/3,8974/1,8975/1,8980/3,8981/3,8982/0,8982/3,8983/0,8983/3,8990/0,8990/1,8990/3,8991/3,9000/0,9000/1,9000/3,9010/0,9011/0,9012/0,9013/0,9014/0,9014/1,9014/3,9015/0,9015/1,9015/3,9016/0,9020/0,9020/1,9020/3,9030/0,9040/0,9040/3,9041/3,9042/3,9043/3,9044/3,9045/3,9050/0,9050/3,9051/0,9051/3,9052/0,9052/3,9053/3,9054/0,9055/0,9055/1,9060/3,9061/3,9062/3,9063/3,9064/2,9064/3,9065/3,9070/3,9071/3,9072/3,9073/1,9080/0,9080/1,9080/3,9081/3,9082/3,9083/3,9084/0,9084/3,9085/3,9086/3,9090/0,9090/3,9091/1,9100/0,9100/1,9100/3,9101/3,9102/3,9103/0,9104/1,9105/3,9110/0,9110/1,9110/3,9120/0,9120/3,9121/0,9122/0,9123/0,9124/3,9125/0,9130/0,9130/1,9130/3,9131/0,9132/0,9133/1,9133/3,9135/1,9136/1,9137/3,9140/3,9141/0,9142/0,9150/0,9150/1,9150/3,9160/0,9161/0,9161/1,9170/0,9170/3,9171/0,9172/0,9173/0,9174/0,9174/1,9175/0,9180/0,9180/3,9181/3,9182/3,9183/3,9184/3,9185/3,9186/3,9187/3,9191/0,9192/3,9193/3,9194/3,9195/3,9200/0,9200/1,9210/0,9210/1,9220/0,9220/1,9220/3,9221/0,9221/3,9230/0,9230/3,9231/3,9240/3,9241/0,9242/3,9243/3,9250/1,9250/3,9251/1,9251/3,9252/0,9252/3,9260/3,9261/3,9262/0,9270/0,9270/1,9270/3,9271/0,9272/0,9273/0,9274/0,9275/0,9280/0,9281/0,9282/0,9290/0,9290/3,9300/0,9301/0,9302/0,9302/3,9310/0,9310/3,9311/0,9312/0,9320/0,9321/0,9322/0,9330/0,9330/3,9340/0,9341/1,9341/3,9342/3,9350/1,9351/1,9352/1,9360/1,9361/1,9362/3,9363/0,9364/3,9365/3,9370/3,9371/3,9372/3,9373/0,9380/3,9381/3,9382/3,9383/1,9384/1,9385/3,9390/0,9390/1,9390/3,9391/3,9392/3,9393/3,9394/1,9395/3,9396/3,9400/3,9401/3,9410/3,9411/3,9412/1,9413/0,9420/3,9421/1,9423/3,9424/3,9425/3,9430/3,9431/1,9432/1,9440/3,9441/3,9442/1,9442/3,9444/1,9445/3,9450/3,9451/3,9460/3,9470/3,9471/3,9472/3,9473/3,9474/3,9475/3,9476/3,9477/3,9478/3,9480/3,9490/0,9490/3,9491/0,9492/0,9493/0,9500/3,9501/0,9501/3,9502/0,9502/3,9503/3,9504/3,9505/1,9505/3,9506/1,9507/0,9508/3,9509/1,9510/0,9510/3,9511/3,9512/3,9513/3,9514/1,9520/3,9521/3,9522/3,9523/3,9530/0,9530/1,9530/3,9531/0,9532/0,9533/0,9534/0,9535/0,9537/0,9538/1,9538/3,9539/1,9539/3,9540/0,9540/1,9540/3,9541/0,9542/3,9550/0,9560/0,9560/1,9560/3,9561/3,9562/0,9570/0,9571/0,9571/3,9580/0,9580/3,9581/3,9582/0,9590/3,9591/3,9596/3,9597/3,9650/3,9651/3,9652/3,9653/3,9654/3,9655/3,9659/3,9661/3,9662/3,9663/3,9664/3,9665/3,9667/3,9670/3,9671/3,9673/3,9675/3,9678/3,9679/3,9680/3,9684/3,9687/3,9688/3,9689/3,9690/3,9691/3,9695/3,9698/3,9699/3,9700/3,9701/3,9702/3,9705/3,9708/3,9709/3,9712/3,9714/3,9716/3,9717/3,9718/3,9719/3,9724/3,9725/3,9726/3,9727/3,9728/3,9729/3,9731/3,9732/3,9733/3,9734/3,9735/3,9737/3,9738/3,9740/1,9740/3,9741/1,9741/3,9742/3,9750/3,9751/1,9751/3,9752/1,9753/1,9754/3,9755/3,9756/3,9757/3,9758/3,9759/3,9760/3,9761/3,9762/3,9764/3,9765/1,9766/1,9767/1,9768/1,9769/1,9800/3,9801/3,9805/3,9806/3,9807/3,9808/3,9809/3,9811/3,9812/3,9813/3,9814/3,9815/3,9816/3,9817/3,9818/3,9820/3,9823/3,9826/3,9827/3,9831/3,9832/3,9833/3,9834/3,9835/3,9836/3,9837/3,9840/3,9860/3,9861/3,9863/3,9865/3,9866/3,9867/3,9869/3,9870/3,9871/3,9872/3,9873/3,9874/3,9875/3,9876/3,9891/3,9895/3,9896/3,9897/3,9898/1,9898/3,9910/3,9911/3,9920/3,9930/3,9931/3,9940/3,9945/3,9946/3,9948/3,9950/3,9960/3,9961/3,9962/3,9963/3,9964/3,9965/3,9966/3,9967/3,9970/1,9971/1,9971/3,9975/3,9980/3,9982/3,9983/3,9984/3,9985/3,9986/3,9987/3,9989/3,9991/3,9992/3,Unknown,Not Reported, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0 -Primary Diagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS,Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,Unknown",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0 -Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3382736&version=2.0 -Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,, -Site of Resection or Biopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161034&version=1.0 -Tissue or Organ of Origin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,Unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,Unknown,Not Reported",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161035&version=1.0 -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Low Grade, Unknown, Not Reported, Not Applicable",,,TRUE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2785839&version=2.0 -AJCC Clinical M,"Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment.","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440331&version=1.0 -AJCC Clinical N,"Extent of the regional lymph node involvement for the cancer based on evidence obtained from - clinical assessment parameters determined prior to treatment.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440330&version=1.0 -AJCC Clinical Stage,"Stage group determined from clinical information on the tumor (T), regional node (N) and - metastases (M) and by grouping cases with similar prognosis for cancer.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440332&version=1.0 -AJCC Clinical T,"Extent of the primary cancer based on evidence obtained from clinical assessment parameters - determined prior to treatment.","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440328&version=1.0 -AJCC Pathologic M,"Code to represent the defined absence or presence of distant spread or metastases (M) to - locations via vascular channels or lymphatics beyond the regional lymph nodes, using - criteria established by the American Joint Committee on Cancer (AJCC).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045439&version=1.0 -AJCC Pathologic N,"The codes that represent the stage of cancer based on the nodes present (N stage) according - to criteria based on multiple editions of the AJCC's Cancer Staging Manual.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203106&version=1.0 -AJCC Pathologic Stage,"The extent of a cancer, especially whether the disease has spread from the original site to - other parts of the body based on AJCC staging criteria.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203222&version=1.0 -AJCC Pathologic T,"Code of pathological T (primary tumor) to define the size or contiguous extension of the - primary tumor (T), using staging criteria from the American Joint Committee on Cancer - (AJCC).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045435&version=1.0 -AJCC Staging System Edition,"The text term used to describe the version or edition of the American Joint Committee on Cancer - Staging Handbooks, a publication by the group formed for the purpose of developing a system of - staging for cancer that is acceptable to the American medical profession and is compatible with - other accepted classifications.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2722309&version=1.0 -Anaplasia Present,"Yes/no/unknown/not reported indicator used to describe whether anaplasia was present at the -time of diagnosis.","Yes - Anaplasia Present, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6059599&version=1.0 -Yes - Anaplasia Present,Indicates anaplasia is present,,Anaplasia Present Type,,FALSE,Diagnosis,, -Anaplasia Present Type,"The text term used to describe the morphologic findings indicating the presence of a malignant - cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and - high mitotic activity in a tissue sample.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925534&version=1.0 -Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003324&version=4.0 -Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis -and the deepest point of tumor penetration.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64809&version=3.0 -Classification of Tumor,"Text that describes the kind of disease present in the tumor specimen as related to a specific - timepoint.","Primary, Metastasis, Recurrence, Other, Unknown, Not reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0 -Days to Diagnosis,"Number of days between the date used for index and the date the patient was diagnosed with the - malignant disease.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154733&version=1.0 -First Symptom Prior to Diagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,"Altered Mental Status, Headaches, Motor or Movement Changes, Seizures, Sensory Changes, Visual Changes, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133605&version=1.0 -Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133606&version=1.0 -Laterality,"For tumors in paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=827&version=3.0 -Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=89&version=3.0 -Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3&version=3.0 -Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64171&version=3.0 -Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133614&version=1.0 -Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver, Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum, Omentum, Ovary, Pelvis, Peritoneal Cavity, Peritoneum, Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3029815&version=1.0 -Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Imaging,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,Unknown,Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161031&version=1.0 -Mitotic Count,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",,,,FALSE,Diagnosis,, -Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,,,,FALSE,Diagnosis,, -Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6690681&version=1.0 -Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64181&version=3.0 -Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2608702&version=1.0 -Synchronous Malignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.","Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142390&version=1.0 -Tumor Confined to Organ of Origin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,"Yes, No, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925494&version=1.0 -Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3174022&version=1.0 -Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64215&version=3.0 -Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, Unknown, Not Reported, Not Allowed To Collect",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64358&version=3.0 -Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,,Vascular Invasion Type,,FALSE,Diagnosis,, -Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, Unknown, Not Reported",,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3168001&version=1.0 -Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,,,,FALSE,Diagnosis,,https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896960&version=1.0 \ No newline at end of file diff --git a/data/schema_org_schemas/HTAN.jsonld b/data/schema_org_schemas/HTAN.jsonld index 879f6c62c..4bd5632a7 100644 --- a/data/schema_org_schemas/HTAN.jsonld +++ b/data/schema_org_schemas/HTAN.jsonld @@ -2428,6 +2428,9 @@ }, { "@id": "bts:Therapy" + }, + { + "@id": "bts:MolecularTest" } ], "sms:requiresDependency": [ @@ -2726,6 +2729,18 @@ }, { "@id": "bts:Cloupe" + }, + { + "@id": "bts:Am" + }, + { + "@id": "bts:Cellam" + }, + { + "@id": "bts:Mpg" + }, + { + "@id": "bts:M" } ], "sms:displayName": "File Format", @@ -2735,7 +2750,7 @@ { "@id": "bts:Checksum", "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the fasta file", + "rdfs:comment": "MD5 checksum of the BAM file", "rdfs:label": "Checksum", "rdfs:subClassOf": [ { @@ -2820,7 +2835,7 @@ { "@id": "bts:HTANParentBiospecimenID", "@type": "rdfs:Class", - "rdfs:comment": "HTAN Biospecimen Identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", "rdfs:label": "HTANParentBiospecimenID", "rdfs:subClassOf": [ { @@ -2852,10 +2867,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Demographics", + "@id": "bts:ClinicalDataTier2", "@type": "rdfs:Class", - "rdfs:comment": "Individual biomedical demographics attributes", - "rdfs:label": "Demographics", + "rdfs:comment": "Cancer related clinical data", + "rdfs:label": "ClinicalDataTier2", "rdfs:subClassOf": [ { "@id": "bts:Patient" @@ -2864,8 +2879,13 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Demographics", + "sms:displayName": "Clinical Data Tier 2", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -2874,226 +2894,175 @@ "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Ethnicity" - }, - { - "@id": "bts:Gender" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Race" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:VitalStatus" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:DaystoBirth" + "@id": "bts:SentinelLymphNodeCount" }, { - "@id": "bts:AgeIsObfuscated" + "@id": "bts:SentinelNodePositiveAssessmentCount" }, { - "@id": "bts:YearOfBirth" + "@id": "bts:TumorExtranodalExtensionIndicator" }, { - "@id": "bts:OccupationDurationYears" + "@id": "bts:SatelliteMetastasisPresentIndicator" }, { - "@id": "bts:PrematureAtBirth" + "@id": "bts:OtherBiopsyResectionSite" }, { - "@id": "bts:WeeksGestationatBirth" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyHistory", - "@type": "rdfs:Class", - "rdfs:comment": "Individual's family cancer history", - "rdfs:label": "FamilyHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Family History", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:PrecancerousConditionType" }, { - "@id": "bts:RelativewithCancerHistory" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Exposure", - "@type": "rdfs:Class", - "rdfs:comment": "Individual's exposure to carcenogens", - "rdfs:label": "Exposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Exposure", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:PriorSitesofRadiation" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:SmokingExposure" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:AsbestosExposure" + "@id": "bts:FamilyMemberVitalStatusIndicator" }, { - "@id": "bts:CoalDustExposure" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" + "@id": "bts:COVID19CurrentStatus" }, { - "@id": "bts:RadonExposure" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:RespirableCrystallineSilicaExposure" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:FollowUp", - "@type": "rdfs:Class", - "rdfs:comment": "Individual's follow up exams", - "rdfs:label": "FollowUp", - "rdfs:subClassOf": [ - { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Follow Up", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:DaystoFollowUp" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:AdverseEvent" + "@id": "bts:Ecigvapeuse" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:Ecigvape30dayusenum" }, { - "@id": "bts:BarrettsEsophagusGobletCellsPresent" + "@id": "bts:Ecigvapetimesperday" }, { - "@id": "bts:BMI" + "@id": "bts:Typeofsmokeexposurecumulativeyears" }, { - "@id": "bts:CauseofResponse" + "@id": "bts:Chewingtobaccodailyusecount" }, { - "@id": "bts:Comorbidity" + "@id": "bts:Secondhandsmokeexposureyears" }, { - "@id": "bts:ComorbidityMethodofDiagnosis" + "@id": "bts:KnownGeneticPredispositionMutation" }, { - "@id": "bts:DaystoAdverseEvent" + "@id": "bts:HereditaryCancerPredispositionSyndrome" }, { - "@id": "bts:DaystoComorbidity" + "@id": "bts:CancerAssociatedGeneMutations" }, { - "@id": "bts:DiabetesTreatmentType" + "@id": "bts:MutationalSignatures" }, { - "@id": "bts:DiseaseResponse" + "@id": "bts:MismatchRepairSystemStatus" }, { - "@id": "bts:DLCORefPredictivePercent" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:ECOGPerformanceStatus" - }, + "@id": "bts:ModeofCancerDetection" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:LungCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "LungCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:FEV1FVCPostBronchPercent" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lung Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:FEV1FVCPreBronchPercent" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:FEV1RefPostBronchPercent" + "@id": "bts:Component" }, { - "@id": "bts:FEV1RefPreBronchPercent" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Height" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:HepatitisSustainedVirologicalResponse" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:HPVPositiveType" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:KarnofskyPerformanceStatus" + "@id": "bts:LungCancerDetectionMethodType" }, { - "@id": "bts:MenopauseStatus" + "@id": "bts:LungCancerParticipantProcedureHistory" }, { - "@id": "bts:PancreatitisOnsetYear" + "@id": "bts:LungAdjacentHistologyType" }, { - "@id": "bts:RefluxTreatmentType" + "@id": "bts:LungTumorLocationAnatomicSite" }, { - "@id": "bts:RiskFactor" + "@id": "bts:LungTumorLobeBronchialLocation" }, { - "@id": "bts:RiskFactorTreatment" + "@id": "bts:CurrentLungCancerSymptoms" }, { - "@id": "bts:ViralHepatitisSerologies" + "@id": "bts:LungTopography" }, { - "@id": "bts:Weight" + "@id": "bts:LungCancerHarboringGenomicAberrations" } ], "sms:validationRules": [] }, { - "@id": "bts:Therapy", + "@id": "bts:ColorectalCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Individual's first line of therapy or treatment", - "rdfs:label": "Therapy", + "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ColorectalCancerTier3", "rdfs:subClassOf": [ { "@id": "bts:Patient" @@ -3102,8 +3071,13 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Therapy", + "sms:displayName": "Colorectal Cancer Tier 3", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -3112,46 +3086,79 @@ "@id": "bts:HTANParticipantID" }, { - "@id": "bts:TreatmentorTherapy" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:TreatmentType" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:TreatmentEffect" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:TreatmentOutcome" + "@id": "bts:ColorectalCancerDetectionMethodType" }, { - "@id": "bts:DaystoTreatmentEnd" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:TreatmentAnatomicSite" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:DaystoTreatmentStart" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:InitialDiseaseStatus" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:RegimenorLineofTherapy" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:TherapeuticAgents" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:TreatmentIntentType" + "@id": "bts:PatientColonoscopyPerformedIndicator" + }, + { + "@id": "bts:ColorectalCancerTumorBorderConfiguration" + }, + { + "@id": "bts:MLH1PromoterMethylationStatus" + }, + { + "@id": "bts:ColorectalCancerKRASIndicator" + }, + { + "@id": "bts:ColonPolypOccurenceIndicator" + }, + { + "@id": "bts:FamilyHistoryColorectalPolyp" + }, + { + "@id": "bts:ColorectalPolypNewIndicator" + }, + { + "@id": "bts:ColorectalPolypShape" + }, + { + "@id": "bts:SizeofPolypRemoved" + }, + { + "@id": "bts:ColorectalPolypCount" + }, + { + "@id": "bts:ColorectalPolypType" + }, + { + "@id": "bts:ColorectalPolypAdenomaType" } ], "sms:validationRules": [] }, { - "@id": "bts:Diagnosis", + "@id": "bts:BreastCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Individual's diagnosis", - "rdfs:label": "Diagnosis", + "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "BreastCancerTier3", "rdfs:subClassOf": [ { "@id": "bts:Patient" @@ -3160,8 +3167,13 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Diagnosis", + "sms:displayName": "Breast Cancer Tier 3", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], "sms:requiresDependency": [ { "@id": "bts:Component" @@ -3170,166 +3182,181 @@ "@id": "bts:HTANParticipantID" }, { - "@id": "bts:AgeatDiagnosis" - }, - { - "@id": "bts:YearofDiagnosis" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:BreastCarcinomaDetectionMethodType" }, { - "@id": "bts:Morphology" + "@id": "bts:BreastCarcinomaHistologyCategory" }, { - "@id": "bts:TumorGrade" + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:BreastBiopsyProcedureFindingType" }, { - "@id": "bts:DaystoLastFollowup" + "@id": "bts:BreastQuadrantSite" }, { - "@id": "bts:DaystoLastKnownDiseaseStatus" + "@id": "bts:BreastCancerAssessmentTests" }, { - "@id": "bts:MethodofDiagnosis" + "@id": "bts:BreastCancerGenomicTestPerformed" }, { - "@id": "bts:PriorMalignancy" + "@id": "bts:MammaprintRiskGroup" }, { - "@id": "bts:PriorTreatment" + "@id": "bts:OncotypeRiskGroup" }, { - "@id": "bts:MetastasisatDiagnosis" + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" }, { - "@id": "bts:MetastasisatDiagnosisSite" + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" }, { - "@id": "bts:FirstSymptomPriortoDiagnosis" + "@id": "bts:BreastCancerAllredEstrogenReceptorScore" }, { - "@id": "bts:DaystoDiagnosis" + "@id": "bts:PriorInvasiveBreastDisease" }, { - "@id": "bts:PercentTumorInvasion" + "@id": "bts:BreastCarcinomaERStatusPercentageValue" }, { - "@id": "bts:ResidualDisease" + "@id": "bts:BreastCarcinomaPRStatusPercentageValue" }, { - "@id": "bts:SynchronousMalignancy" + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" }, { - "@id": "bts:TumorConfinedtoOrganofOrigin" + "@id": "bts:BreastCarcinomaCentromere17CopyNumber" }, { - "@id": "bts:TumorFocality" + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" }, { - "@id": "bts:TumorLargestDimensionDiameter" + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" }, { - "@id": "bts:GrossTumorWeight" + "@id": "bts:BreastCarcinomaSurgicalProcedureName" }, { - "@id": "bts:BreslowThickness" + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" }, { - "@id": "bts:VascularInvasionPresent" + "@id": "bts:BreastCarcinomaHER2Status" }, { - "@id": "bts:VascularInvasionType" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:AnaplasiaPresent" + "@id": "bts:BreastCarcinomaERStainingIntensity" }, { - "@id": "bts:AnaplasiaPresentType" + "@id": "bts:BreastCarcinomaPRStainingIntensity" }, { - "@id": "bts:Laterality" + "@id": "bts:OncotypeScore" }, { - "@id": "bts:PerineuralInvasionPresent" + "@id": "bts:BreastImagingPerformedType" }, { - "@id": "bts:LymphaticInvasionPresent" + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" }, { - "@id": "bts:LymphNodesPositive" + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" }, { - "@id": "bts:LymphNodesTested" - }, + "@id": "bts:BIRADSMammographyBreastDensityCategory" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:BrainCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Brain cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "BrainCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:PeritonealFluidCytologicalStatus" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Brain Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:ClassificationofTumor" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:BestOverallResponse" + "@id": "bts:Component" }, { - "@id": "bts:MitoticCount" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:AJCCClinicalM" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AJCCClinicalN" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:AJCCClinicalStage" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:AJCCClinicalT" + "@id": "bts:CNSTumorPrimaryAnatomicSite" }, { - "@id": "bts:AJCCPathologicM" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:AJCCPathologicN" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:AJCCPathologicStage" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AJCCPathologicT" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:AJCCStagingSystemEdition" + "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus" } ], "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:AcuteLymphoblasticLeukemiaTier3", "@type": "rdfs:Class", - "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3", + "rdfs:label": "AcuteLymphoblasticLeukemiaTier3", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", + "sms:displayName": "Acute Lymphoblastic Leukemia Tier 3", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -3341,143 +3368,206 @@ "@id": "bts:Component" }, { - "@id": "bts:HTANBiospecimenID" - }, - { - "@id": "bts:HTANParentID" + "@id": "bts:HTANParticipantID" }, { "@id": "bts:TimepointLabel" }, { - "@id": "bts:CollectionDaysfromIndex" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:AdjacentBiospecimenID" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:BiospecimenType" + "@id": "bts:SpecimenBlastCountPercentageValue" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:NCIALLRiskGroup" }, { - "@id": "bts:FixativeType" + "@id": "bts:MRDALLDiagnosticSensitivity" }, { - "@id": "bts:SiteofResectionorBiopsy" - }, + "@id": "bts:CNSLeukemiaStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Ovarian cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "OvarianCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:StorageMethod" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ovarian Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:ProcessingDaysfromIndex" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:ProtocolLink" + "@id": "bts:Component" }, { - "@id": "bts:SiteDataSource" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:MountingMedium" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:ProcessingLocation" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:HistologyAssessmentBy" + "@id": "bts:OvarianCancerHistologicSubtype" }, { - "@id": "bts:HistologyAssessmentMedium" + "@id": "bts:OvarianCancerSurgicalOutcome" }, { - "@id": "bts:PreinvasiveMorphology" - }, + "@id": "bts:OvarianCancerPlatinumStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ProstateCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:TumorInfiltratingLymphocytes" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Prostate Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:DegreeofDysplasia" + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:DysplasiaFraction" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:NumberProliferatingCells" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:PercentEosinophilInfiltration" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:PercentGranulocyteInfiltration" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:PercentInflamInfiltration" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:PercentLymphocyteInfiltration" + "@id": "bts:LocationNaturePositiveMargins" }, { - "@id": "bts:PercentMonocyteInfiltration" + "@id": "bts:SeminalVesicleInvasion" }, { - "@id": "bts:PercentNecrosis" + "@id": "bts:ProstateCarcinomaHistologicType" }, { - "@id": "bts:PercentNeutrophilInfiltration" + "@id": "bts:ProstateCancerLocalExtent" }, { - "@id": "bts:PercentNormalCells" + "@id": "bts:AdditonalFindingsUninvolvedProstate" }, { - "@id": "bts:PercentStromalCells" + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "SarcomaTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sarcoma Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:PercentTumorCells" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:PercentTumorNuclei" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:FiducialMarker" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:SlicingMethod" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:SarcomaSubtype" }, { - "@id": "bts:LysisBuffer" + "@id": "bts:SarcomaDiagnosisClassificationCategory" }, { - "@id": "bts:MethodofNucleicAcidIsolation" + "@id": "bts:SarcomaTumorExtensionType" } ], "sms:validationRules": [] }, { - "@id": "bts:OtherAssay", + "@id": "bts:PancreaticCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", - "rdfs:label": "OtherAssay", + "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", + "rdfs:label": "PancreaticCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Assay", + "sms:displayName": "Pancreatic