From b60d1e00732a4c937a9b55718dc2b92242be94f9 Mon Sep 17 00:00:00 2001 From: StellaEggels Date: Thu, 5 Sep 2024 10:49:54 +0200 Subject: [PATCH] update dpbo --- DPBO.owl | 2273 ++++++++++++++++++++++++++++-------------------------- dpbo.obo | 57 ++ 2 files changed, 1243 insertions(+), 1087 deletions(-) diff --git a/DPBO.owl b/DPBO.owl index a9ebb91..eb3cca1 100644 --- a/DPBO.owl +++ b/DPBO.owl @@ -1,19 +1,19 @@ - - - + + https://orcid.org/0000-0001-9021-3197 https://orcid.org/0000-0003-1476-2121 DataPLANT Biology Ontology @@ -106,33 +106,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -732,7 +732,7 @@ - + DNA or deoxyribonucleic acid is the genetic material in all the living things, and some viruses. It is a polymer of nucleotides, with a backbone made of deoxyribose sugar and phosphate groups joined together by ester bonds. DPBO BAO:0000269 @@ -744,7 +744,7 @@ - + DNA that is linear and not circular. Examples of linear DNA include synthetic oligonucleotide, restriction endonuclease digestion product, polymerase chain reaction product, mechanically sheared genomic DNA, etc. DPBO BAO:0000316 @@ -986,7 +986,7 @@ - + biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. DPBO CHEBI:36080 @@ -1045,7 +1045,7 @@ drying - + @@ -1104,13 +1104,13 @@ LSE - + SPE - + @@ -1320,7 +1320,7 @@ - + Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. methoxyamination derivatization DPBO @@ -1342,7 +1342,7 @@ - + Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. TMS derivatisation trimethylsilyl derivatization @@ -1384,10 +1384,10 @@ - + - - + + A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted DPBO Experimental Randomisation @@ -1397,9 +1397,9 @@ - + - + The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478 DPBO DPBO:0000002 @@ -1409,9 +1409,9 @@ - + - + The version of the read alignment software (DPBO:0000002). DPBO DPBO:0000003 @@ -1420,9 +1420,9 @@ - + - + The parameters of the read alignment software (DPBO:0000002). DPBO DPBO:0000004 @@ -1431,9 +1431,9 @@ - + - + This term defines the relative humidity of the air at daytime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) DPBO DPBO:0000005 @@ -1443,9 +1443,9 @@ - + - + This term defines the relative humidity of the air at nighttime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) DPBO DPBO:0000006 @@ -1455,9 +1455,9 @@ - + - + This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) DPBO DPBO:0000007 @@ -1467,9 +1467,9 @@ - + - + This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) DPBO DPBO:0000008 @@ -1479,9 +1479,9 @@ - + - + Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ” DPBO DPBO:0000009 @@ -1490,9 +1490,9 @@ - + - + Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.” DPBO DPBO:0000010 @@ -1502,9 +1502,9 @@ - + - + The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample” DPBO DPBO:0000011 @@ -1514,9 +1514,9 @@ - + - + The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.” DPBO DPBO:0000012 @@ -1526,9 +1526,9 @@ - + - + The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.” DPBO DPBO:0000013 @@ -1538,9 +1538,9 @@ - + - + The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.” DPBO DPBO:0000014 @@ -1550,9 +1550,9 @@ - + - + Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment” DPBO DPBO:0000015 @@ -1562,9 +1562,9 @@ - + - + Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)” DPBO DPBO:0000016 @@ -1574,9 +1574,9 @@ - + - + The name of the software used for base-calling. DPBO DPBO:0000017 @@ -1586,9 +1586,9 @@ - + - + The version of the base-calling software (DPBO:0000017).” DPBO DPBO:0000018 @@ -1598,9 +1598,9 @@ - + - + The parameters of the base-calling software (DPBO:0000017).” DPBO DPBO:0000019 @@ -1610,9 +1610,9 @@ - + - + Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)” DPBO DPBO:0000020 @@ -1622,9 +1622,9 @@ - + - + File format of the raw data file” DPBO DPBO:0000021 @@ -1634,9 +1634,9 @@ - + - + Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum DPBO DPBO:0000022 @@ -1645,9 +1645,9 @@ - + - + Name of the software applied for data filtering DPBO DPBO:0000023 @@ -1657,9 +1657,9 @@ - + - + The