Cancer Tier 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -3485,58 +3575,47 @@ "@id": "bts:Component" }, { - "@id": "bts:filename" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:fileFormat" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:AssayType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AssayType", - "@type": "rdfs:Class", - "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)", - "rdfs:label": "AssayType", - "rdfs:subClassOf": [ + "@id": "bts:PancreasPrecancerHistopathologicGrade" + }, { - "@id": "bts:Assay" + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" + }, + { + "@id": "bts:PancreaticDuctFinalPathologyType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Assay Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel1", + "@id": "bts:MelanomaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", - "rdfs:label": "ScRNA-seqLevel1", + "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "MelanomaTier3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 1", + "sms:displayName": "Melanoma Tier 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -3544,1100 +3623,876 @@ "@id": "bts:Component" }, { - "@id": "bts:filename" - }, - { - "@id": "bts:fileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Read1" + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" }, { - "@id": "bts:Read2" + "@id": "bts:CutaneousMelanomaTumorRegressionRange" }, { - "@id": "bts:EndBias" + "@id": "bts:MelanomaSpecimenClarkLevelValue" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:CutaneousMelanomaSurgicalMargins" }, { - "@id": "bts:SpikeIn" + "@id": "bts:MelanomaLesionSize" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:HistoryofAtypicalNevi" }, { - "@id": "bts:TotalNumberofInputCells" + "@id": "bts:FitzpatrickSkinTone" }, { - "@id": "bts:InputCellsandNuclei" + "@id": "bts:HistoryofChronicUVExposure" }, { - "@id": "bts:LibraryPreparationDate" + "@id": "bts:HistoryofBlisteringSunburn" }, { - "@id": "bts:SingleCellDissociationDate" + "@id": "bts:HistoryofTanningBedUse" }, { - "@id": "bts:SequencingLibraryConstructionDate" + "@id": "bts:ImmediateFamilyHistoryMelanoma" }, { - "@id": "bts:NucleicAcidCaptureDate" + "@id": "bts:MelanomaBiopsyResectionSites" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:CutaneousMelanomaUlceration" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:CutaneousMelanomaAdditionalFindings" } ], "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel2", + "@id": "bts:Demographics", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", - "rdfs:label": "ScRNA-seqLevel2", + "rdfs:comment": "Individual biomedical demographics attributes", + "rdfs:label": "Demographics", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 2", + "sms:displayName": "Demographics", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel1" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" }, { - "@id": "bts:filename" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:fileFormat" + "@id": "bts:Ethnicity" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Gender" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Race" }, { - "@id": "bts:ScRNA-seqWorkflowType" + "@id": "bts:VitalStatus" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:DaystoBirth" }, { - "@id": "bts:WorkflowParametersDescription" + "@id": "bts:CountryofResidence" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:AgeIsObfuscated" }, { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:GenomeAnnotationURL" - }, - { - "@id": "bts:Checksum" - }, - { - "@id": "bts:White-listCellBarcodeFileLink" + "@id": "bts:YearOfBirth" }, { - "@id": "bts:CellBarcodeTag" + "@id": "bts:OccupationDurationYears" }, { - "@id": "bts:UMITag" + "@id": "bts:PrematureAtBirth" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:WeeksGestationatBirth" } ], "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel3", + "@id": "bts:FamilyHistory", "@type": "rdfs:Class", - "rdfs:comment": "Gene and Isoform expression files", - "rdfs:label": "ScRNA-seqLevel3", + "rdfs:comment": "Individual's family cancer history", + "rdfs:label": "FamilyHistory", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 3", + "sms:displayName": "Family History", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel2" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" }, { - "@id": "bts:filename" - }, - { - "@id": "bts:fileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:DataCategory" - }, - { - "@id": "bts:MatrixType" - }, - { - "@id": "bts:LinkedMatrices" - }, - { - "@id": "bts:CellMedianNumberReads" - }, - { - "@id": "bts:CellMedianNumberGenes" - }, - { - "@id": "bts:CellTotal" - }, - { - "@id": "bts:ScRNA-seqWorkflowType" - }, - { - "@id": "bts:ScRNA-seqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:WorkflowStartDate-time" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:WorkflowEndDate-time" + "@id": "bts:RelativewithCancerHistory" } ], "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel4", + "@id": "bts:Exposure", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScRNA-seqLevel4", + "rdfs:comment": "Individual's exposure to carcenogens", + "rdfs:label": "Exposure", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 4", + "sms:displayName": "Exposure", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:ScRNA-seqLevel3" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" }, { - "@id": "bts:filename" - }, - { - "@id": "bts:fileFormat" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:SmokingExposure" }, { - "@id": "bts:ScRNA-seqWorkflowType" + "@id": "bts:AlcoholExposure" }, { - "@id": "bts:ScRNA-seqWorkflowParametersDescription" + "@id": "bts:AsbestosExposure" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:CoalDustExposure" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:EnvironmentalTobaccoSmokeExposure" }, { - 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} - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BulkWESLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk WES Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:filename" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:fileFormat" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:MethodofDiagnosis" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:PriorMalignancy" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:PriorTreatment" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:MetastasisatDiagnosis" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:MetastasisatDiagnosisSite" }, { - 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"@id": "bts:GenomicReference" + "@id": "bts:GeneSymbol" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:GermlineVariantsWorkflowURL" + "@id": "bts:TestResult" }, { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:AAChange" }, { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:Antigen" }, { - "@id": "bts:SomaticVariantsWorkflowURL" + "@id": "bts:ClinicalBiospecimenType" }, { - "@id": "bts:SomaticVariantsWorkflowType" + "@id": "bts:BloodTestNormalRangeUpper" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:BloodTestNormalRangeLower" }, { - "@id": "bts:StructuralVariantWorkflowURL" + "@id": "bts:CellCount" }, { - "@id": "bts:StructuralVariantWorkflowType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ScATAC-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", - "rdfs:label": "ScATAC-seqLevel1", - 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"@id": "bts:NucleiBarcodeLength" + "@id": "bts:Locus" }, { - "@id": "bts:NucleiBarcodeRead" + "@id": "bts:MismatchRepairMutation" }, { - "@id": "bts:ScATAC-seqRead1" + "@id": "bts:MolecularConsequence" }, { - "@id": "bts:ScATAC-seqRead2" + "@id": "bts:Pathogenicity" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Ploidy" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:SecondExon" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:SecondGeneSymbol" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:SpecializedMolecularTest" }, { - "@id": "bts:MedianFractionofReadsinPeaks-FRIP" + "@id": "bts:TestAnalyteType" }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcis-DNAElements-FRIADE" + "@id": "bts:TestUnits" }, { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:TestValue" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:Transcript" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:VariantOrigin" }, { - "@id": "bts:TotalReads" + "@id": "bts:VariantType" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Zygosity" } ], "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel2", + "@id": "bts:Biospecimen", "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", + "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", + "rdfs:label": "Biospecimen", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 2", + "sms:displayName": "Biospecimen", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" - }, - { - "@id": "bts:ImagingLevel1and2Channels" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -4645,1299 +4500,1467 @@ "@id": "bts:Component" }, { - "@id": "bts:filename" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:fileFormat" + "@id": "bts:HTANParentID" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:ChannelMetadataFilename" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:FixativeType" }, { - "@id": "bts:WorkflowStartDate-time" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:WorkflowEndDate-time" + "@id": "bts:StorageMethod" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:ImageAcquisitionDate" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Microscope" + "@id": "bts:SiteDataSource" }, { - "@id": "bts:Objective" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:MountingMedium" }, { - "@id": "bts:LensNA" + "@id": "bts:ProcessingLocation" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:HistologyAssessmentBy" }, { - 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(eg \"Channel:0:1\")", - "rdfs:label": "ChannelID", + "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", + "rdfs:label": "ScRNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ChannelName", - "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg “Blue” or “CD45” or “E-cadherin”)", - "rdfs:label": "ChannelName", - "rdfs:subClassOf": [ + "sms:displayName": "scRNA-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:ScRNA-seqLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Channel Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ChannelPassedQC", - "@type": "rdfs:Class", - "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", - "rdfs:label": "ChannelPassedQC", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Yes" + "@id": "bts:filename" }, { - "@id": "bts:No" + "@id": "bts:fileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:GenomicReferenceURL" + }, + { + "@id": "bts:GenomeAnnotationURL" + }, + { + "@id": "bts:Checksum" + }, + { + "@id": "bts:WhitelistCellBarcodeFileLink" + }, + { + "@id": "bts:CellBarcodeTag" + }, + { + "@id": "bts:UMITag" + }, + { + "@id": "bts:AppliedHardTrimming" } ], - "sms:displayName": "Channel Passed QC", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CycleNumber", + "@id": "bts:ScRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", - "rdfs:label": "CycleNumber", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cycle Number", + "sms:displayName": "scRNA-seq Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Sub-CycleNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Sub-cycle number", - "rdfs:label": "Sub-CycleNumber", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:ScRNA-seqLevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sub-Cycle Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetName", - "@type": "rdfs:Class", - "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", - "rdfs:label": "TargetName", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:Component" + }, + { + "@id": "bts:filename" + }, + { + "@id": "bts:fileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:LinkedMatrices" + }, + { + "@id": "bts:CellMedianNumberReads" + }, + { + "@id": "bts:CellMedianNumberGenes" + }, + { + "@id": "bts:CellTotal" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowStartDatetime" + }, + { + "@id": "bts:WorkflowEndDatetime" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Name", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AntibodyName", + "@id": "bts:ScRNA-seqLevel4", "@type": "rdfs:Class", - 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}, - "sms:displayName": "RRID identifier", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Fluorophore", - "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", - "rdfs:label": "Fluorophore", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2Channels" + "@id": "bts:Component" + }, + { + "@id": "bts:filename" + }, + { + "@id": "bts:fileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowStartDatetime" + }, + { + "@id": "bts:WorkflowEndDatetime" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fluorophore", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clone", + "@id": "bts:BulkRNA-seqLevel1", "@type": "rdfs:Class", - 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"@id": "bts:Objective", + "@id": "bts:BulkWESLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", + "rdfs:comment": "Bulk Whole Exome Sequencing raw files", + "rdfs:label": "BulkWESLevel1", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Objective", + "sms:displayName": "Bulk WES Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NominalMagnification", - "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - 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Floating point value > 0.", - "rdfs:label": "LensNA", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "LensNA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistance", - "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WorkingDistance", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:filename" + }, { - "@id": "bts:WorkingDistanceUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistanceUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", - "rdfs:subClassOf": [ + "@id": "bts:fileFormat" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HTANParentBiospecimenID" + }, { - "@id": "bts:Cm" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Mm" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:Μm" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:Nm" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Immersion", - "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", - "rdfs:subClassOf": [ + "@id": "bts:LibrarySelectionMethod" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ReadLength" + }, { - "@id": "bts:Air" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:Oil" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pyramid", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", - "rdfs:subClassOf": [ + "@id": "bts:LibraryPreparationKitVendor" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LibraryPreparationKitVersion" + }, { - "@id": "bts:Yes" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Z-stack", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Z-stack", - "rdfs:subClassOf": [ + "@id": "bts:AdapterName" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AdapterSequence" + }, { - "@id": "bts:Yes" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Z-stack", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:T-series", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "T-series", - "rdfs:subClassOf": [ + "@id": "bts:BaseCallerVersion" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:FlowCellBarcode" + }, { - "@id": "bts:Yes" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "T-series", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PassedQC", - "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", - "rdfs:subClassOf": [ + "@id": "bts:FragmentMeanLength" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:FragmentMinimumLength" + }, { - "@id": "bts:Yes" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:No-ChannelsQC", - "@type": "rdfs:Class", - "rdfs:comment": "Not all channels passed QC", - "rdfs:label": "No-ChannelsQC", - "rdfs:subClassOf": [ + "@id": "bts:LaneNumber" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No - Channels QC", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:MultiplexBarcode" + }, { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ + "@id": "bts:LibraryPreparationDaysfromIndex" + }, { - "@id": "bts:ImagingLevel2" + "@id": "bts:SizeSelectionRange" + }, + { + "@id": "bts:TargetDepth" + }, + { + "@id": "bts:ToTrimAdapterSequence" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Comment", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVnumber", + "@id": "bts:BulkWESLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", + "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", + "rdfs:label": "BulkWESLevel2", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOV number", + "sms:displayName": "Bulk WES Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVX", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:BulkWESLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVX", - "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:FOVXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", - "rdfs:subClassOf": [ + "@id": "bts:Component" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:filename" + }, { - "@id": "bts:Cm" + "@id": "bts:fileFormat" }, { - "@id": "bts:Mm" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Μm" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Nm" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:Å" + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:GenomicReferenceURL" + }, + { + "@id": "bts:IndexFileName" + }, + { + "@id": "bts:AverageBaseQuality" + }, + { + "@id": "bts:AverageInsertSize" + }, + { + "@id": "bts:AverageReadLength" + }, + { + "@id": "bts:Contamination" + }, + { + "@id": "bts:ContaminationError" + }, + { + "@id": "bts:MeanCoverage" + }, + { + "@id": "bts:AdapterContent" + }, + { + "@id": "bts:BasicStatistics" + }, + { + "@id": "bts:Encoding" + }, + { + "@id": "bts:OverrepresentedSequences" + }, + { + "@id": "bts:PerBaseNContent" + }, + { + "@id": "bts:PerBaseSequenceContent" + }, + { + "@id": "bts:PerBaseSequenceQuality" + }, + { + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" + }, + { + "@id": "bts:MSIWorkflowLink" + }, + { + "@id": "bts:MSIScore" + }, + { + "@id": "bts:MSIStatus" + }, + { + "@id": "bts:PairsOnDiffCHR" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:TotalUniquelyMapped" + }, + { + "@id": "bts:TotalUnmappedreads" + }, + { + "@id": "bts:ProportionReadsDuplicated" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:ShortReads" + }, + { + "@id": "bts:ProportionCoverage10x" + }, + { + "@id": "bts:ProportionCoverage30X" } ], - "sms:displayName": "FOVXUnit", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVY", + "@id": "bts:BulkWESLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", + "rdfs:comment": "Bulk Whole Exome Sequencing called variants", + "rdfs:label": "BulkWESLevel3", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVY", + "sms:displayName": "Bulk WES Level 3", "sms:required": "sms:false", - "sms:requiresDependency": [ + "sms:requiresComponent": [ { - "@id": "bts:FOVYUnit" + "@id": "bts:BulkWESLevel2" } ], - "sms:validationRules": [] - }, - { - "@id": "bts:FOVYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Cm" + "@id": "bts:filename" }, { - "@id": "bts:Mm" + "@id": "bts:fileFormat" }, { - "@id": "bts:Μm" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Nm" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Å" + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:GenomicReferenceURL" + }, + { + "@id": "bts:GermlineVariantsWorkflowURL" + }, + { + "@id": "bts:GermlineVariantsWorkflowType" + }, + { + "@id": "bts:GermlineVariantsWorkflowType" + }, + { + "@id": "bts:SomaticVariantsWorkflowURL" + }, + { + "@id": "bts:SomaticVariantsWorkflowType" + }, + { + "@id": "bts:SomaticVariantsSampleType" + }, + { + "@id": "bts:StructuralVariantWorkflowURL" + }, + { + "@id": "bts:StructuralVariantWorkflowType" } ], - "sms:displayName": "FOVYUnit", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FrameAveraging", + "@id": "bts:ScATAC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", + "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", + "rdfs:label": "ScATAC-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Frame Averaging", + "sms:displayName": "scATAC-seq Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImageID", - "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DimensionOrder", - "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:XYZCT" + "@id": "bts:filename" }, { - "@id": "bts:XYZTC" + "@id": "bts:fileFormat" }, { - "@id": "bts:XYCTZ" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:XYCZT" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:XYTZC" + "@id": "bts:NucleicAcidSource" + }, + { + "@id": "bts:DissociationMethod" + }, + { + "@id": "bts:SingleNucleusBuffer" + }, + { + "@id": "bts:SingleCellIsolationMethod" + }, + { + "@id": "bts:TranspositionReaction" + }, + { + "@id": "bts:ScATACseqLibraryLayout" + }, + { + "@id": "bts:NucleusIdentifier" + }, + { + "@id": "bts:NucleiBarcodeLength" + }, + { + "@id": "bts:NucleiBarcodeRead" + }, + { + "@id": "bts:ScATACseqRead1" + }, + { + "@id": "bts:ScATACseqRead2" + }, + { + "@id": "bts:ScATACseqRead3" + }, + { + "@id": "bts:LibraryConstructionMethod" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:MedianFractionofReadsinPeaks" + }, + { + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" + }, + { + "@id": "bts:MedianPassingReadPercentage" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeX", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "sms:displayName": "Imaging Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:PhysicalSizeXUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", - "rdfs:subClassOf": [ + "@id": "bts:Biospecimen" + }, { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Cm" + "@id": "bts:Component" }, { - "@id": "bts:Mm" + "@id": "bts:filename" }, { - "@id": "bts:Μm" + "@id": "bts:fileFormat" }, { - "@id": "bts:Nm" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeY", - "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentBiospecimenID" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ChannelMetadataFilename" + }, + { + "@id": "bts:ImagingAssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:WorkflowStartDatetime" + }, + { + "@id": "bts:WorkflowEndDatetime" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:Microscope" + }, + { + "@id": "bts:Objective" + }, + { + "@id": "bts:NominalMagnification" + }, + { + "@id": "bts:LensNA" + }, + { + "@id": "bts:WorkingDistance" + }, + { + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:Immersion" + }, + { + "@id": "bts:Pyramid" + }, + { + "@id": "bts:Zstack" + }, + { + "@id": "bts:Tseries" + }, + { + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:FrameAveraging" + }, + { + "@id": "bts:ImageID" + }, + { + "@id": "bts:DimensionOrder" + }, + { + "@id": "bts:PhysicalSizeX" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeY" + }, { "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZ" + }, + { + "@id": "bts:PhysicalSizeZUnit" + }, + { + "@id": "bts:PixelsBigEndian" + }, + { + "@id": "bts:PlaneCount" + }, + { + "@id": "bts:SizeC" + }, + { + "@id": "bts:SizeT" + }, + { + "@id": "bts:SizeX" + }, + { + "@id": "bts:SizeY" + }, + { + "@id": "bts:SizeZ" + }, + { + "@id": "bts:PixelType" } ], "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:ImagingLevel2Channels", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel2Channels", "rdfs:subClassOf": [ { "@id": "bts:ImagingLevel2" @@ -5946,89 +5969,123 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging Level 2 Channels", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Cm" + "@id": "bts:ChannelID" }, { - "@id": "bts:Mm" + "@id": "bts:ChannelName" }, { - "@id": "bts:Μm" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:Nm" + "@id": "bts:CycleNumber" }, { - "@id": "bts:Å" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:Cm" + "@id": "bts:TargetName" }, { - "@id": "bts:Mm" + "@id": "bts:AntibodyName" }, { - "@id": "bts:Μm" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:Nm" + "@id": "bts:Fluorophore" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:Clone" + }, { - "@id": "bts:PhysicalSizeZUnit" + "@id": "bts:Lot" + }, + { + "@id": "bts:Vendor" + }, + { + "@id": "bts:CatalogNumber" + }, + { + "@id": "bts:ExcitationWavelength" + }, + { + "@id": "bts:EmissionWavelength" + }, + { + "@id": "bts:ExcitationBandwidth" + }, + { + "@id": "bts:EmissionBandwidth" + }, + { + "@id": "bts:MetalIsotopeElement" + }, + { + "@id": "bts:MetalIsotopeMass" + }, + { + "@id": "bts:OligoBarcodeUpperStrand" + }, + { + "@id": "bts:OligoBarcodeLowerStrand" + }, + { + "@id": "bts:Dilution" + }, + { + "@id": "bts:Concentration" } ], "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:ChannelID", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg \"Channel:0:1\")", + "rdfs:label": "ChannelID", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeYUnit", + "sms:displayName": "Channel ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:ChannelName", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg “Blue” or “CD45” or “E-cadherin”)", + "rdfs:label": "ChannelName", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeYUnit", + "sms:displayName": "Channel Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PixelsBigEndian", + "@id": "bts:ChannelPassedQC", "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", + "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", + "rdfs:label": "ChannelPassedQC", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { @@ -6036,443 +6093,364 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:True" + "@id": "bts:Yes" }, { - "@id": "bts:False" + "@id": "bts:No" } ], - "sms:displayName": "Pixels BigEndian", + "sms:displayName": "Channel Passed QC", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PlaneCount", + "@id": "bts:CycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", + "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", + "rdfs:label": "CycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PlaneCount", - "sms:required": "sms:true", + "sms:displayName": "Cycle Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeC", + "@id": "bts:SubCycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", + "rdfs:comment": "Sub cycle number", + "rdfs:label": "SubCycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", + "sms:displayName": "Sub Cycle Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeT", + "@id": "bts:TargetName", "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", + "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", + "rdfs:label": "TargetName", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeT", - "sms:required": "sms:true", + "sms:displayName": "Target Name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeX", + "@id": "bts:AntibodyName", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", + "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", + "rdfs:label": "AntibodyName", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", + "sms:displayName": "Antibody Name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeY", + "@id": "bts:RRIDidentifier", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", + "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", + "rdfs:label": "RRIDidentifier", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeY", - "sms:required": "sms:true", + "sms:displayName": "RRID identifier", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeZ", + "@id": "bts:Fluorophore", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", + "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", + "rdfs:label": "Fluorophore", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeZ", - "sms:required": "sms:true", + "sms:displayName": "Fluorophore", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PixelType", + "@id": "bts:Clone", "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", + "rdfs:comment": "Clone", + "rdfs:label": "Clone", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Int8" - }, - { - "@id": "bts:Int16" - }, - { - "@id": "bts:Int32" - }, - { - "@id": "bts:Uint8" - }, - { - "@id": "bts:Uint16" - }, - { - "@id": "bts:Uint32" - }, - { - "@id": "bts:Float" - }, - { - "@id": "bts:Double" - }, + "sms:displayName": "Clone", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Lot", + "@type": "rdfs:Class", + "rdfs:comment": "Lot number from vendor", + "rdfs:label": "Lot", + "rdfs:subClassOf": [ { - "@id": "bts:Bit" + "@id": "bts:ImagingLevel2Channels" } ], - "sms:displayName": "PixelType", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lot", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidSource", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - "rdfs:label": "NucleicAcidSource", + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:SingleCell" - }, - { - "@id": "bts:BulkWholeCell" - }, - { - "@id": "bts:SingleNucleus" - }, - { - "@id": "bts:BulkNuclei" - } - ], - "sms:displayName": "Nucleic Acid Source", - "sms:required": "sms:true", + "sms:displayName": "Vendor", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleCellIsolationMethod", + "@id": "bts:CatalogNumber", "@type": "rdfs:Class", - "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "rdfs:label": "SingleCellIsolationMethod", + "rdfs:comment": "Catalog Number", + "rdfs:label": "CatalogNumber", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MicrofluidicsChip" - }, - { - "@id": "bts:Droplets" - }, - { - "@id": "bts:FACS" - }, - { - "@id": "bts:Plates" - }, - { - "@id": "bts:10x" - } - ], - "sms:displayName": "Single Cell Isolation Method", - "sms:required": "sms:true", + "sms:displayName": "Catalog Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DissociationMethod", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", - "rdfs:label": "DissociationMethod", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GentleMACS" - }, - { - "@id": "bts:Dounce" - }, - { - "@id": "bts:EnzymaticDigestion" - } - ], - "sms:displayName": "Dissociation Method", - "sms:required": "sms:true", + "sms:displayName": "Excitation Wavelength", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryLayout", + "@id": "bts:EmissionWavelength", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "LibraryLayout", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:PairedEnd" - }, - { - "@id": "bts:SingleRead" - } - ], - "sms:displayName": "Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Emission Wavelength", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleusIdentifier", + "@id": "bts:ExcitationBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "rdfs:label": "NucleusIdentifier", + "rdfs:comment": "Nominal width of excitation spectrum (nm)", + "rdfs:label": "ExcitationBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NucleiBarcode" - } - ], - "sms:displayName": "Nucleus Identifier", - "sms:required": "sms:true", + "sms:displayName": "Excitation Bandwidth", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleiBarcode", + "@id": "bts:EmissionBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode", - "rdfs:label": "NucleiBarcode", + "rdfs:comment": "Nominal width of emission spectrum (nm)", + "rdfs:label": "EmissionBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NucleiBarcodeRead" - }, - { - "@id": "bts:NucleiBarcodeLength" - } - ], - "sms:displayName": "Nuclei Barcode", + "sms:displayName": "Emission Bandwidth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLibraryLayout", + "@id": "bts:MetalIsotopeElement", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "ScATAC-seqLibraryLayout", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:ScATAC-seqPairedEnd" - } - ], - "sms:displayName": "scATAC-seq Library Layout", - "sms:required": "sms:true", + "sms:displayName": "Metal Isotope Element", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleiBarcodeRead", + "@id": "bts:MetalIsotopeMass", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Read", - "rdfs:label": "NucleiBarcodeRead", + "rdfs:comment": "Element mass number", + "rdfs:label": "MetalIsotopeMass", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Barcode Read", - "sms:required": "sms:true", + "sms:displayName": "Metal Isotope Mass", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NucleiBarcodeLength", + "@id": "bts:OligoBarcodeUpperStrand", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Length", - "rdfs:label": "NucleiBarcodeLength", + "rdfs:comment": "Oligo Barcode - Upper Strand", + "rdfs:label": "OligoBarcodeUpperStrand", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Barcode Length", - "sms:required": "sms:true", + "sms:displayName": "Oligo Barcode Upper Strand", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqPairedEnd", + "@id": "bts:OligoBarcodeLowerStrand", "@type": "rdfs:Class", - "rdfs:comment": "A library layout type", - "rdfs:label": "ScATAC-seqPairedEnd", + "rdfs:comment": "Oligo Barcode - Lower Strand", + "rdfs:label": "OligoBarcodeLowerStrand", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:ScATAC-seqRead1" - }, - { - "@id": "bts:ScATAC-seqRead2" - } - ], - "sms:displayName": "scATAC-seq Paired End", + "sms:displayName": "Oligo Barcode Lower Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqRead1", + "@id": "bts:Dilution", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScATAC-seqRead1", + "rdfs:comment": "Dilution (eg 1:1000)", + "rdfs:label": "Dilution", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandDNAInsert" - }, + "sms:displayName": "Dilution", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Concentration", + "@type": "rdfs:Class", + "rdfs:comment": "Concentration (eg 10ug/mL)", + "rdfs:label": "Concentration", + "rdfs:subClassOf": [ { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:ImagingLevel2Channels" } ], - "sms:displayName": "scATAC-seq Read1", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Concentration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqRead2", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScATAC-seqRead2", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -6480,153 +6458,178 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:H&E" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:CyCIF" + }, + { + "@id": "bts:T-CyCIF" + }, + { + "@id": "bts:IHC" + }, + { + "@id": "bts:MIHC" + }, + { + "@id": "bts:MxIF" + }, + { + "@id": "bts:SABER" + }, + { + "@id": "bts:IMC" + }, + { + "@id": "bts:CODEX" + }, + { + "@id": "bts:GeoMX-DSP" + }, + { + "@id": "bts:MIBI" + }, + { + "@id": "bts:MERFISH" } ], - "sms:displayName": "scATAC-seq Read2", + "sms:displayName": "Imaging Assay Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ThresholdforMinimumPassingReads", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "Threshold for calling cells", - "rdfs:label": "ThresholdforMinimumPassingReads", + "rdfs:comment": "Full path of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Threshold for Minimum Passing Reads", + "sms:displayName": "Channel Metadata Filename", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofPassingNuclei", + "@id": "bts:ImageAcquisitionDate", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei sequenced", - "rdfs:label": "TotalNumberofPassingNuclei", + "rdfs:comment": "Date of image acquisition", + "rdfs:label": "ImageAcquisitionDate", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Passing Nuclei", - "sms:required": "sms:true", + "sms:displayName": "Image Acquisition Date", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinPeaks-FRIP", + "@id": "bts:Microscope", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in peaks (FRIP)", - "rdfs:label": "MedianFractionofReadsinPeaks-FRIP", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Peaks - FRIP", + "sms:displayName": "Microscope", "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PeaksCallingSoftware" - } - ], "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcis-DNAElements-FRIADE", + "@id": "bts:Objective", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", - "rdfs:label": "MedianFractionofReadsinAnnotatedcis-DNAElements-FRIADE", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Annotated cis-DNA Elements - FRIADE", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PeaksCallingSoftware" - } - ], + "sms:displayName": "Objective", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPassingReadPercentage", + "@id": "bts:NominalMagnification", "@type": "rdfs:Class", - "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label": "MedianPassingReadPercentage", + "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label": "NominalMagnification", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Passing Read Percentage", + "sms:displayName": "NominalMagnification", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@id": "bts:LensNA", "@type": "rdfs:Class", - "rdfs:comment": "Contamination from mitochondrial sequences", - "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", - "sms:required": "sms:true", + "sms:displayName": "LensNA", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PeaksCallingSoftware", + "@id": "bts:WorkingDistance", "@type": "rdfs:Class", - "rdfs:comment": "Generic name of peaks calling tool", - "rdfs:label": "PeaksCallingSoftware", + "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label": "WorkingDistance", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Peaks Calling Software", - "sms:required": "sms:true", + "sms:displayName": "WorkingDistance", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:WorkingDistanceUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Read1", + "@id": "bts:WorkingDistanceUnit", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "Read1", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -6634,24 +6637,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:Cm" }, { - "@id": "bts:CDNA" + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "sms:displayName": "Read1", + "sms:displayName": "WorkingDistanceUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Read2", + "@id": "bts:Immersion", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "Read2", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -6659,273 +6671,329 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandUMI" + "@id": "bts:Air" }, { - "@id": "bts:CDNA" + "@id": "bts:Oil" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Read2", - "sms:required": "sms:true", + "sms:displayName": "Immersion", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CDNA", + "@id": "bts:Pyramid", "@type": "rdfs:Class", - "rdfs:comment": "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", - "rdfs:label": "CDNA", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cDNA", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:CDNAOffset" + "@id": "bts:Yes" }, { - "@id": "bts:CDNALength" + "@id": "bts:No" } ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CDNAOffset", + "@id": "bts:Zstack", "@type": "rdfs:Class", - "rdfs:comment": "Offset in sequence for cDNA read (in bp): number", - "rdfs:label": "CDNAOffset", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cDNA Offset", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CDNALength", - "@type": "rdfs:Class", - "rdfs:comment": "Length of cDNA read (in bp): number", - "rdfs:label": "CDNALength", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "cDNA Length", + "sms:displayName": "Zstack", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeandUMI", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "Cell and transcript identifiers", - "rdfs:label": "CellBarcodeandUMI", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode and UMI", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:UMIBarcodeOffset" - }, - { - "@id": "bts:UMIBarcodeLength" - }, - { - "@id": "bts:MedianUMIsperCellNumber" - }, - { - "@id": "bts:CellBarcodeOffset" - }, + "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeLength" + "@id": "bts:Yes" }, { - "@id": "bts:ValidBarcodesCellNumber" + "@id": "bts:No" } ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeOffset", + "@id": "bts:PassedQC", "@type": "rdfs:Class", - "rdfs:comment": "Offset in sequence for cell barcode read (in bp): number", - "rdfs:label": "CellBarcodeOffset", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Offset", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeLength", + "@id": "bts:No-ChannelsQC", "@type": "rdfs:Class", - "rdfs:comment": "Length of cell barcode read (in bp): number", - "rdfs:label": "CellBarcodeLength", + "rdfs:comment": "Not all channels passed QC", + "rdfs:label": "No-ChannelsQC", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Length", - "sms:required": "sms:true", + "sms:displayName": "No - Channels QC", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Comment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:ValidBarcodesCellNumber", + "@id": "bts:Comment", "@type": "rdfs:Class", - "rdfs:comment": "Number", - "rdfs:label": "ValidBarcodesCellNumber", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Valid Barcodes Cell Number", - "sms:required": "sms:true", + "sms:displayName": "Comment", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMIBarcodeOffset", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label": "UMIBarcodeOffset", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Offset", - "sms:required": "sms:true", + "sms:displayName": "FOV number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMIBarcodeLength", + "@id": "bts:FOVX", "@type": "rdfs:Class", - "rdfs:comment": "Length of UMI barcode read (in bp): number", - "rdfs:label": "UMIBarcodeLength", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Length", - "sms:required": "sms:true", + "sms:displayName": "FOVX", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:FOVXUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:MedianUMIsperCellNumber", + "@id": "bts:FOVXUnit", "@type": "rdfs:Class", - "rdfs:comment": "Number", - "rdfs:label": "MedianUMIsperCellNumber", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median UMIs per Cell Number", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVXUnit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberReads", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "Median number of reads per cell. Number", - "rdfs:label": "CellMedianNumberReads", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Reads", - "sms:required": "sms:true", + "sms:displayName": "FOVY", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:FOVYUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberGenes", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "Median number of genes detected per cell. Number", - "rdfs:label": "CellMedianNumberGenes", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Genes", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" + } + ], + "sms:displayName": "FOVYUnit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellTotal", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label": "CellTotal", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Total", + "sms:displayName": "Frame Averaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImageID", + "@type": "rdfs:Class", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Image ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryConstructionMethod", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "LibraryConstructionMethod", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -6933,57 +7001,111 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" + "@id": "bts:XYZCT" }, { - "@id": "bts:Smart-SeqV4" + "@id": "bts:XYZTC" }, { - "@id": "bts:10xV1.0" + "@id": "bts:XYCTZ" }, { - "@id": "bts:10xV1.1" + "@id": "bts:XYCZT" }, { - "@id": "bts:10xV2" - }, + "@id": "bts:XYTZC" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", + "rdfs:subClassOf": [ { - "@id": "bts:10xV3" - }, + "@id": "bts:ImagingLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:10xV3.1" - }, + "@id": "bts:PhysicalSizeXUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeXUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", + "rdfs:subClassOf": [ { - "@id": "bts:CEL-seq2" - }, + "@id": "bts:ImagingLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Drop-seq" + "@id": "bts:Cm" }, { - "@id": "bts:InDropsV2" + "@id": "bts:Mm" }, { - "@id": "bts:InDropsV3" + "@id": "bts:Μm" }, { - "@id": "bts:TruDrop" + "@id": "bts:Nm" }, { - "@id": "bts:Sci-ATAC-seq" + "@id": "bts:Å" } ], - "sms:displayName": "Library Construction Method", + "sms:displayName": "PhysicalSizeXUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibrarySelectionMethod", + "@id": "bts:PhysicalSizeY", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeYUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", + "rdfs:subClassOf": [ + { + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -6991,206 +7113,214 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HybridSelection" + "@id": "bts:Cm" }, { - "@id": "bts:PCR" + "@id": "bts:Mm" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:Μm" }, { - "@id": "bts:Other" + "@id": "bts:Nm" }, { - "@id": "bts:HybridSelection" + "@id": "bts:Å" }, { - "@id": "bts:PCR" + "@id": "bts:Cm" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:Mm" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:Μm" }, { - "@id": "bts:Random" + "@id": "bts:Nm" }, { - "@id": "bts:RRNADepletion" - }, + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:MiRNASizeFractionation" - }, + "@id": "bts:PhysicalSizeZUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeYUnit", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:ImagingLevel2" } ], - "sms:displayName": "Library Selection Method", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeYUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InputCellsandNuclei", + "@id": "bts:PhysicalSizeYUnit", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label": "InputCellsandNuclei", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Input Cells and Nuclei", + "sms:displayName": "PhysicalSizeYUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CEL-seq2", + "@id": "bts:PixelsBigEndian", "@type": "rdfs:Class", - "rdfs:comment": "Highly-multiplexed plate-based single-cell RNA-Seq assay", - "rdfs:label": "CEL-seq2", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CEL-seq2", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:EmptyWellBarcode" + "@id": "bts:True" }, { - "@id": "bts:WellIndex" + "@id": "bts:False" } ], + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:EmptyWellBarcode", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.", - "rdfs:label": "EmptyWellBarcode", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Empty Well Barcode", + "sms:displayName": "PlaneCount", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WellIndex", + "@id": "bts:SizeC", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays", - "rdfs:label": "WellIndex", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Well Index", - "sms:required": "sms:false", + "sms:displayName": "SizeC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationDate", + "@id": "bts:SizeT", "@type": "rdfs:Class", - "rdfs:comment": "The date that the libraries were prepared for sequencing (in number of days since sample received in lab). A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm] or \"null\"", - "rdfs:label": "LibraryPreparationDate", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Date", - "sms:required": "sms:false", + "sms:displayName": "SizeT", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SingleCellDissociationDate", + "@id": "bts:SizeX", "@type": "rdfs:Class", - "rdfs:comment": "The date when the sample was dissociated and cells were isolated (date format)", - "rdfs:label": "SingleCellDissociationDate", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell Dissociation Date", + "sms:displayName": "SizeX", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequencingLibraryConstructionDate", + "@id": "bts:SizeY", "@type": "rdfs:Class", - "rdfs:comment": "Date of sequencing library construction part of library construction (in number of days since sample received in lab)", - "rdfs:label": "SequencingLibraryConstructionDate", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Library Construction Date", + "sms:displayName": "SizeY", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidCaptureDate", + "@id": "bts:SizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Date of nucleic acid capture part of library construction (in number of days since sample received in lab)", - "rdfs:label": "NucleicAcidCaptureDate", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleic Acid Capture Date", + "sms:displayName": "SizeZ", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CryopreservedCellsinSample", + "@id": "bts:PixelType", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { @@ -7198,24 +7328,45 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Int8" }, { - "@id": "bts:No" + "@id": "bts:Int16" + }, + { + "@id": "bts:Int32" + }, + { + "@id": "bts:Uint8" + }, + { + "@id": "bts:Uint16" + }, + { + "@id": "bts:Uint32" + }, + { + "@id": "bts:Float" + }, + { + "@id": "bts:Double" + }, + { + "@id": "bts:Bit" } ], - "sms:displayName": "Cryopreserved Cells in Sample", + "sms:displayName": "PixelType", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:EndBias", + "@id": "bts:NucleicAcidSource", "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", + "rdfs:comment": "The source of the input nucleic molecule", + "rdfs:label": "NucleicAcidSource", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -7223,24 +7374,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:3Prime" + "@id": "bts:SingleCell" }, { - "@id": "bts:5Prime" + "@id": "bts:BulkWholeCell" }, { - "@id": "bts:FullLengthTranscript" + "@id": "bts:SingleNucleus" + }, + { + "@id": "bts:BulkNuclei" } ], - "sms:displayName": "End Bias", + "sms:displayName": "Nucleic Acid Source", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ReverseTranscriptionPrimer", + "@id": "bts:SingleCellIsolationMethod", "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", + "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "rdfs:label": "SingleCellIsolationMethod", "rdfs:subClassOf": [ { "@id": "bts:ScRNA-seqLevel1" @@ -7251,27 +7405,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Oligo-dT" + "@id": "bts:MicrofluidicsChip" }, { - "@id": "bts:Poly-dT" + "@id": "bts:Droplets" }, { - "@id": "bts:Featurebarcoding" + "@id": "bts:FACS" }, { - "@id": "bts:Random" + "@id": "bts:Plates" + }, + { + "@id": "bts:10x" + }, + { + "@id": "bts:NucleiIsolation" } ], - "sms:displayName": "Reverse Transcription Primer", + "sms:displayName": "Single Cell Isolation Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Featurebarcoding", + "@id": "bts:DissociationMethod", "@type": "rdfs:Class", - "rdfs:comment": "A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc]", - "rdfs:label": "Featurebarcoding", + "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "rdfs:label": "DissociationMethod", "rdfs:subClassOf": [ { "@id": "bts:ScRNA-seqLevel1" @@ -7280,40 +7440,57 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Feature barcoding", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:FeatureReferenceId" + "@id": "bts:GentleMACS" + }, + { + "@id": "bts:Dounce" + }, + { + "@id": "bts:EnzymaticDigestion" + }, + { + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Dissociation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FeatureReferenceId", + "@id": "bts:LibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", - "rdfs:label": "FeatureReferenceId", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "LibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Feature Reference Id", + "schema:rangeIncludes": [ + { + "@id": "bts:PairedEnd" + }, + { + "@id": "bts:SingleRead" + } + ], + "sms:displayName": "Library Layout", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpikeIn", + "@id": "bts:NucleusIdentifier", "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", + "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "rdfs:label": "NucleusIdentifier", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -7321,220 +7498,124 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ERCC" - }, - { - "@id": "bts:OtherSpikeIn" - }, - { - "@id": "bts:NoSpikeIn" - }, - { - "@id": "bts:PhiX" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Spike In", + "sms:displayName": "Nucleus Identifier", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ERCC", + "@id": "bts:NucleiBarcode", "@type": "rdfs:Class", - "rdfs:comment": "The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization", - "rdfs:label": "ERCC", + "rdfs:comment": "Nuclei Barcode", + "rdfs:label": "NucleiBarcode", "rdfs:subClassOf": [ { - "@id": "bts:SpikeIn" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ERCC", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:SpikeInConcentration" - }, - { - "@id": "bts:SpikeInMix1" - }, + "schema:rangeIncludes": [ { - "@id": "bts:SpikeInMix2" + "@id": "bts:NucleiBarcodeRead" }, { - "@id": "bts:BothSpikeinMixes" + "@id": "bts:NucleiBarcodeLength" } ], + "sms:displayName": "Nuclei Barcode", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpikeInConcentration", + "@id": "bts:ScATACseqLibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", - "rdfs:label": "SpikeInConcentration", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "ScATACseqLibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:ERCC" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spike In Concentration", + "schema:rangeIncludes": [ + { + "@id": "bts:ScATACseqPairedEnd" + } + ], + "sms:displayName": "scATACseq Library Layout", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequencingPlatform", + "@id": "bts:NucleiBarcodeRead", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "SequencingPlatform", + "rdfs:comment": "Nuclei Barcode Read", + "rdfs:label": "NucleiBarcodeRead", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:IlluminaNextSeq500" - }, - { - "@id": "bts:IlluminaNextSeq550" - }, - { - "@id": "bts:IlluminaNextSeq2500" - }, - { - "@id": "bts:IlluminaNovaSeq6000" - }, - { - "@id": "bts:IlluminaMiSeq" - }, - { - "@id": "bts:454GSFLXTitanium" - }, - { - "@id": "bts:ABSOLiD4ABSOLiD2" - }, - { - "@id": "bts:ABSOLiD3" - }, - { - "@id": "bts:CompleteGenomics" - }, - { - "@id": "bts:IlluminaHiSeqXTen" - }, - { - "@id": "bts:IlluminaHiSeqXFive" - }, - { - "@id": "bts:IlluminaGenomeAnalyzerII" - }, - { - "@id": "bts:IlluminaGenomeAnalyzerIIx" - }, - { - "@id": "bts:IlluminaHiSeq2000" - }, - { - "@id": "bts:IlluminaHiSeq2500" - }, - { - "@id": "bts:IlluminaHiSeq4000" - }, - { - "@id": "bts:IlluminaMiSeq" - }, - { - "@id": "bts:IlluminaNextSeq" - }, - { - "@id": "bts:IonTorrentPGM" - }, - { - "@id": "bts:IonTorrentProton" - }, - { - "@id": "bts:IonTorrentS5" - }, - { - "@id": "bts:PacBioRS" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequencing Platform", + "sms:displayName": "Nuclei Barcode Read", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TechnicalReplicateGroup", + "@id": "bts:NucleiBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", - "rdfs:label": "TechnicalReplicateGroup", + "rdfs:comment": "Nuclei Barcode Length", + "rdfs:label": "NucleiBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Technical Replicate Group", - "sms:required": "sms:false", + "sms:displayName": "Nuclei Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofInputCells", + "@id": "bts:ScATACseqPairedEnd", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", + "rdfs:comment": "A library layout type", + "rdfs:label": "ScATACseqPairedEnd", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SequencingBatchID", - "@type": "rdfs:Class", - "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", - "rdfs:label": "SequencingBatchID", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATACseqRead1" + }, + { + "@id": "bts:ScATACseqRead2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Batch ID", - "sms:required": "sms:true", + "sms:displayName": "scATACseq Paired End", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusBuffer", + "@id": "bts:ScATACseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScATACseqRead1", "rdfs:subClassOf": [ { "@id": "bts:ScATAC-seqLevel1" @@ -7545,24 +7626,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NIB" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:10x" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Omni" + "@id": "bts:DNAInsert" + }, + { + "@id": "bts:SampleIndex" + }, + { + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Single Nucleus Buffer", + "sms:displayName": "scATACseq Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranspositionReaction", + "@id": "bts:ScATACseqRead2", "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScATACseqRead2", "rdfs:subClassOf": [ { "@id": "bts:ScATAC-seqLevel1" @@ -7573,50 +7660,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Tn5" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:EZ-Tn5" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Tn5-059" + "@id": "bts:DNAInsert" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:SampleIndex" }, { - "@id": "bts:In-House" - } - ], - "sms:displayName": "Transposition Reaction", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ReadLength", - "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:CellBarcode" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Read Length", + "sms:displayName": "scATACseq Read2", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:ScATACseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScATACseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -7624,292 +7694,159 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:CustomTargetsFileProvided" - }, - { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" - }, - { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" - }, - { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" - }, - { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" - }, - { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" - }, - { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" - }, - { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" - }, - { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" - }, - { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" - }, - { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" - }, - { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" - }, - { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" - }, - { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" - }, - { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" - }, - { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" - }, - { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" - }, - { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" - }, - { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" - }, - { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" - }, - { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" - }, - { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" - }, - { - "@id": "bts:FoundationMedicineT7Panel-429Genes" - }, - { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" - }, - { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" - }, - { - "@id": "bts:NexteraDNAExome" - }, - { - "@id": "bts:NexteraRapidCaptureExomev1.2" - }, - { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" - }, - { - "@id": "bts:SeqCapEZHumanExomev2.0" - }, - { - "@id": "bts:SeqCapEZHumanExomev3.0" - }, - { - "@id": "bts:SureSelectHumanAllExonv3" - }, - { - "@id": "bts:SureSelectHumanAllExonv4" - }, - { - "@id": "bts:SureSelectHumanAllExonv5" - }, - { - "@id": "bts:SureSelectHumanAllExonv5+UTR" - }, - { - "@id": "bts:TruSeqAmpliconCancerPanel" - }, - { - "@id": "bts:TruSeqExomeEnrichment-62Mb" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:TruSeqRNAExome" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:TruSightMyeloidSequencingPanel" + "@id": "bts:DNAInsert" }, { - "@id": "bts:XGenExomeResearchPanelv1.0" + "@id": "bts:SampleIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Target Capture Kit", - "sms:required": "sms:true", + "sms:displayName": "scATACseq Read3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibrarySelectionMethod", + "@id": "bts:ThresholdforMinimumPassingReads", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", + "rdfs:comment": "Threshold for calling cells", + "rdfs:label": "ThresholdforMinimumPassingReads", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Selection Method", + "sms:displayName": "Threshold for Minimum Passing Reads", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitName", + "@id": "bts:TotalNumberofPassingNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", + "rdfs:comment": "Number of nuclei sequenced", + "rdfs:label": "TotalNumberofPassingNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Name", + "sms:displayName": "Total Number of Passing Nuclei", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVendor", + "@id": "bts:MedianFractionofReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", + "rdfs:comment": "Median fraction of reads in peaks (FRIP)", + "rdfs:label": "MedianFractionofReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Vendor", + "sms:displayName": "Median Fraction of Reads in Peaks", "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PeaksCallingSoftware" + } + ], "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationKitVersion", + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", + "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Kit Version", + "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:PeaksCallingSoftware" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Name", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdapterSequence", + "@id": "bts:MedianPassingReadPercentage", "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", + "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label": "MedianPassingReadPercentage", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", + "sms:displayName": "Median Passing Read Percentage", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerName", + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", + "rdfs:comment": "Contamination from mitochondrial sequences", + "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", + "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerVersion", + "@id": "bts:PeaksCallingSoftware", "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", + "rdfs:comment": "Generic name of peaks calling tool", + "rdfs:label": "PeaksCallingSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Version", - "sms:required": "sms:false", + "sms:displayName": "Peaks Calling Software", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FlowCellBarcode", + "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", + "rdfs:comment": "Indicate if this is Read 1 (R1) or Read 2 (R2)", + "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -7918,49 +7855,73 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Flow Cell Barcode", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:R1" + }, + { + "@id": "bts:R2" + } + ], + "sms:displayName": "Read Indicator", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FragmentMaximumLength", + "@id": "bts:Read1", "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "Read1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FragmentMeanLength", + "@id": "bts:Read2", "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "Read2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FragmentMinimumLength", + "@id": "bts:CDNA", "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", + "rdfs:comment": "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase", + "rdfs:label": "CDNA", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -7969,15 +7930,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fragment Minimum Length", + "sms:displayName": "cDNA", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:CDNAOffset" + }, + { + "@id": "bts:CDNALength" + } + ], "sms:validationRules": [] }, { - "@id": "bts:FragmentStandardDeviationLength", + "@id": "bts:CDNAOffset", "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", + "rdfs:comment": "Offset in sequence for cDNA read (in bp): number", + "rdfs:label": "CDNAOffset", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -7986,15 +7955,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", + "sms:displayName": "cDNA Offset", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LaneNumber", + "@id": "bts:CDNALength", "@type": "rdfs:Class", - "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label": "LaneNumber", + "rdfs:comment": "Length of cDNA read (in bp): number", + "rdfs:label": "CDNALength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8003,218 +7972,205 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", + "sms:displayName": "cDNA Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryStrand", + "@id": "bts:CellBarcodeandUMI", "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", + "rdfs:comment": "Cell and transcript identifiers", + "rdfs:label": "CellBarcodeandUMI", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Cell Barcode and UMI", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Unstranded" + "@id": "bts:UMIBarcodeOffset" }, { - "@id": "bts:FirstStranded" + "@id": "bts:UMIBarcodeLength" }, { - "@id": "bts:SecondStranded" + "@id": "bts:MedianUMIsperCellNumber" }, { - "@id": "bts:NotApplicable" + "@id": "bts:CellBarcodeOffset" + }, + { + "@id": "bts:CellBarcodeLength" + }, + { + "@id": "bts:ValidBarcodesCellNumber" } ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MultiplexBarcode", + "@id": "bts:CellBarcodeOffset", "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", + "rdfs:comment": "Offset in sequence for cell barcode read (in bp): number", + "rdfs:label": "CellBarcodeOffset", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Offset", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SizeSelectionRange", + "@id": "bts:CellBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", + "rdfs:comment": "Length of cell barcode read (in bp): number", + "rdfs:label": "CellBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetDepth", + "@id": "bts:ValidBarcodesCellNumber", "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", + "rdfs:comment": "Number", + "rdfs:label": "ValidBarcodesCellNumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", + "sms:displayName": "Valid Barcodes Cell Number", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ToTrimAdapterSequence", + "@id": "bts:UMIBarcodeOffset", "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", + "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", + "rdfs:label": "UMIBarcodeOffset", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-TrimAdapterSequence" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", + "sms:displayName": "UMI Barcode Offset", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Yes-TrimAdapterSequence", + "@id": "bts:UMIBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Trim adapter sequence", - "rdfs:label": "Yes-TrimAdapterSequence", + "rdfs:comment": "Length of UMI barcode read (in bp): number", + "rdfs:label": "UMIBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AdapterTrimmerName" - }, - { - "@id": "bts:AdapterTrimmerVersion" - }, - { - "@id": "bts:AdapterTrimmerOptions" - } - ], - "sms:displayName": "Yes - Trim Adapter Sequence", - "sms:required": "sms:false", + "sms:displayName": "UMI Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterTrimmerName", + "@id": "bts:MedianUMIsperCellNumber", "@type": "rdfs:Class", - "rdfs:comment": "Name of adapter trimmer", - "rdfs:label": "AdapterTrimmerName", + "rdfs:comment": "Number", + "rdfs:label": "MedianUMIsperCellNumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Trimmer Name", - "sms:required": "sms:false", + "sms:displayName": "Median UMIs per Cell Number", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterTrimmerVersion", + "@id": "bts:CellMedianNumberReads", "@type": "rdfs:Class", - "rdfs:comment": "Version of the adapter trimmer", - "rdfs:label": "AdapterTrimmerVersion", + "rdfs:comment": "Median number of reads per cell. Number", + "rdfs:label": "CellMedianNumberReads", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Trimmer Version", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Reads", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterTrimmerOptions", + "@id": "bts:CellMedianNumberGenes", "@type": "rdfs:Class", - "rdfs:comment": "Options used by adapter trimmer", - "rdfs:label": "AdapterTrimmerOptions", + "rdfs:comment": "Median number of genes detected per cell. Number", + "rdfs:label": "CellMedianNumberGenes", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adapter Trimmer Options", - "sms:required": "sms:false", + "sms:displayName": "Cell Median Number Genes", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranscriptIntegrityNumber(TIN)", + "@id": "bts:CellTotal", "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber(TIN)", + "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", + "rdfs:label": "CellTotal", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcript Integrity Number (TIN)", - "sms:required": "sms:false", + "sms:displayName": "Cell Total", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RIN", + "@id": "bts:LibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "LibraryConstructionMethod", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8223,66 +8179,56 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RIN", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DV200", - "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DV200", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", - "rdfs:subClassOf": [ + "@id": "bts:Smart-seq2" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Smart-SeqV4" + }, { - "@id": "bts:FAIL" + "@id": "bts:10xV1.0" }, { - "@id": "bts:PASS" + "@id": "bts:10xV1.1" }, { - "@id": "bts:WARN" + "@id": "bts:10xV2" }, { - "@id": "bts:Unknown" + "@id": "bts:10xV3" }, { - "@id": "bts:NotReported" + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:CEL-seq2" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:Sci-ATAC-seq" } ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", + "sms:displayName": "Library Construction Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BasicStatistics", + "@id": "bts:LibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8293,84 +8239,113 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:HybridSelection" }, { - "@id": "bts:PASS" + "@id": "bts:PCR" }, { - "@id": "bts:WARN" + "@id": "bts:AffinityEnrichment" }, { - "@id": "bts:Unknown" + "@id": "bts:Other" }, { - "@id": "bts:NotReported" + "@id": "bts:HybridSelection" + }, + { + "@id": "bts:PCR" + }, + { + "@id": "bts:AffinityEnrichment" + }, + { + "@id": "bts:Poly-TEnrichment" + }, + { + "@id": "bts:Random" + }, + { + "@id": "bts:RRNADepletion" + }, + { + "@id": "bts:MiRNASizeFractionation" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", + "sms:displayName": "Library Selection Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Encoding", + "@id": "bts:InputCellsandNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", + "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label": "InputCellsandNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Encoding", - "sms:required": "sms:false", + "sms:displayName": "Input Cells and Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:KmerContent", + "@id": "bts:CEL-seq2", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", + "rdfs:comment": "Highly-multiplexed plate-based single-cell RNA-Seq assay", + "rdfs:label": "CEL-seq2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, + "sms:displayName": "CEL-seq2", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:WARN" + "@id": "bts:EmptyWellBarcode" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:WellIndex" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:EmptyWellBarcode", + "@type": "rdfs:Class", + "rdfs:comment": "Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.", + "rdfs:label": "EmptyWellBarcode", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ScRNA-seqLevel1" } ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Empty Well Barcode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OverrepresentedSequences", + "@id": "bts:WellIndex", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", + "rdfs:comment": "Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays", + "rdfs:label": "WellIndex", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -8378,30 +8353,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "Overrepresented Sequences", + "sms:displayName": "Well Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PerBaseNContent", + "@id": "bts:LibraryPreparationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", + "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]", + "rdfs:label": "LibraryPreparationDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8410,32 +8376,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Library Preparation Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SingleCellDissociationDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]", + "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ScRNA-seqLevel1" } ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Single Cell Dissociation Days from Index", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceContent", + "@id": "bts:SequencingLibraryConstructionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", + "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]", + "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8444,35 +8410,35 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Sequencing Library Construction Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]", + "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nucleic Acid Capture Days from Index", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceQuality", + "@id": "bts:CryopreservedCellsinSample", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", + "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", + "rdfs:label": "CryopreservedCellsinSample", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -8480,33 +8446,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", + "sms:displayName": "Cryopreserved Cells in Sample", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerSequenceGCContent", + "@id": "bts:EndBias", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", + "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "rdfs:label": "EndBias", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -8514,33 +8471,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" + "@id": "bts:3Prime" }, { - "@id": "bts:Unknown" + "@id": "bts:5Prime" }, { - "@id": "bts:NotReported" + "@id": "bts:FullLengthTranscript" } ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", + "sms:displayName": "End Bias", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerSequenceQualityScore", + "@id": "bts:ReverseTranscriptionPrimer", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", + "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", + "rdfs:label": "ReverseTranscriptionPrimer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -8548,84 +8499,69 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:Oligo-dT" }, { - "@id": "bts:WARN" + "@id": "bts:Poly-dT" }, { - "@id": "bts:Unknown" + "@id": "bts:Featurebarcoding" }, { - "@id": "bts:NotReported" + "@id": "bts:Random" } ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", + "sms:displayName": "Reverse Transcription Primer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerTileSequenceQuality", + "@id": "bts:Featurebarcoding", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", + "rdfs:comment": "A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc]", + "rdfs:label": "Featurebarcoding", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Feature barcoding", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:NotReported" + "@id": "bts:FeatureReferenceId" } ], - "sms:displayName": "Per Tile Sequence Quality", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentGCContent", + "@id": "bts:FeatureReferenceId", "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", + "rdfs:comment": "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", + "rdfs:label": "FeatureReferenceId", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent GC Content", - "sms:required": "sms:false", + "sms:displayName": "Feature Reference Id", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceDuplicationLevels", + "@id": "bts:SpikeIn", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", + "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label": "SpikeIn", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -8633,81 +8569,169 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" + "@id": "bts:ERCC" }, { - "@id": "bts:WARN" + "@id": "bts:OtherSpikeIn" }, { - "@id": "bts:Unknown" + "@id": "bts:NoSpikeIn" }, { - "@id": "bts:NotReported" + "@id": "bts:PhiX" } ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", + "sms:displayName": "Spike In", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceLengthDistribution", + "@id": "bts:ERCC", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", + "rdfs:comment": "The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization", + "rdfs:label": "ERCC", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpikeIn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "ERCC", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:FAIL" + "@id": "bts:SpikeInConcentration" }, { - "@id": "bts:PASS" + "@id": "bts:SpikeInMix1" }, { - "@id": "bts:WARN" + "@id": "bts:SpikeInMix2" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:BothSpikeinMixes" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SpikeInConcentration", + "@type": "rdfs:Class", + "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", + "rdfs:label": "SpikeInConcentration", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ERCC" } ], - "sms:displayName": "Sequence Length Distribution", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spike In Concentration", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalReads", + "@id": "bts:SequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "SequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Device" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:IlluminaNextSeq500" + }, + { + "@id": "bts:IlluminaNextSeq550" + }, + { + "@id": "bts:IlluminaNextSeq2500" + }, + { + "@id": "bts:IlluminaNovaSeq6000" + }, + { + "@id": "bts:IlluminaMiSeq" + }, + { + "@id": "bts:454GSFLXTitanium" + }, + { + "@id": "bts:ABSOLiD4ABSOLiD2" + }, + { + "@id": "bts:ABSOLiD3" + }, + { + "@id": "bts:CompleteGenomics" + }, + { + "@id": "bts:IlluminaHiSeqXTen" + }, + { + "@id": "bts:IlluminaHiSeqXFive" + }, + { + "@id": "bts:IlluminaGenomeAnalyzerII" + }, + { + "@id": "bts:IlluminaGenomeAnalyzerIIx" + }, + { + "@id": "bts:IlluminaHiSeq2000" + }, + { + "@id": "bts:IlluminaHiSeq2500" + }, + { + "@id": "bts:IlluminaHiSeq4000" + }, + { + "@id": "bts:IlluminaMiSeq" + }, + { + "@id": "bts:IlluminaNextSeq" + }, + { + "@id": "bts:IonTorrentPGM" + }, + { + "@id": "bts:IonTorrentProton" + }, + { + "@id": "bts:IonTorrentS5" + }, + { + "@id": "bts:PacBioRS" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequencing Platform", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:White-listCellBarcodeFileLink", + "@id": "bts:TechnicalReplicateGroup", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "White-listCellBarcodeFileLink", + "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label": "TechnicalReplicateGroup", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8716,15 +8740,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "White-list Cell Barcode File Link", - "sms:required": "sms:true", + "sms:displayName": "Technical Replicate Group", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeTag", + "@id": "bts:TotalNumberofInputCells", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag", - "rdfs:label": "CellBarcodeTag", + "rdfs:comment": "Number of cells loaded/placed on plates", + "rdfs:label": "TotalNumberofInputCells", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8733,15 +8757,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Tag", + "sms:displayName": "Total Number of Input Cells", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UMITag", + "@id": "bts:SequencingBatchID", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for UMI field; please provide a valid UB, UMI", - "rdfs:label": "UMITag", + "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", + "rdfs:label": "SequencingBatchID", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8750,54 +8774,77 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Tag", + "sms:displayName": "Sequencing Batch ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AppliedHardTrimming", + "@id": "bts:SingleNucleusBuffer", "@type": "rdfs:Class", - "rdfs:comment": "Yes - Applied Hard Trimming, No", - "rdfs:label": "AppliedHardTrimming", + "rdfs:comment": "Nuclei isolation buffer", + "rdfs:label": "SingleNucleusBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Applied Hard Trimming", + "schema:rangeIncludes": [ + { + "@id": "bts:NIB" + }, + { + "@id": "bts:10x" + }, + { + "@id": "bts:Omni" + } + ], + "sms:displayName": "Single Nucleus Buffer", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Yes-AppliedHardTrimming", + "@id": "bts:TranspositionReaction", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Yes-AppliedHardTrimming", + "rdfs:comment": "Name of the transposase, transposon sequences", + "rdfs:label": "TranspositionReaction", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Applied Hard Trimming", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:AlignedReadLength" + "@id": "bts:Tn5" + }, + { + "@id": "bts:EZ-Tn5" + }, + { + "@id": "bts:Tn5-059" + }, + { + "@id": "bts:NexteraTn5" + }, + { + "@id": "bts:In-House" } ], + "sms:displayName": "Transposition Reaction", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AlignedReadLength", + "@id": "bts:ReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Read length used for alignment if hard trimming was applied", - "rdfs:label": "AlignedReadLength", + "rdfs:comment": "The length of the sequencing reads. Can be integer, null", + "rdfs:label": "ReadLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8806,15 +8853,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned Read Length", + "sms:displayName": "Read Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqWorkflowType", + "@id": "bts:TargetCaptureKit", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNA-seqWorkflowType", + "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", + "rdfs:label": "TargetCaptureKit", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8825,48 +8872,156 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellRanger" + "@id": "bts:NotApplicable" }, { - "@id": "bts:STARsolo" + "@id": "bts:CustomTargetsFileProvided" }, { - "@id": "bts:HCAOptimus" + "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" }, { - "@id": "bts:DropEST" + "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" }, { - "@id": "bts:SEQC" + "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" }, { - "@id": "bts:Cufflinks" + "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" }, { - "@id": "bts:DEXSeq" + "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" }, { - "@id": "bts:HTSeq-FPKM" + "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" }, { - "@id": "bts:Cellannotation" + "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" }, { - "@id": "bts:Differentiationtrajectoryanalysis" + "@id": "bts:CustomMSKIMPACTPanel-341Genes" }, { - "@id": "bts:Other" + "@id": "bts:CustomMSKIMPACTPanel-410Genes" + }, + { + "@id": "bts:CustomMSKIMPACTPanel-468Genes" + }, + { + "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + }, + { + "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + }, + { + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + }, + { + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" + }, + { + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" + }, + { + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" + }, + { + "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" + }, + { + "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" + }, + { + "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" + }, + { + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" + }, + { + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" + }, + { + "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" + }, + { + "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" + }, + { + "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" + }, + { + "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" + }, + { + "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" + }, + { + "@id": "bts:FoundationMedicineT5aPanel-322Genes" + }, + { + "@id": "bts:FoundationMedicineT7Panel-429Genes" + }, + { + "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" + }, + { + "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" + }, + { + "@id": "bts:NexteraDNAExome" + }, + { + "@id": "bts:NexteraRapidCaptureExomev1.2" + }, + { + "@id": "bts:SeqCapEZHGSCVCRomev2.1" + }, + { + "@id": "bts:SeqCapEZHumanExomev2.0" + }, + { + "@id": "bts:SeqCapEZHumanExomev3.0" + }, + { + "@id": "bts:SureSelectHumanAllExonv3" + }, + { + "@id": "bts:SureSelectHumanAllExonv4" + }, + { + "@id": "bts:SureSelectHumanAllExonv5" + }, + { + "@id": "bts:SureSelectHumanAllExonv5+UTR" + }, + { + "@id": "bts:TruSeqAmpliconCancerPanel" + }, + { + "@id": "bts:TruSeqExomeEnrichment-62Mb" + }, + { + "@id": "bts:TruSeqRNAExome" + }, + { + "@id": "bts:TruSightMyeloidSequencingPanel" + }, + { + "@id": "bts:XGenExomeResearchPanelv1.0" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "scRNA-seq Workflow Type", + "sms:displayName": "Target Capture Kit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WorkflowType", + "@id": "bts:LibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "WorkflowType", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8875,15 +9030,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Type", + "sms:displayName": "Library Selection Method", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WorkflowVersion", + "@id": "bts:LibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8892,15 +9047,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Version", + "sms:displayName": "Library Preparation Kit Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqWorkflowParametersDescription", + "@id": "bts:LibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNA-seqWorkflowParametersDescription", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVendor", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8909,15 +9064,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Workflow Parameters Description", + "sms:displayName": "Library Preparation Kit Vendor", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WorkflowParametersDescription", + "@id": "bts:LibraryPreparationKitVersion", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow.", - "rdfs:label": "WorkflowParametersDescription", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8926,15 +9081,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Parameters Description", + "sms:displayName": "Library Preparation Kit Version", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WorkflowLink", + "@id": "bts:AdapterName", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", + "rdfs:comment": "Name of the sequencing adapter. String", + "rdfs:label": "AdapterName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8943,15 +9098,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", + "sms:displayName": "Adapter Name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowStartDate-time", + "@id": "bts:AdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]", - "rdfs:label": "WorkflowStartDate-time", + "rdfs:comment": "Base sequence of the sequencing adapter. String", + "rdfs:label": "AdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8960,15 +9115,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Start Date-time", + "sms:displayName": "Adapter Sequence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowEndDate-time", + "@id": "bts:BaseCallerName", "@type": "rdfs:Class", - "rdfs:comment": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]", - "rdfs:label": "WorkflowEndDate-time", + "rdfs:comment": "Name of the base caller. String", + "rdfs:label": "BaseCallerName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8977,15 +9132,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow End Date-time", + "sms:displayName": "Base Caller Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowType", + "@id": "bts:BaseCallerVersion", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", + "rdfs:comment": "Version of the base caller. String", + "rdfs:label": "BaseCallerVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -8994,15 +9149,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Type", + "sms:displayName": "Base Caller Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowVersion", + "@id": "bts:FlowCellBarcode", "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", + "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", + "rdfs:label": "FlowCellBarcode", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9011,15 +9166,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Version", + "sms:displayName": "Flow Cell Barcode", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowLink", + "@id": "bts:FragmentMaximumLength", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", + "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMaximumLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9028,15 +9183,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Link", + "sms:displayName": "Fragment Maximum Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowURL", + "@id": "bts:FragmentMeanLength", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentMeanLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9045,15 +9200,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Germline Variants Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Fragment Mean Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowType", + "@id": "bts:FragmentMinimumLength", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMinimumLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9062,23 +9217,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GATK4" - }, + "sms:displayName": "Fragment Minimum Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentStandardDeviationLength", + "@type": "rdfs:Class", + "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentStandardDeviationLength", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Germline Variants Workflow Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Standard Deviation Length", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowURL", + "@id": "bts:LaneNumber", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label": "LaneNumber", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9087,15 +9251,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Somatic Variants Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Lane Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsWorkflowType", + "@id": "bts:LibraryStrand", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:comment": "Library stranded-ness.", + "rdfs:label": "LibraryStrand", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9106,39 +9270,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CaVEMan" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:MuTect2" - }, - { - "@id": "bts:MuSE" - }, - { - "@id": "bts:MuTect2" + "@id": "bts:Unstranded" }, { - "@id": "bts:Pindel" + "@id": "bts:FirstStranded" }, { - "@id": "bts:SomaticSniper" + "@id": "bts:SecondStranded" }, { - "@id": "bts:VarScan2" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Somatic Variants Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "Library Strand", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SomaticVariantsSampleType", + "@id": "bts:MultiplexBarcode", "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", + "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", + "rdfs:label": "MultiplexBarcode", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9147,23 +9299,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaseSample" - }, - { - "@id": "bts:ControlSample" - } - ], - "sms:displayName": "Somatic Variants Sample Type", - "sms:required": "sms:true", + "sms:displayName": "Multiplex Barcode", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowURL", + "@id": "bts:SizeSelectionRange", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", + "rdfs:comment": "Range of size selection. String", + "rdfs:label": "SizeSelectionRange", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9172,15 +9316,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "Size Selection Range", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowType", + "@id": "bts:TargetDepth", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", + "rdfs:comment": "The targeted read depth prior to sequencing. Integer", + "rdfs:label": "TargetDepth", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9189,29 +9333,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BRASS" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:CNV" - }, - { - "@id": "bts:CNVkit" - } - ], - "sms:displayName": "Structural Variant Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "Target Depth", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowUrl", + "@id": "bts:ToTrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", + "rdfs:comment": "Does the user suggest adapter trimming?", + "rdfs:label": "ToTrimAdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9220,15 +9350,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-TrimAdapterSequence" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "To Trim Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlignmentWorkflowType", + "@id": "bts:Yes-TrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", + "rdfs:comment": "Trim adapter sequence", + "rdfs:label": "Yes-TrimAdapterSequence", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9239,42 +9377,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BWA" - }, - { - "@id": "bts:BWAwithBQSR" - }, - { - "@id": "bts:BWA-aln" - }, - { - "@id": "bts:BWA-mem" - }, - { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" - }, - { - "@id": "bts:STAR2-Pass" - }, - { - "@id": "bts:STAR2-PassChimeric" + "@id": "bts:AdapterTrimmerName" }, { - "@id": "bts:STAR2-PassGenome" + "@id": "bts:AdapterTrimmerVersion" }, { - "@id": "bts:STAR2-PassTranscriptome" + "@id": "bts:AdapterTrimmerOptions" } ], - "sms:displayName": "Alignment Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "Yes - Trim Adapter Sequence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:AdapterTrimmerName", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "Name of adapter trimmer", + "rdfs:label": "AdapterTrimmerName", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9283,15 +9403,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", + "sms:displayName": "Adapter Trimmer Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIScore", + "@id": "bts:AdapterTrimmerVersion", "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", + "rdfs:comment": "Version of the adapter trimmer", + "rdfs:label": "AdapterTrimmerVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9300,15 +9420,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Score", + "sms:displayName": "Adapter Trimmer Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:AdapterTrimmerOptions", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Options used by adapter trimmer", + "rdfs:label": "AdapterTrimmerOptions", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9317,29 +9437,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MSI" - }, - { - "@id": "bts:MSI-low" - }, - { - "@id": "bts:MSI-high" - }, - { - "@id": "bts:MSS" - } - ], - "sms:displayName": "MSI Status", + "sms:displayName": "Adapter Trimmer Options", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:TranscriptIntegrityNumber", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). URL", - "rdfs:label": "GenomicReference", + "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", + "rdfs:label": "TranscriptIntegrityNumber", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9348,15 +9454,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", + "sms:displayName": "Transcript Integrity Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:RIN", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", + "rdfs:label": "RIN", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9365,15 +9471,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", - "sms:required": "sms:true", + "sms:displayName": "RIN", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomeAnnotationURL", + "@id": "bts:DV200", "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", + "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", + "rdfs:label": "DV200", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9382,15 +9488,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genome Annotation URL", - "sms:required": "sms:true", + "sms:displayName": "DV200", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IndexFileName", + "@id": "bts:AdapterContent", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9399,15 +9505,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", - "sms:required": "sms:true", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:BasicStatistics", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9416,15 +9539,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Basic Statistics", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageInsertSize", + "@id": "bts:Encoding", "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9433,15 +9573,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Insert Size", + "sms:displayName": "Encoding", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:KmerContent", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9450,15 +9590,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Kmer Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Contamination", + "@id": "bts:OverrepresentedSequences", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9467,15 +9624,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Overrepresented Sequences", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ContaminationError", + "@id": "bts:PerBaseNContent", "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9484,15 +9658,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination Error", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base N Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MeanCoverage", + "@id": "bts:PerBaseSequenceContent", "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9501,15 +9692,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean Coverage", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PairsOnDiffCHR", + "@id": "bts:PerBaseSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9518,15 +9726,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pairs On Diff CHR", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalUniquelyMapped", + "@id": "bts:PerSequenceGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9535,15 +9760,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Uniquely Mapped", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence GC Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalUnmappedreads", + "@id": "bts:PerSequenceQualityScore", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9552,15 +9794,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Unmapped reads", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence Quality Score", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsDuplicated", + "@id": "bts:PerTileSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerTileSequenceQuality", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9569,15 +9828,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Duplicated", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Tile Sequence Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMapped", + "@id": "bts:PercentGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", + "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", + "rdfs:label": "PercentGCContent", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9586,15 +9862,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped", + "sms:displayName": "Percent GC Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionTargetsNoCoverage", + "@id": "bts:SequenceDuplicationLevels", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9603,15 +9879,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Targets No Coverage", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Duplication Levels", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionBaseMismatch", + "@id": "bts:SequenceLengthDistribution", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", - "rdfs:label": "ProportionBaseMismatch", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9620,15 +9913,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Base Mismatch", + "schema:rangeIncludes": [ + { + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Length Distribution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage10x", + "@id": "bts:TotalReads", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage10x", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9637,15 +9947,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 10x", + "sms:displayName": "Total Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage30X", + "@id": "bts:WhitelistCellBarcodeFileLink", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage30X", + "rdfs:comment": "Link to file listing all possible cell barcodes. URL", + "rdfs:label": "WhitelistCellBarcodeFileLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9654,15 +9964,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 30X", - "sms:required": "sms:false", + "sms:displayName": "Whitelist Cell Barcode File Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ShortReads", + "@id": "bts:CellBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that were too short. Integer", - "rdfs:label": "ShortReads", + "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag", + "rdfs:label": "CellBarcodeTag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9671,15 +9981,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Short Reads", - "sms:required": "sms:false", + "sms:displayName": "Cell Barcode Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PseudoAlignmentUsed", + "@id": "bts:UMITag", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", - "rdfs:label": "PseudoAlignmentUsed", + "rdfs:comment": "SAM tag for UMI field; please provide a valid UB, UMI", + "rdfs:label": "UMITag", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9688,23 +9998,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-PseudoAlignmentUsed" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pseudo Alignment Used", + "sms:displayName": "UMI Tag", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SoftwareandVersion", + "@id": "bts:AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", + "rdfs:comment": "TBD", + "rdfs:label": "AppliedHardTrimming", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9713,15 +10015,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Software and Version", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AppliedHardTrimming" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Applied Hard Trimming", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Yes-PseudoAlignmentUsed", + "@id": "bts:Yes-AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligner was used", - "rdfs:label": "Yes-PseudoAlignmentUsed", + "rdfs:comment": "TBD", + "rdfs:label": "Yes-AppliedHardTrimming", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9730,46 +10040,20 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Pseudo Alignment Used", + "sms:displayName": "Yes - Applied Hard Trimming", "sms:required": "sms:false", "sms:requiresDependency": [ { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:GenomicReference", - "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/)", - "rdfs:label": "GenomicReference", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" + "@id": "bts:AlignedReadLength" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:AlignedReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) [URL]", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Read length used for alignment if hard trimming was applied", + "rdfs:label": "AlignedReadLength", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9778,15 +10062,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", + "sms:displayName": "Aligned Read Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DataCategory", + "@id": "bts:ScRNAseqWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Specific content type of the data file.", - "rdfs:label": "DataCategory", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScRNAseqWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9797,36 +10081,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GeneExpression" + "@id": "bts:CellRanger" }, { - "@id": "bts:TranscriptExpression" + "@id": "bts:STARsolo" }, { - "@id": "bts:ExonExpressionQuantification" + "@id": "bts:HCAOptimus" }, { - "@id": "bts:GeneExpressionQuantification" + "@id": "bts:DropEST" }, { - "@id": "bts:IsoformExpressionQuantification" + "@id": "bts:SEQC" }, { - "@id": "bts:SpliceJunctionQuantification" + "@id": "bts:Cufflinks" + }, + { + "@id": "bts:DEXSeq" + }, + { + "@id": "bts:HTSeq-FPKM" + }, + { + "@id": "bts:Cellannotation" + }, + { + "@id": "bts:Differentiationtrajectoryanalysis" }, { "@id": "bts:Other" } ], - "sms:displayName": "Data Category", + "sms:displayName": "scRNAseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExpressionUnits", + "@id": "bts:WorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "How quantities are corrected for gene length", - "rdfs:label": "ExpressionUnits", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "WorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9835,35 +10131,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:TPM" - }, - { - "@id": "bts:RPKM" - }, - { - "@id": "bts:FPKM" - }, - { - "@id": "bts:Counts" - }, - { - "@id": "bts:Other" - }, + "sms:displayName": "Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WorkflowVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", + "rdfs:label": "WorkflowVersion", + "rdfs:subClassOf": [ { - "@id": "bts:NA" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Expression Units", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Workflow Version", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneDetected", + "@id": "bts:ScRNAseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "Was a fusion gene identified?", - "rdfs:label": "FusionGeneDetected", + "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", + "rdfs:label": "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9872,26 +10165,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-FusionGeneDetected" - }, - { - "@id": "bts:No" - }, + "sms:displayName": "scRNAseq Workflow Parameters Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WorkflowParametersDescription", + "@type": "rdfs:Class", + "rdfs:comment": "Parameters used to run the workflow.", + "rdfs:label": "WorkflowParametersDescription", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Fusion Gene Detected", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Workflow Parameters Description", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Yes-FusionGeneDetected", + "@id": "bts:WorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "A fusion gene was detected", - "rdfs:label": "Yes-FusionGeneDetected", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "WorkflowLink", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9900,20 +10199,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Fusion Gene Detected", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "sms:displayName": "Workflow Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WorkflowStartDatetime", + "@type": "rdfs:Class", + "rdfs:comment": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]", + "rdfs:label": "WorkflowStartDatetime", + "rdfs:subClassOf": [ { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Workflow Start Datetime", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneIdentity", + "@id": "bts:WorkflowEndDatetime", "@type": "rdfs:Class", - "rdfs:comment": "The gene symbols of fused genes.", - "rdfs:label": "FusionGeneIdentity", + "rdfs:comment": "A combination of date and time of day in the form [-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]", + "rdfs:label": "WorkflowEndDatetime", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9922,37 +10233,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:EWS-FLI" - }, - { - "@id": "bts:EWS-ERG" - }, - { - "@id": "bts:SYT-SSX1" - }, - { - "@id": "bts:SYT-SSX2" - }, - { - "@id": "bts:EWS-WT1" - }, + "sms:displayName": "Workflow End Datetime", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", + "rdfs:subClassOf": [ { - "@id": "bts:OtherFusionGene" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Fusion Gene Identity", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Type", "sms:required": "sms:false", - "sms:validationRules": [ - "list" - ] + "sms:validationRules": [] }, { - "@id": "bts:OtherFusionGene", + "@id": "bts:QCWorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Other fusion gene detected.", - "rdfs:label": "OtherFusionGene", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9961,20 +10267,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Fusion Gene", + "sms:displayName": "QC Workflow Version", "sms:required": "sms:false", - "sms:requiresDependency": [ + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow used. String", + "rdfs:label": "QCWorkflowLink", + "rdfs:subClassOf": [ { - "@id": "bts:SpecifyOtherFusionGene" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Link", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpecifyOtherFusionGene", + "@id": "bts:GermlineVariantsWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Specify fusion gene detected, if not in list", - "rdfs:label": "SpecifyOtherFusionGene", + "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", + "rdfs:label": "GermlineVariantsWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -9983,15 +10301,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Specify Other Fusion Gene", - "sms:required": "sms:false", + "sms:displayName": "Germline Variants Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MatrixType", + "@id": "bts:GermlineVariantsWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Type of data stored in matrix.", - "rdfs:label": "MatrixType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "GermlineVariantsWorkflowType", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -10002,27 +10320,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RawCounts" - }, - { - "@id": "bts:NormalizedCounts" - }, - { - "@id": "bts:ScaledCounts" + "@id": "bts:GATK4" }, { - "@id": "bts:BatchCorrectedCounts" + "@id": "bts:Other" } ], - "sms:displayName": "Matrix Type", + "sms:displayName": "Germline Variants Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LinkedMatrices", + "@id": "bts:SomaticVariantsWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", - "rdfs:label": "LinkedMatrices", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowURL", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -10031,18 +10343,18 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Linked Matrices", - "sms:required": "sms:false", + "sms:displayName": "Somatic Variants Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenType", + "@id": "bts:SomaticVariantsWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -10050,1037 +10362,690 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TissueBiospecimenType" - }, - { - "@id": "bts:BloodBiospecimenType" - }, - { - "@id": "bts:AnalyteBiospecimenType" - }, - { - "@id": "bts:MouthRinseBiospecimenType" + "@id": "bts:CaVEMan" }, { - "@id": "bts:StoolBiospecimenType" + "@id": "bts:GATK4" }, { - "@id": "bts:UrineBiospecimenType" + "@id": "bts:MuTect2" }, { - "@id": "bts:AscitesBiospecimenType" + "@id": "bts:MuSE" }, { - "@id": "bts:SputumBiospecimenType" + "@id": "bts:MuTect2" }, { - "@id": "bts:FluidsBiospecimenType" + "@id": "bts:Pindel" }, { - "@id": "bts:BoneMarrowBiospecimenType" + "@id": "bts:SomaticSniper" }, { - "@id": "bts:CellsBiospecimenType" + "@id": "bts:VarScan2" } ], - "sms:displayName": "Biospecimen Type", + "sms:displayName": "Somatic Variants Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AnalyteBiospecimenType", + "@id": "bts:SomaticVariantsSampleType", "@type": "rdfs:Class", - "rdfs:comment": "A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteBiospecimenType", + "rdfs:comment": "Is the sample case or control in somatic variant analysis", + "rdfs:label": "SomaticVariantsSampleType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Analyte Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AnalyteType" - }, - { - "@id": "bts:FixationDuration" - }, - { - "@id": "bts:SlideChargeType" - }, - { - "@id": "bts:SectionThicknessValue" - }, - { - "@id": "bts:SectioningDaysfromIndex" - }, - { - "@id": "bts:ShippingConditionType" - }, + "schema:rangeIncludes": [ { - "@id": "bts:IschemicTime" + "@id": "bts:CaseSample" }, { - "@id": "bts:IschemicTemperature" + "@id": "bts:ControlSample" } ], + "sms:displayName": "Somatic Variants Sample Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TissueBiospecimenType", + "@id": "bts:StructuralVariantWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Tissue biospecimen", - "rdfs:label": "TissueBiospecimenType", + "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", + "rdfs:label": "StructuralVariantWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tissue Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:SpecimenLaterality" - }, - { - "@id": "bts:PortionWeight" - }, - { - "@id": "bts:TotalVolume" - }, - { - "@id": "bts:TumorTissueType" - }, - { - "@id": "bts:HistologicMorphologyCode" - }, - { - "@id": "bts:PreservationMethod" - } - ], + "sms:displayName": "Structural Variant Workflow URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BoneMarrowBiospecimenType", + "@id": "bts:StructuralVariantWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Bone Marrow biospecimen", - "rdfs:label": "BoneMarrowBiospecimenType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "StructuralVariantWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bone Marrow Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:SpecimenLaterality" - }, + "schema:rangeIncludes": [ { - "@id": "bts:PortionWeight" + "@id": "bts:BRASS" }, { - "@id": "bts:TotalVolume" + "@id": "bts:GATK4" }, { - "@id": "bts:TumorTissueType" + "@id": "bts:CNV" }, { - "@id": "bts:HistologicMorphologyCode" - }, + "@id": "bts:CNVkit" + } + ], + "sms:displayName": "Structural Variant Workflow Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AlignmentWorkflowUrl", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", + "rdfs:label": "AlignmentWorkflowUrl", + "rdfs:subClassOf": [ { - "@id": "bts:PreservationMethod" + "@id": "bts:Sequencing" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UrineBiospecimenType", + "@id": "bts:AlignmentWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Urine biospecimen", - "rdfs:label": "UrineBiospecimenType", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "AlignmentWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Urine Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:IschemicTime" + "@id": "bts:BWA" }, { - "@id": "bts:IschemicTemperature" + "@id": "bts:BWAwithBQSR" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:BWA-aln" }, { - "@id": "bts:SpecimenLaterality" + "@id": "bts:BWA-mem" }, { - "@id": "bts:PortionWeight" + "@id": "bts:BWAwithMarkDuplicatesandBQSR" }, { - "@id": "bts:TotalVolume" + "@id": "bts:STAR2-Pass" }, { - "@id": "bts:TumorTissueType" + "@id": "bts:STAR2-PassChimeric" }, { - "@id": "bts:HistologicMorphologyCode" + "@id": "bts:STAR2-PassGenome" }, { - "@id": "bts:PreservationMethod" + "@id": "bts:STAR2-PassTranscriptome" } ], + "sms:displayName": "Alignment Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BloodBiospecimenType", + "@id": "bts:MSIWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Blood biospecimen", - "rdfs:label": "BloodBiospecimenType", + "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", + "rdfs:label": "MSIWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Biospecimen Type", + "sms:displayName": "MSI Workflow Link", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:ShippingConditionType" - } - ], "sms:validationRules": [] }, { - "@id": "bts:TimepointLabel", + "@id": "bts:MSIScore", "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", + "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", + "rdfs:label": "MSIScore", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", + "sms:displayName": "MSI Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CollectionDaysfromIndex", + "@id": "bts:MSIStatus", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained.", - "rdfs:label": "CollectionDaysfromIndex", + "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", + "rdfs:label": "MSIStatus", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [] - }, + "schema:rangeIncludes": [ + { + "@id": "bts:MSI" + }, + { + "@id": "bts:MSI-low" + }, + { + "@id": "bts:MSI-high" + }, + { + "@id": "bts:MSS" + } + ], + "sms:displayName": "MSI Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { - "@id": "bts:ProtocolLink", + "@id": "bts:GenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). URL", + "rdfs:label": "GenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protocol Link", + "sms:displayName": "Genomic Reference", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdjacentBiospecimenID", + "@id": "bts:GenomicReferenceURL", "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenID", + "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", + "rdfs:label": "GenomicReferenceURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adjacent Biospecimen ID", - "sms:required": "sms:false", + "sms:displayName": "Genomic Reference URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MountingMedium", + "@id": "bts:GenomeAnnotationURL", "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", + "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", + "rdfs:label": "GenomeAnnotationURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" - }, - { - "@id": "bts:Toluene" - }, - { - "@id": "bts:AntifadewithDAPI" - }, - { - "@id": "bts:AntifadewithoutDAPI" - }, - { - "@id": "bts:PBS" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", + "sms:displayName": "Genome Annotation URL", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AnalyteType", + "@id": "bts:IndexFileName", "@type": "rdfs:Class", - "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteType", + "rdfs:comment": "The name (or part of a name) of a file (of any type). String", + "rdfs:label": "IndexFileName", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CfDNAAnalyte" - }, - { - "@id": "bts:DNAAnalyte" - }, - { - "@id": "bts:RNAAnalyte" - }, - { - "@id": "bts:TotalRNAAnalyte" - }, - { - "@id": "bts:TissueBlockAnalyte" - }, - { - "@id": "bts:TissueSectionAnalyte" - }, - { - "@id": "bts:PBMCsorPlasmaorSerumAnalyte" - }, - { - "@id": "bts:CDNALibrariesAnalyte" - } - ], - "sms:displayName": "Analyte Type", + "sms:displayName": "Index File Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AcquisitionMethodType", + "@id": "bts:AverageBaseQuality", "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", + "rdfs:comment": "Average base quality collected from samtools. 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"@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -11088,80 +11053,126 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Ambienttemperature" + "@id": "bts:GeneExpression" }, { - "@id": "bts:Cutslide" + "@id": "bts:TranscriptExpression" }, { - "@id": "bts:Fresh" + "@id": "bts:ExonExpressionQuantification" }, { - "@id": "bts:Frozenat-70C" + "@id": "bts:GeneExpressionQuantification" }, { - "@id": "bts:Frozenat-80C" + "@id": "bts:IsoformExpressionQuantification" }, { - "@id": "bts:Frozenat-150C" + "@id": "bts:SpliceJunctionQuantification" }, { - "@id": "bts:Frozeninliquidnitrogen" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Data Category", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ExpressionUnits", + "@type": "rdfs:Class", + "rdfs:comment": "How quantities are corrected for gene length", + "rdfs:label": "ExpressionUnits", + "rdfs:subClassOf": [ { - "@id": "bts:Frozeninvaporphase" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:TPM" }, { - "@id": "bts:Raraffinblock" + "@id": "bts:RPKM" }, { - "@id": "bts:RNAlaterat4C" + "@id": "bts:FPKM" }, { - "@id": "bts:RNAlaterat25C" + "@id": "bts:Counts" }, { - "@id": "bts:RNAlaterat-20C" + "@id": "bts:Other" }, { - "@id": "bts:Refrigeratedat4degrees" + "@id": "bts:NA" + } + ], + "sms:displayName": "Expression Units", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:FusionGeneDetected", + "@type": "rdfs:Class", + "rdfs:comment": "Was a fusion gene identified?", + "rdfs:label": "FusionGeneDetected", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-FusionGeneDetected" }, { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:No" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", + "sms:displayName": "Fusion Gene Detected", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProcessingDaysfromIndex", + "@id": "bts:Yes-FusionGeneDetected", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed", - "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:comment": "A fusion gene was detected", + "rdfs:label": "Yes-FusionGeneDetected", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", + "sms:displayName": "Yes - Fusion Gene Detected", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:FusionGeneIdentity" + } + ], "sms:validationRules": [] }, { - "@id": "bts:ShippingConditionType", + "@id": "bts:FusionGeneIdentity", "@type": "rdfs:Class", - "rdfs:comment": "Text descriptor of the shipping environment of a biospecimen.", - "rdfs:label": "ShippingConditionType", + "rdfs:comment": "The gene symbols of fused genes.", + "rdfs:label": "FusionGeneIdentity", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -11169,73 +11180,77 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AmbientPack" - }, - { - "@id": "bts:ColdPack" + "@id": "bts:EWS-FLI" }, { - "@id": "bts:DryIce" + "@id": "bts:EWS-ERG" }, { - "@id": "bts:IcePack" + "@id": "bts:SYT-SSX1" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:SYT-SSX2" }, { - "@id": "bts:OtherShippingEnvironment" + "@id": "bts:EWS-WT1" }, { - "@id": "bts:SpecimenatRoomTemperature" + "@id": "bts:OtherFusionGene" } ], - "sms:displayName": "Shipping Condition Type", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "Fusion Gene Identity", + "sms:required": "sms:false", + "sms:validationRules": [ + "list" + ] }, { - "@id": "bts:SiteDataSource", + "@id": "bts:OtherFusionGene", "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", + "rdfs:comment": "Other fusion gene detected.", + "rdfs:label": "OtherFusionGene", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Site Data Source", + "sms:displayName": "Other Fusion Gene", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:SpecifyOtherFusionGene" + } + ], "sms:validationRules": [] }, { - "@id": "bts:ProcessingLocation", + "@id": "bts:SpecifyOtherFusionGene", "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", + "rdfs:comment": "Specify fusion gene detected, if not in list", + "rdfs:label": "SpecifyOtherFusionGene", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Location", + "sms:displayName": "Specify Other Fusion Gene", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentBy", + "@id": "bts:MatrixType", "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", + "rdfs:comment": "Type of data stored in matrix.", + "rdfs:label": "MatrixType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -11243,27 +11258,44 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pathologist" + "@id": "bts:RawCounts" }, { - "@id": "bts:ResearchScientist" + "@id": "bts:NormalizedCounts" }, { - "@id": "bts:Other" + "@id": "bts:ScaledCounts" }, { - "@id": "bts:Unknown" + "@id": "bts:BatchCorrectedCounts" } ], - "sms:displayName": "Histology Assessment By", + "sms:displayName": "Matrix Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LinkedMatrices", + "@type": "rdfs:Class", + "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", + "rdfs:label": "LinkedMatrices", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Linked Matrices", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentMedium", + "@id": "bts:BiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11274,27 +11306,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Digital" + "@id": "bts:TissueBiospecimenType" }, { - "@id": "bts:Microscope" + "@id": "bts:BloodBiospecimenType" }, { - "@id": "bts:Other" + "@id": "bts:AnalyteBiospecimenType" }, { - "@id": "bts:Unknown" + "@id": "bts:MouthRinseBiospecimenType" + }, + { + "@id": "bts:StoolBiospecimenType" + }, + { + "@id": "bts:UrineBiospecimenType" + }, + { + "@id": "bts:AscitesBiospecimenType" + }, + { + "@id": "bts:SputumBiospecimenType" + }, + { + "@id": "bts:FluidsBiospecimenType" + }, + { + "@id": "bts:BoneMarrowBiospecimenType" + }, + { + "@id": "bts:CellsBiospecimenType" } ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TumorInfiltratingLymphocytes", + "@id": "bts:AnalyteBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:comment": "A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteBiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11303,15 +11356,41 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", + "sms:displayName": "Analyte Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:AnalyteType" + }, + { + "@id": "bts:FixationDuration" + }, + { + "@id": "bts:SlideChargeType" + }, + { + "@id": "bts:SectionThicknessValue" + }, + { + "@id": "bts:SectioningDaysfromIndex" + }, + { + "@id": "bts:ShippingConditionType" + }, + { + "@id": "bts:IschemicTime" + }, + { + "@id": "bts:IschemicTemperature" + } + ], "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:TissueBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "Tissue biospecimen", + "rdfs:label": "TissueBiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11320,35 +11399,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Tissue Biospecimen Type", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" + "@id": "bts:IschemicTime" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:IschemicTemperature" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:SpecimenLaterality" }, { - "@id": "bts:CarcinomainSitu" + "@id": "bts:PortionWeight" }, { - "@id": "bts:Unknown" + "@id": "bts:TotalVolume" + }, + { + "@id": "bts:TumorTissueType" + }, + { + "@id": "bts:HistologicMorphologyCode" + }, + { + "@id": "bts:PreservationMethod" } ], - "sms:displayName": "Degree of Dysplasia", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DysplasiaFraction", + "@id": "bts:BoneMarrowBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", + "rdfs:comment": "Bone Marrow biospecimen", + "rdfs:label": "BoneMarrowBiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11357,32 +11445,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dysplasia Fraction", + "sms:displayName": "Bone Marrow Biospecimen Type", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberProliferatingCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Biospecimen" + "@id": "bts:IschemicTime" + }, + { + "@id": "bts:IschemicTemperature" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:SpecimenLaterality" + }, + { + "@id": "bts:PortionWeight" + }, + { + "@id": "bts:TotalVolume" + }, + { + "@id": "bts:TumorTissueType" + }, + { + "@id": "bts:HistologicMorphologyCode" + }, + { + "@id": "bts:PreservationMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number Proliferating Cells", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:UrineBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "Urine biospecimen", + "rdfs:label": "UrineBiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11391,15 +11491,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", + "sms:displayName": "Urine Biospecimen Type", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentGranulocyteInfiltration", + "sms:requiresDependency": [ + { + "@id": "bts:IschemicTime" + }, + { + "@id": "bts:IschemicTemperature" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:SpecimenLaterality" + }, + { + "@id": "bts:PortionWeight" + }, + { + "@id": "bts:TotalVolume" + }, + { + "@id": "bts:TumorTissueType" + }, + { + "@id": "bts:HistologicMorphologyCode" + }, + { + "@id": "bts:PreservationMethod" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:BloodBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", + "rdfs:comment": "Blood biospecimen", + "rdfs:label": "BloodBiospecimenType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11408,15 +11537,20 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Granulocyte Infiltration", + "sms:displayName": "Blood Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ShippingConditionType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:TimepointLabel", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label": "TimepointLabel", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11425,15 +11559,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", - "sms:required": "sms:false", + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:CollectionDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained.", + "rdfs:label": "CollectionDaysfromIndex", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11442,32 +11576,32 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", - "sms:required": "sms:false", + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentMonocyteInfiltration", + "@id": "bts:ProtocolLink", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:InformationContentEntity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Monocyte Infiltration", - "sms:required": "sms:false", + "sms:displayName": "Protocol Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentNecrosis", + "@id": "bts:AdjacentBiospecimenIDs", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11476,15 +11610,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Necrosis", + "sms:displayName": "Adjacent Biospecimen IDs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:MountingMedium", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11493,15 +11627,44 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Aqueouswaterbased" + }, + { + "@id": "bts:Non-AqueousSolventbased" + }, + { + "@id": "bts:Xylene" + }, + { + "@id": "bts:Toluene" + }, + { + "@id": "bts:AntifadewithDAPI" + }, + { + "@id": "bts:AntifadewithoutDAPI" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mounting Medium", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:AnalyteType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11510,15 +11673,41 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:CfDNAAnalyte" + }, + { + "@id": "bts:DNAAnalyte" + }, + { + "@id": "bts:RNAAnalyte" + }, + { + "@id": "bts:TotalRNAAnalyte" + }, + { + "@id": "bts:TissueBlockAnalyte" + }, + { + "@id": "bts:TissueSectionAnalyte" + }, + { + "@id": "bts:PBMCsorPlasmaorSerumAnalyte" + }, + { + "@id": "bts:CDNALibrariesAnalyte" + } + ], + "sms:displayName": "Analyte Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:AcquisitionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11527,15 +11716,53 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Autopsy" + }, + { + "@id": "bts:Biopsy" + }, + { + "@id": "bts:FineNeedleAspirate" + }, + { + "@id": "bts:SurgicalResection" + }, + { + "@id": "bts:PunchBiopsy" + }, + { + "@id": "bts:ShaveBiopsy" + }, + { + "@id": "bts:Excision" + }, + { + "@id": "bts:Re-excision" + }, + { + "@id": "bts:SentinelNodeBiopsy" + }, + { + "@id": "bts:Lymphadenectomy-RegionalNodes" + }, + { + "@id": "bts:OtherAcquisitionMethod" + }, + { + "@id": "bts:Notspecified" + } + ], + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorCells", + "@id": "bts:OtherAcquisitionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", + "rdfs:comment": "A custom acquisition method", + "rdfs:label": "OtherAcquisitionMethod", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11544,15 +11771,20 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Cells", + "sms:displayName": "Other Acquisition Method", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:AcquisitionMethodOtherSpecify" + } + ], "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:AcquisitionMethodOtherSpecify", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "A custom acquisition method [Text - max length 100 characters]", + "rdfs:label": "AcquisitionMethodOtherSpecify", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11561,15 +11793,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", - "sms:required": "sms:false", + "sms:displayName": "Acquisition Method Other Specify", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:PreservationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Text term that represents the method used to preserve the sample.", + "rdfs:label": "PreservationMethod", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11580,19 +11812,55 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NuclearStain-DAPI" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:FluorescentBeads" + "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" }, { - "@id": "bts:GridSlides-Hemocytometer" + "@id": "bts:Cryopreservationindryice-deadtissue" }, { - "@id": "bts:AdhesiveMarkers" + "@id": "bts:Cryopreservationinliquidnitrogen-livecells" }, { - "@id": "bts:Other" + "@id": "bts:Formalinfixedparaffinembedded-FFPE" + }, + { + "@id": "bts:Formalinfixed-unbuffered" + }, + { + "@id": "bts:Formalinfixed-buffered" + }, + { + "@id": "bts:Fresh" + }, + { + "@id": "bts:OCT" + }, + { + "@id": "bts:SnapFrozen" + }, + { + "@id": "bts:Frozen" + }, + { + "@id": "bts:Negative80DegC" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:Freshdissociated" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsorted" + }, + { + "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + }, + { + "@id": "bts:Methacarnfixedparaffinembedded-MFPE" }, { "@id": "bts:Unknown" @@ -11601,15 +11869,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Fiducial Marker", - "sms:required": "sms:false", + "sms:displayName": "Preservation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:FixativeType", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11620,39 +11888,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Vibratome" + "@id": "bts:Acetone" }, { - "@id": "bts:Cryosectioning" + "@id": "bts:Alcohol" }, { - "@id": "bts:Tissuemolds" + "@id": "bts:Formalin" }, { - "@id": "bts:Slidingmicrotome" + "@id": "bts:Glutaraldehyde" }, { - "@id": "bts:Sectioning" + "@id": "bts:OCTmedia" + }, + { + "@id": "bts:RNAlater" + }, + { + "@id": "bts:Saline" + }, + { + "@id": "bts:95%Ethanol" + }, + { + "@id": "bts:Dimidoester" + }, + { + "@id": "bts:Carbodiimide" + }, + { + "@id": "bts:Dimethylacetamide" + }, + { + "@id": "bts:Para-benzoquinone" + }, + { + "@id": "bts:PAXgenetissue" + }, + { + "@id": "bts:TCLlysisbuffer" + }, + { + "@id": "bts:NP40lysisbuffer" + }, + { + "@id": "bts:Methacarn" + }, + { + "@id": "bts:Cryo-store" }, { "@id": "bts:Other" }, { - "@id": "bts:Unknown" + "@id": "bts:None" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "Slicing Method", - "sms:required": "sms:false", + "sms:displayName": "Fixative Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AntigenRetrieval", + "@id": "bts:FixationDuration", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ", - "rdfs:label": "AntigenRetrieval", + "rdfs:comment": "The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)", + "rdfs:label": "FixationDuration", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11661,15 +11965,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antigen Retrieval", - "sms:required": "sms:false", + "sms:displayName": "Fixation Duration", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenSlideLocation", + "@id": "bts:IschemicTime", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable", - "rdfs:label": "BiospecimenSlideLocation", + "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label": "IschemicTime", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11678,15 +11982,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen Slide Location", + "sms:displayName": "Ischemic Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StainingMarkers", + "@id": "bts:IschemicTemperature", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: text to identify proteins/ antibodies selected for staining", - "rdfs:label": "StainingMarkers", + "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", + "rdfs:label": "IschemicTemperature", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11695,32 +11999,35 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Staining Markers", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LysisBuffer", - "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:WarmIschemia" + }, + { + "@id": "bts:ColdIschemia" + }, + { + "@id": "bts:Ambientair" + }, + { + "@id": "bts:4Cwetice" + }, + { + "@id": "bts:Negative-20DegCDryIce" + }, + { + "@id": "bts:LiquidNitrogen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lysis Buffer", + "sms:displayName": "Ischemic Temperature", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofNucleicAcidIsolation", + "@id": "bts:CollectionMedia", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", "rdfs:subClassOf": [ { "@id": "bts:Biospecimen" @@ -11729,18 +12036,38 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Method of Nucleic Acid Isolation", + "schema:rangeIncludes": [ + { + "@id": "bts:DMEM" + }, + { + "@id": "bts:DMEM+Serum" + }, + { + "@id": "bts:RPMI" + }, + { + "@id": "bts:RPMI+Serum" + }, + { + "@id": "bts:PBS" + }, + { + "@id": "bts:PBS+Serum" + } + ], + "sms:displayName": "Collection Media", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ethnicity", + "@id": "bts:SpecimenLaterality", "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", + "rdfs:comment": "For tumors in paired organs, designates the side on which the specimen was obtained.", + "rdfs:label": "SpecimenLaterality", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -11748,67 +12075,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Hispanicorlatino" + "@id": "bts:Bilateral" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:Left" + }, + { + "@id": "bts:Right" }, { "@id": "bts:Unknown" }, { - "@id": "bts:Notreported" + "@id": "bts:NotReported" }, { - "@id": "bts:Notallowedtocollect" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Ethnicity", + "sms:displayName": "Specimen Laterality", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Gender", + "@id": "bts:PortionWeight", "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", + "rdfs:comment": "Numeric value that represents the sample portion weight, measured in milligrams.", + "rdfs:label": "PortionWeight", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Female" - }, - { - "@id": "bts:Male" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Unspecified" - }, + "sms:displayName": "Portion Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TotalVolume", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value for the total amount of sample or specimen, measured in milliliters (mL).", + "rdfs:label": "TotalVolume", + "rdfs:subClassOf": [ { - "@id": "bts:Notreported" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Gender", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Total Volume", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Race", + "@id": "bts:TumorTissueType", "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", + "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", + "rdfs:label": "TumorTissueType", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -11816,163 +12146,197 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:White" + "@id": "bts:AdditionalPrimary" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:Localrecurrence" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:Metastatic" }, { - "@id": "bts:Asian" + "@id": "bts:Premalignant" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:Primary" }, { - "@id": "bts:Other" + "@id": "bts:Recurrent" }, { - "@id": "bts:Unknown" + "@id": "bts:NotOtherwiseSpecified" }, { - "@id": "bts:Notreported" + "@id": "bts:Premalignant-insitu" }, { - "@id": "bts:Notallowedtocollect" + "@id": "bts:Atypia-hyperplasia" } ], - "sms:displayName": "Race", + "sms:displayName": "Tumor Tissue Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:VitalStatus", + "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", + "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alive" - }, - { - "@id": "bts:Dead" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", + "sms:displayName": "Histologic Morphology Code", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Dead", + "@id": "bts:PreinvasiveMorphology", "@type": "rdfs:Class", - "rdfs:comment": "This indicates the participant is dead and defines further required metadata", - "rdfs:label": "Dead", + "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", + "rdfs:label": "PreinvasiveMorphology", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dead", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:YearofDeath" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:CauseofDeath" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:CauseofDeathSource" + "@id": "bts:Melanomainsitu-superficialspreading" }, { - "@id": "bts:DaystoDeath" + "@id": "bts:Melanomainsitu-lentigomalignatype" + }, + { + "@id": "bts:Melanomainsitu-acral-lentiginous" + }, + { + "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + }, + { + "@id": "bts:Persistentmelanomainsitu" + }, + { + "@id": "bts:Melanomainsitu-nototherwiseclassified" + }, + { + "@id": "bts:Scar-noresidualmelanoma" + }, + { + "@id": "bts:Invasivemelanoma-superficialspreading" + }, + { + "@id": "bts:Invasivemelanoma-nodulartype" + }, + { + "@id": "bts:Invasivemelanoma-lentigomaligna" + }, + { + "@id": "bts:Invasivemelanoma-acrallentiginous" + }, + { + "@id": "bts:Invasivemelanoma-desmoplastic" + }, + { + "@id": "bts:Invasivemelanoma-nevoid" + }, + { + "@id": "bts:Invasivemelanoma-other" } ], + "sms:displayName": "Preinvasive Morphology", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoBirth", + "@id": "bts:SlideChargeType", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.", - "rdfs:label": "DaystoBirth", + "rdfs:comment": "A description of the charge on the glass slide.", + "rdfs:label": "SlideChargeType", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Birth", + "schema:rangeIncludes": [ + { + "@id": "bts:Uncharged" + }, + { + "@id": "bts:Charged" + }, + { + "@id": "bts:Coverslip" + }, + { + "@id": "bts:Notapplicable" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Slide Charge Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:YearofDeath", + "@id": "bts:SectionThicknessValue", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of the death of an individual.", - "rdfs:label": "YearofDeath", + "rdfs:comment": "Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).", + "rdfs:label": "SectionThicknessValue", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Year of Death", + "sms:displayName": "Section Thickness Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AgeatIndex", + "@id": "bts:SectioningDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "For GDC submission only - this is going to be always 0 since HTAN's index is the date of birth", - "rdfs:label": "AgeatIndex", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was sectioned after collection", + "rdfs:label": "SectioningDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Age at Index", - "sms:required": "sms:false", + "sms:displayName": "Sectioning Days from Index", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AgeIsObfuscated", + "@id": "bts:StorageMethod", "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -11980,96 +12344,80 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:True" + "@id": "bts:Ambienttemperature" }, { - "@id": "bts:False" - } - ], - "sms:displayName": "Age Is Obfuscated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:YearOfBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", - "rdfs:subClassOf": [ + "@id": "bts:Cutslide" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year Of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CauseofDeath", - "@type": "rdfs:Class", - "rdfs:comment": "The cause of death", - "rdfs:label": "CauseofDeath", - "rdfs:subClassOf": [ + "@id": "bts:Fresh" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Frozenat-70C" + }, { - "@id": "bts:CancerRelated" + "@id": "bts:Frozenat-80C" }, { - "@id": "bts:CardiovascularDisorderNOS" + "@id": "bts:Frozenat-150C" }, { - "@id": "bts:End-stageRenalDisease" + "@id": "bts:Frozeninliquidnitrogen" }, { - "@id": "bts:Infection" + "@id": "bts:Frozeninvaporphase" }, { - "@id": "bts:NotCancerRelated" + "@id": "bts:Paraffinblock" }, { - "@id": "bts:RenalDisorderNOS" + "@id": "bts:RNAlaterat4C" }, { - "@id": "bts:SpinalMuscularAtrophy" + "@id": "bts:RNAlaterat25C" }, { - "@id": "bts:SurgicalComplications" + "@id": "bts:RNAlaterat-20C" }, { - "@id": "bts:Toxicity" + "@id": "bts:Refrigeratedat4degrees" }, { - "@id": "bts:NotReported" + "@id": "bts:Refrigeratedvacuumchamber" }, { "@id": "bts:Unknown" - }, + } + ], + "sms:displayName": "Storage Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed", + "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Cause of Death", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Days from Index", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CauseofDeathSource", + "@id": "bts:ShippingConditionType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the source used to determine the patient's cause of death.", - "rdfs:label": "CauseofDeathSource", + "rdfs:comment": "Text descriptor of the shipping environment of a biospecimen.", + "rdfs:label": "ShippingConditionType", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12077,70 +12425,76 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" + "@id": "bts:AmbientPack" }, { - "@id": "bts:DeathCertificate" + "@id": "bts:ColdPack" }, { - "@id": "bts:MedicalRecord" + "@id": "bts:DryIce" }, { - "@id": "bts:SocialSecurityDeathIndex" + "@id": "bts:IcePack" }, { - "@id": "bts:Unknown" + "@id": "bts:LiquidNitrogen" }, { - "@id": "bts:NotReported" + "@id": "bts:SpecimenatRoomTemperature" + }, + { + "@id": "bts:OtherShippingEnvironment" + }, + { + "@id": "bts:NotShipped" } ], - "sms:displayName": "Cause of Death Source", - "sms:required": "sms:false", + "sms:displayName": "Shipping Condition Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DaystoDeath", + "@id": "bts:SiteDataSource", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.", - "rdfs:label": "DaystoDeath", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Death", + "sms:displayName": "Site Data Source", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OccupationDurationYears", + "@id": "bts:ProcessingLocation", "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", + "rdfs:label": "ProcessingLocation", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Occupation Duration Years", + "sms:displayName": "Processing Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrematureAtBirth", + "@id": "bts:HistologyAssessmentBy", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", + "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", + "rdfs:label": "HistologyAssessmentBy", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12148,47 +12502,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Pathologist" }, { - "@id": "bts:No" + "@id": "bts:ResearchScientist" }, { - "@id": "bts:Unknown" + "@id": "bts:Other" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Premature At Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WeeksGestationatBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weeks Gestation at Birth", + "sms:displayName": "Histology Assessment By", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipGender", + "@id": "bts:HistologyAssessmentMedium", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the gender of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipGender", + "rdfs:comment": "The method of assessment used to characterize histology", + "rdfs:label": "HistologyAssessmentMedium", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12196,50 +12533,47 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Female" - }, - { - "@id": "bts:Male" + "@id": "bts:Digital" }, { - "@id": "bts:Unknown" + "@id": "bts:Microscopy" }, { - "@id": "bts:Unspecified" + "@id": "bts:Other" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "Relationship Gender", + "sms:displayName": "Histology Assessment Medium", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipAgeatDiagnosis", + "@id": "bts:TumorInfiltratingLymphocytes", "@type": "rdfs:Class", - "rdfs:comment": "The age (in years) when the patient's relative was first diagnosed.", - "rdfs:label": "RelationshipAgeatDiagnosis", + "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", + "rdfs:label": "TumorInfiltratingLymphocytes", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Relationship Age at Diagnosis", + "sms:displayName": "Tumor Infiltrating Lymphocytes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipPrimaryDiagnosis", + "@id": "bts:DegreeofDysplasia", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipPrimaryDiagnosis", + "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", + "rdfs:label": "DegreeofDysplasia", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12247,471 +12581,257 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AdrenalGlandCancer" - }, - { - "@id": "bts:BasalCellCancer" - }, - { - "@id": "bts:BileDuctCancer" - }, - { - "@id": "bts:BladderCancer" - }, - { - "@id": "bts:BloodCancer" - }, - { - "@id": "bts:BoneCancer" - }, - { - "@id": "bts:BrainCancer" - }, - { - "@id": "bts:BreastCancer" - }, - { - "@id": "bts:Cancer" - }, - { - "@id": "bts:CervicalCancer" - }, - { - "@id": "bts:Chondrosarcoma" - }, - { - "@id": "bts:CNSCancer" - }, - { - "@id": "bts:ColorectalCancer" - }, - { - "@id": "bts:EsophagealCancer" - }, - { - "@id": "bts:EwingSarcoma" - }, - { - "@id": "bts:GallbladderCancer" - }, - { - "@id": "bts:GastricCancer" - }, - { - "@id": "bts:Glioblastoma" - }, - { - "@id": "bts:GynecologicCancer" - }, - { - "@id": "bts:HeadandNeckCancer" - }, - { - "@id": "bts:HematologicCancer" - }, - { - "@id": "bts:KaposiSarcoma" - }, - { - "@id": "bts:KidneyCancer" - }, - { - "@id": "bts:LaryngealCancer" - }, - { - "@id": "bts:Leukemia" - }, - { - "@id": "bts:LiverCancer" - }, - { - "@id": "bts:LungCancer" - }, - { - "@id": "bts:LymphNodeCancer" - }, - { - "@id": "bts:Lymphoma" - }, - { - "@id": "bts:Melanoma" - }, - { - "@id": "bts:Mesothelioma" - }, - { - "@id": "bts:MultipleMyeloma" - }, - { - "@id": "bts:Neuroblastoma" - }, - { - "@id": "bts:Osteosarcoma" - }, - { - "@id": "bts:OvarianCancer" - }, - { - "@id": "bts:PancreasCancer" - }, - { - "@id": "bts:ProstateCancer" - }, - { - "@id": "bts:RectalCancer" - }, - { - "@id": "bts:Rhabdomyosarcoma" - }, - { - "@id": "bts:Sarcoma" - }, - { - "@id": "bts:SkinCancer" - }, - { - "@id": "bts:SpleenCancer" - }, - { - "@id": "bts:TesticularCancer" - }, - { - "@id": "bts:ThroatCancer" - }, - { - "@id": "bts:ThyroidCancer" + "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" }, { - "@id": "bts:TongueCancer" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:TonsillarCancer" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:UterineCancer" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:WilmsTumor" + "@id": "bts:CarcinomainSitu" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" } ], - "sms:displayName": "Relationship Primary Diagnosis", + "sms:displayName": "Degree of Dysplasia", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipType", + "@id": "bts:DysplasiaFraction", "@type": "rdfs:Class", - "rdfs:comment": "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.", - "rdfs:label": "RelationshipType", + "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", + "rdfs:label": "DysplasiaFraction", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Relationship Type", + "sms:displayName": "Dysplasia Fraction", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelativewithCancerHistory", + "@id": "bts:NumberProliferatingCells", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", + "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", + "rdfs:label": "NumberProliferatingCells", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-CancerHistoryRelative" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Notreported" - } - ], - "sms:displayName": "Relative with Cancer History", + "sms:displayName": "Number Proliferating Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelativeswithCancerHistoryCount", + "@id": "bts:PercentEosinophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The number of relatives the patient has with a known history of cancer.", - "rdfs:label": "RelativeswithCancerHistoryCount", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", + "rdfs:label": "PercentEosinophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Relatives with Cancer History Count", + "sms:displayName": "Percent Eosinophil Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yes-CancerHistoryRelative", + "@id": "bts:PercentGranulocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Individual has a relative with cancer history", - "rdfs:label": "Yes-CancerHistoryRelative", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", + "rdfs:label": "PercentGranulocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Cancer History Relative", + "sms:displayName": "Percent Granulocyte Infiltration", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:RelativeswithCancerHistoryCount" - }, - { - "@id": "bts:RelationshipType" - }, - { - "@id": "bts:RelationshipPrimaryDiagnosis" - }, - { - "@id": "bts:RelationshipGender" - }, - { - "@id": "bts:RelationshipAgeatDiagnosis" - } - ], "sms:validationRules": [] }, { - "@id": "bts:SmokingExposure", + "@id": "bts:PercentInflamInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", + "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", + "rdfs:label": "PercentInflamInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-SmokingExposure" - }, - { - "@id": "bts:No-SmokingExposure" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", + "sms:displayName": "Percent Inflam Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yes-SmokingExposure", + "@id": "bts:PercentLymphocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Individual has been exposed to smoke; requires additional metadata", - "rdfs:label": "Yes-SmokingExposure", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", + "rdfs:label": "PercentLymphocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Smoking Exposure", + "sms:displayName": "Percent Lymphocyte Infiltration", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:YearsSmoked" - }, - { - "@id": "bts:PackYearsSmoked" - }, - { - "@id": "bts:CigarettesperDay" - }, - { - "@id": "bts:SmokingFrequency" - }, - { - "@id": "bts:TimebetweenWakingandFirstSmoke" - }, - { - "@id": "bts:TobaccoSmokingOnsetYear" - }, - { - "@id": "bts:TobaccoSmokingQuitYear" - }, - { - "@id": "bts:TobaccoSmokingStatus" - }, - { - "@id": "bts:TypeofTobaccoUsed" - } - ], "sms:validationRules": [] }, { - "@id": "bts:PackYearsSmoked", + "@id": "bts:PercentMonocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", - "rdfs:label": "PackYearsSmoked", + "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", + "rdfs:label": "PercentMonocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pack Years Smoked", - "sms:required": "sms:true", + "sms:displayName": "Percent Monocyte Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearsSmoked", + "@id": "bts:PercentNecrosis", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", - "rdfs:label": "YearsSmoked", + "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNecrosis", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Years Smoked", - "sms:required": "sms:true", + "sms:displayName": "Percent Necrosis", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholExposure", + "@id": "bts:PercentNeutrophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", + "rdfs:label": "PercentNeutrophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AlcoholExposure" - }, - { - "@id": "bts:No-AlcoholExposure" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", + "sms:displayName": "Percent Neutrophil Infiltration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yes-AlcoholExposure", + "@id": "bts:PercentNormalCells", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Yes-AlcoholExposure", + "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNormalCells", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Alcohol Exposure", + "sms:displayName": "Percent Normal Cells", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AlcoholDaysPerWeek" - }, - { - "@id": "bts:AlcoholDrinksPerDay" - }, - { - "@id": "bts:AlcoholHistory" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:PercentStromalCells", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", + "rdfs:label": "PercentStromalCells", + "rdfs:subClassOf": [ { - "@id": "bts:AlcoholIntensity" + "@id": "bts:Biospecimen" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Percent Stromal Cells", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholDaysPerWeek", + "@id": "bts:PercentTumorCells", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.", - "rdfs:label": "AlcoholDaysPerWeek", + "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", + "rdfs:label": "PercentTumorCells", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Alcohol Days Per Week", + "sms:displayName": "Percent Tumor Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholDrinksPerDay", + "@id": "bts:PercentTumorNuclei", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the average number of alcoholic beverages a person consumes per day.", - "rdfs:label": "AlcoholDrinksPerDay", + "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", + "rdfs:label": "PercentTumorNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Alcohol Drinks Per Day", + "sms:displayName": "Percent Tumor Nuclei", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholHistory", + "@id": "bts:FiducialMarker", "@type": "rdfs:Class", - "rdfs:comment": "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.", - "rdfs:label": "AlcoholHistory", + "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", + "rdfs:label": "FiducialMarker", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12719,10 +12839,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:NuclearStain-DAPI" }, { - "@id": "bts:No" + "@id": "bts:FluorescentBeads" + }, + { + "@id": "bts:GridSlides-Hemocytometer" + }, + { + "@id": "bts:AdhesiveMarkers" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -12731,18 +12860,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Alcohol History", + "sms:displayName": "Fiducial Marker", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholIntensity", + "@id": "bts:SlicingMethod", "@type": "rdfs:Class", - "rdfs:comment": "Category to describe the patient's current level of alcohol use as self-reported by the patient.", - "rdfs:label": "AlcoholIntensity", + "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", + "rdfs:label": "SlicingMethod", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -12750,19 +12879,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Drinker" + "@id": "bts:Vibratome" }, { - "@id": "bts:HeavyDrinker" + "@id": "bts:Cryosectioning" }, { - "@id": "bts:LifelongNon-Drinker" + "@id": "bts:Tissuemolds" }, { - "@id": "bts:Non-Drinker" + "@id": "bts:Slidingmicrotome" }, { - "@id": "bts:OccasionalDrinker" + "@id": "bts:Sectioning" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -12771,94 +12903,137 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Alcohol Intensity", + "sms:displayName": "Slicing Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AsbestosExposure", + "@id": "bts:AntigenRetrieval", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", + "rdfs:comment": "Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ", + "rdfs:label": "AntigenRetrieval", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Antigen Retrieval", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenSlideLocation", + "@type": "rdfs:Class", + "rdfs:comment": "Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable", + "rdfs:label": "BiospecimenSlideLocation", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Asbestos Exposure", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Biospecimen Slide Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CigarettesperDay", + "@id": "bts:StainingMarkers", "@type": "rdfs:Class", - "rdfs:comment": "The average number of cigarettes smoked per day.", - "rdfs:label": "CigarettesperDay", + "rdfs:comment": "Imaging specific: text to identify proteins/ antibodies selected for staining", + "rdfs:label": "StainingMarkers", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cigarettes per Day", + "sms:displayName": "Staining Markers", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CoalDustExposure", + "@id": "bts:LysisBuffer", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", + "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", + "rdfs:label": "LysisBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Lysis Buffer", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MethodofNucleicAcidIsolation", + "@type": "rdfs:Class", + "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", + "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:subClassOf": [ { - "@id": "bts:Yes" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Method of Nucleic Acid Isolation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:StartDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:No" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Patient" } ], - "sms:displayName": "Coal Dust Exposure", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@id": "bts:Ethnicity", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -12866,27 +13041,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Hispanicorlatino" }, { - "@id": "bts:No" + "@id": "bts:Nothispanicorlatino" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" } ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", - "sms:required": "sms:false", + "sms:displayName": "Ethnicity", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RadonExposure", + "@id": "bts:Gender", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -12894,30 +13075,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Female" }, { - "@id": "bts:No" + "@id": "bts:Male" }, { "@id": "bts:Unknown" }, + { + "@id": "bts:Unspecified" + }, { "@id": "bts:NotReported" } ], - "sms:displayName": "Radon Exposure", - "sms:required": "sms:false", + "sms:displayName": "Gender", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RespirableCrystallineSilicaExposure", + "@id": "bts:Race", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -12925,27 +13109,45 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:White" }, { - "@id": "bts:No" + "@id": "bts:Americanindianoralaskanative" + }, + { + "@id": "bts:Blackorafricanamerican" + }, + { + "@id": "bts:Asian" + }, + { + "@id": "bts:Nativehawaiianorotherpacificislander" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" } ], - "sms:displayName": "Respirable Crystalline Silica Exposure", - "sms:required": "sms:false", + "sms:displayName": "Race", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SmokingFrequency", + "@id": "bts:VitalStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", - "rdfs:label": "SmokingFrequency", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -12953,95 +13155,95 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Everyday" + "@id": "bts:Alive" }, { - "@id": "bts:Somedays" + "@id": "bts:Dead" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Smoking Frequency", - "sms:required": "sms:false", + "sms:displayName": "Vital Status", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TimeBetweenWakingandFirstSmoke", + "@id": "bts:Dead", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.", - "rdfs:label": "TimeBetweenWakingandFirstSmoke", + "rdfs:comment": "This indicates the participant is dead and defines further required metadata", + "rdfs:label": "Dead", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Within5Minutes" - }, + "sms:displayName": "Dead", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:6-30Minutes" + "@id": "bts:YearofDeath" }, { - "@id": "bts:31-60Minutes" + "@id": "bts:CauseofDeath" }, { - "@id": "bts:After60Minutes" + "@id": "bts:CauseofDeathSource" }, { - "@id": "bts:Unknown" + "@id": "bts:DaystoDeath" } ], - "sms:displayName": "Time Between Waking and First Smoke", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TobaccoSmokingOnsetYear", + "@id": "bts:DaystoBirth", "@type": "rdfs:Class", - "rdfs:comment": "The year in which the participant began smoking.", - "rdfs:label": "TobaccoSmokingOnsetYear", + "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.", + "rdfs:label": "DaystoBirth", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tobacco Smoking Onset Year", + "sms:displayName": "Days to Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TobaccoSmokingQuitYear", + "@id": "bts:YearofDeath", "@type": "rdfs:Class", - "rdfs:comment": "The year in which the participant quit smoking.", - "rdfs:label": "TobaccoSmokingQuitYear", + "rdfs:comment": "Numeric value to represent the year of the death of an individual.", + "rdfs:label": "YearofDeath", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tobacco Smoking Quit Year", - "sms:required": "sms:false", + "sms:displayName": "Year of Death", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TobaccoSmokingStatus", + "@id": "bts:CountryofResidence", "@type": "rdfs:Class", - "rdfs:comment": "Category describing current smoking status and smoking history as self-reported by a patient", - "rdfs:label": "TobaccoSmokingStatus", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -13049,5876 +13251,6467 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:LifelongNon-Smoker" + "@id": "bts:Afghanistan" }, { - "@id": "bts:CurrentSmoker" + "@id": "bts:Albania" }, { - "@id": "bts:CurrentReformedSmokerfor>15yrs" + "@id": "bts:Algeria" }, { - "@id": "bts:CurrentReformedSmokerfor15yrs" }, { - "@id": "bts:LymphocyteCountIncreased" + "@id": "bts:CurrentReformedSmokerfor15yrs", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "BileDuctCancer", + "rdfs:label": "CurrentReformedSmokerfor>15yrs", "rdfs:subClassOf": [ { - "@id": "bts:RelationshipPrimaryDiagnosis" + "@id": "bts:TobaccoSmokingStatus" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bile Duct Cancer", + "sms:displayName": "Current Reformed Smoker for > 15 yrs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BladderCancer", + "@id": "bts:CurrentReformedSmokerfor15yrs", + "@id": "bts:DuodenalInfection", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CurrentReformedSmokerfor>15yrs", + "rdfs:label": "DuodenalInfection", "rdfs:subClassOf": [ { - "@id": "bts:TobaccoSmokingStatus" + "@id": "bts:AdverseEvent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Current Reformed Smoker for > 15 yrs", + "sms:displayName": "Duodenal Infection", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CurrentReformedSmokerfor 10 and not "list" in validation_rules: + if len(req_vals) > 0 and not "list" in validation_rules: # if more than 10 values in dropdown use ONE_OF_RANGE type of validation since excel and openoffice # do not support other kinds of data validation for larger number of items (even if individual items are not that many # excel has a total number of characters limit per dropdown...) diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py index 7da27078a..8762bc5f4 100644 --- a/schematic/models/metadata.py +++ b/schematic/models/metadata.py @@ -1,8 +1,8 @@ -import pandas as pd -import networkx as nx import json -import re +import logging +import pandas as pd +import networkx as nx from jsonschema import Draft7Validator, exceptions, validate, ValidationError # allows specifying explicit variable types @@ -14,6 +14,8 @@ from schematic.schemas.explorer import SchemaExplorer from schematic.manifest.generator import ManifestGenerator from schematic.schemas.generator import SchemaGenerator +from schematic.synapse.store import SynapseStorage +from schematic.utils.df_utils import trim_commas_df class MetadataModel(object): """Metadata model wrapper around schema.org specification graph. @@ -174,9 +176,37 @@ def validateModelManifest(self, manifestPath: str, rootNode: str, jsonSchema: st jsonSchema = self.sg.get_json_schema_requirements(rootNode, rootNode + "_validation") errors = [] - - # get annotations from manifest (array of json annotations corresponding to manifest rows) - manifest = pd.read_csv(manifestPath).fillna("") + + manifest = pd.read_csv(manifestPath) # read manifest csv file as is from manifest path + + manifest = trim_commas_df(manifest).fillna("") # apply cleaning logic as part of pre-processing step + + # handler for mismatched components/data types + # throw TypeError if the value(s) in the "Component" column differ from the selected template type + if ('Component' in manifest.columns) and ( + (len(manifest['Component'].unique()) > 1) or (manifest['Component'].unique()[0] != rootNode) + ): + logging.error(f"The 'Component' column value(s) {manifest['Component'].unique()} do not match the " + f"selected template type '{rootNode}'.") + + # row indexes for all rows where 'Component' is rootNode + row_idxs = manifest.index[manifest['Component'] != rootNode].tolist() + # column index value for the 'Component' column + col_idx = manifest.columns.get_loc('Component') + # Series with index and 'Component' values from manifest + mismatched_ser = manifest.iloc[row_idxs, col_idx] + for index, component in mismatched_ser.items(): + errors.append([ + index + 2, + 'Component', + f"Component value provided is: '{component}', whereas the Template Type is: '{rootNode}'", + + # tuple of the component in the manifest and selected template type + # check: R/Reticulate cannnot handle dicts? So returning tuple + (component, rootNode) + ]) + + return errors """ diff --git a/schematic/schemas/generator.py b/schematic/schemas/generator.py index 3a813fc3e..fb0c0a326 100644 --- a/schematic/schemas/generator.py +++ b/schematic/schemas/generator.py @@ -1,7 +1,7 @@ import os import json import networkx as nx -from orderedset import OrderedSet +from ordered_set import OrderedSet from typing import Any, Dict, Optional, Text, List diff --git a/schematic/synapse/store.py b/schematic/synapse/store.py index 46b72445e..0493e0dfc 100644 --- a/schematic/synapse/store.py +++ b/schematic/synapse/store.py @@ -174,7 +174,7 @@ def getStorageDatasetsInProject(self, projectId: str) -> List[str]: foldersTable = self.storageFileviewTable[(self.storageFileviewTable["contentType"] == "dataset") & (self.storageFileviewTable["projectId"] == projectId)] areDatasets = True else: - foldersTable = self.storageFileviewTable[(self.storageFileviewTable["type"] == "folder") & (self.storageFileviewTable["projectId"] == projectId)] + foldersTable = self.storageFileviewTable[(self.storageFileviewTable["type"] == "folder") & (self.storageFileviewTable["parentId"] == projectId)] # get an array of tuples (folderId, folderName) # some folders are part of datasets; others contain datasets @@ -186,11 +186,7 @@ def getStorageDatasetsInProject(self, projectId: str) -> List[str]: datasetList = [] folderProperties = ["id", "name"] for folder in list(foldersTable[folderProperties].itertuples(index = False, name = None)): - try: - if self.syn.get(folder[0], downloadFile = False).properties["parentId"] == projectId or areDatasets: - datasetList.append(folder) - except ValueError: - print("The project id {} was not found.".format(projectId)) + datasetList.append(folder) sorted_dataset_list = sorted(datasetList, key=lambda tup: tup[0]) @@ -360,7 +356,7 @@ def get_synapse_table(self, synapse_id:str) -> Tuple[pd.DataFrame, CsvFileTable] return df, results - def associateMetadataWithFiles(self, metadataManifestPath: str, datasetId: str) -> str: + def associateMetadataWithFiles(self, metadataManifestPath: str, datasetId: str, useSchemaLabel:bool=True) -> str: """Associate metadata with files in a storage dataset already on Synapse. Upload metadataManifest in the storage dataset folder on Synapse as well. Return synapseId of the uploaded manifest file. @@ -369,8 +365,9 @@ def associateMetadataWithFiles(self, metadataManifestPath: str, datasetId: str) The manifest should include a column entityId containing synapse IDs of files/entities to be associated with metadata, if that is applicable to the dataset type. Some datasets, e.g. clinical data, do not contain file id's, but data is stored in a table: one row per item. In this case, the system creates a file on Synapse for each row in the table (e.g. patient, biospecimen) and associates the columnset data as metadata/annotations to his file. - datasetId: synapse ID of folder containing the dataset + useSchemaLabel: Default is True - use the schema label. If False, uses the display label from the schema. Attribute display names in the schema must not include characters that are not accepted by Synapse. Annotation names may only contain: letters, numbers, '_' and '.'. + Returns: synapse Id of the uploaded manifest. @@ -438,7 +435,10 @@ def associateMetadataWithFiles(self, metadataManifestPath: str, datasetId: str) # prepare metadata for Synapse storage (resolve display name into a name that Synapse annotations support (e.g no spaces) metadataSyn = {} for k, v in row.to_dict().items(): - keySyn = se.get_class_label_from_display_name(str(k)) + if useSchemaLabel: + keySyn = se.get_class_label_from_display_name(str(k)) + else: + keySyn = str(k) metadataSyn[keySyn] = v diff --git a/schematic/utils/df_utils.py b/schematic/utils/df_utils.py index 12351f9de..a6c5f0324 100644 --- a/schematic/utils/df_utils.py +++ b/schematic/utils/df_utils.py @@ -57,3 +57,18 @@ def update_df(existing_df: pd.DataFrame, new_df: pd.DataFrame, idx_key: str) -> updated_df = updated_df[existing_df.columns] return updated_df + + +def trim_commas_df(df: pd.DataFrame): + """Removes empty (trailing) columns and empty rows from pandas dataframe (manifest data). + Args: + df: pandas dataframe with data from manifest file. + Returns: + df: cleaned-up pandas dataframe. + """ + # remove all columns which have substring "Unnamed" in them + df = df.loc[:, ~df.columns.str.contains('^Unnamed')] + + # remove all completely empty rows + df = df.dropna(how='all', axis=0) + return df diff --git a/schematic/utils/schema_utils.py b/schematic/utils/schema_utils.py index 0a7e396db..ac5dd0577 100644 --- a/schematic/utils/schema_utils.py +++ b/schematic/utils/schema_utils.py @@ -11,97 +11,113 @@ def load_schema_into_networkx(schema): # TODO: clean up obsolete code #if record["@type"] == "rdfs:Class": - # creation of nodes - # adding nodes to the graph - node = {} - for (k, value) in record.items(): - if ":" in k: - key = k.split(":")[1] - node[key] = value - elif "@" in k: - key = k[1:] - node[key] = value - else: - node[k] = value - - # creation of edges - # adding edges to the graph - if "rdfs:subClassOf" in record: - parents = record["rdfs:subClassOf"] - if type(parents) == list: - for _parent in parents: - n1 = extract_name_from_uri_or_curie(_parent["@id"]) - n2 = record["rdfs:label"] - - # do not allow self-loops - if n1 != n2: - G.add_edge(n1, n2, key="parentOf") - elif type(parents) == dict: - n1 = extract_name_from_uri_or_curie(parents["@id"]) + # creation of nodes + # adding nodes to the graph + node = {} + for (k, value) in record.items(): + if ":" in k: + key = k.split(":")[1] + node[key] = value + elif "@" in k: + key = k[1:] + node[key] = value + else: + node[k] = value + + # creation of edges + # adding edges to the graph + if "rdfs:subClassOf" in record: + parents = record["rdfs:subClassOf"] + if type(parents) == list: + for _parent in parents: + n1 = extract_name_from_uri_or_curie(_parent["@id"]) n2 = record["rdfs:label"] # do not allow self-loops if n1 != n2: G.add_edge(n1, n2, key="parentOf") + elif type(parents) == dict: + n1 = extract_name_from_uri_or_curie(parents["@id"]) + n2 = record["rdfs:label"] + + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="parentOf") + + # TODO: refactor: abstract adding relationship method + if "sms:requiresDependency" in record: + dependencies = record["sms:requiresDependency"] + if type(dependencies) == list: + for _dep in dependencies: + n1 = record["rdfs:label"] + n2 = extract_name_from_uri_or_curie(_dep["@id"]) + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="requiresDependency") - # TODO: refactor: abstract adding relationship method - if "sms:requiresDependency" in record: - dependencies = record["sms:requiresDependency"] - if type(dependencies) == list: - for _dep in dependencies: - n1 = record["rdfs:label"] - n2 = extract_name_from_uri_or_curie(_dep["@id"]) - # do not allow self-loops - if n1 != n2: - G.add_edge(n1, n2, key="requiresDependency") - - if "sms:requiresComponent" in record: - components = record["sms:requiresComponent"] - if type(components) == list: - for _comp in components: - n1 = record["rdfs:label"] - n2 = extract_name_from_uri_or_curie(_comp["@id"]) - # do not allow self-loops - if n1 != n2: - G.add_edge(n1, n2, key="requiresComponent") - - if "schema:rangeIncludes" in record: - range_nodes = record["schema:rangeIncludes"] - if type(range_nodes) == list: - for _range_node in range_nodes: - n1 = record["rdfs:label"] - n2 = extract_name_from_uri_or_curie(_range_node["@id"]) - # do not allow self-loops - if n1 != n2: - G.add_edge(n1, n2, key="rangeValue") - elif type(range_nodes) == dict: + if "sms:requiresComponent" in record: + components = record["sms:requiresComponent"] + if type(components) == list: + for _comp in components: + n1 = record["rdfs:label"] + n2 = extract_name_from_uri_or_curie(_comp["@id"]) + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="requiresComponent") + + if "schema:rangeIncludes" in record: + range_nodes = record["schema:rangeIncludes"] + if type(range_nodes) == list: + for _range_node in range_nodes: n1 = record["rdfs:label"] - n2 = extract_name_from_uri_or_curie(range_nodes["@id"]) + n2 = extract_name_from_uri_or_curie(_range_node["@id"]) # do not allow self-loops if n1 != n2: G.add_edge(n1, n2, key="rangeValue") - - # check schema generator (JSON validation schema gen) - if "requiresChildAsValue" in node and node["requiresChildAsValue"]["@id"] == "sms:True": - node["requiresChildAsValue"] = True - - if "required" in node: - if "sms:true" == record["sms:required"]: - node["required"] = True - else: - node["required"] = False - - # not sure if this is required? - if "sms:validationRules" in record: - node["validationRules"] = record["sms:validationRules"] + elif type(range_nodes) == dict: + n1 = record["rdfs:label"] + n2 = extract_name_from_uri_or_curie(range_nodes["@id"]) + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="rangeValue") + + if "schema:domainIncludes" in record: + domain_nodes = record["schema:domainIncludes"] + if type(domain_nodes) == list: + for _domain_node in domain_nodes: + n1 = extract_name_from_uri_or_curie(_domain_node["@id"]) + n2 = record["rdfs:label"] + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="domainValue") + elif type(domain_nodes) == dict: + n1 = extract_name_from_uri_or_curie(domain_nodes["@id"]) + n2 = record["rdfs:label"] + # do not allow self-loops + if n1 != n2: + G.add_edge(n1, n2, key="domainValue") + + # check schema generator (JSON validation schema gen) + if "requiresChildAsValue" in node and node["requiresChildAsValue"]["@id"] == "sms:True": + node["requiresChildAsValue"] = True + + if "required" in node: + if "sms:true" == record["sms:required"]: + node["required"] = True else: - node["validationRules"] = [] + node["required"] = False + + # not sure if this is required? + if "sms:validationRules" in record: + node["validationRules"] = record["sms:validationRules"] + else: + node["validationRules"] = [] - node['uri'] = record["@id"] - node['description'] = record["rdfs:comment"] - G.add_node(record['rdfs:label'], **node) - #print(node) - #print(G.nodes()) + node['uri'] = record["@id"] + node['description'] = record["rdfs:comment"] + G.add_node(record['rdfs:label'], **node) + #print(node) + #print(G.nodes()) return G @@ -213,4 +229,4 @@ def replace_node_in_schema(schema: nx.MultiDiGraph, class_add_mod: dict) -> None def export_schema(schema, file_path): with open(file_path, 'w') as f: - json.dump(schema, f, sort_keys = True, indent = 4, ensure_ascii = False) + json.dump(schema, f, sort_keys = True, indent = 4, ensure_ascii = False) \ No newline at end of file diff --git a/schematic/version.py b/schematic/version.py index 2a8eae68b..71d6f5c2f 100644 --- a/schematic/version.py +++ b/schematic/version.py @@ -1 +1 @@ -__version__ = '0.1.11' \ No newline at end of file +__version__ = '0.1.12' \ No newline at end of file diff --git a/setup.py b/setup.py index f02aeeb32..60d99f1c6 100644 --- a/setup.py +++ b/setup.py @@ -27,10 +27,21 @@ packages=find_packages(include=['schematic', 'schematic.*']), python_requires='>=3.0', install_requires=[ - 'networkx>=2.4', 'rdflib==4.2.2', 'tabletext==0.1', 'graphviz==0.8.4', - 'jsonschema==3.2.0', 'fastjsonschema==2.14.4', 'orderedset==2.0.1', - 'google-api-python-client==1.7.9', 'google-auth-httplib2==0.0.3', 'google-auth-oauthlib==0.4.0', - 'pandas', 'pygsheets>=2.0.1', 'inflection==0.3.1', 'synapseclient==2.1.0', 'setuptools>=41.2.0', + 'networkx>=2.4', + 'rdflib==4.2.2', + 'tabletext==0.1', + 'graphviz==0.8.4', + 'jsonschema==3.2.0', + 'fastjsonschema==2.14.4', + 'ordered-set==*', + 'google-api-python-client==1.7.9', + 'google-auth-httplib2==0.0.3', + 'google-auth-oauthlib==0.4.0', + 'pandas', + 'pygsheets>=2.0.1', + 'inflection==0.3.1', + 'synapseclient==2.1.0', + 'setuptools>=41.2.0', 'pyyaml==5.3.1' ] ) \ No newline at end of file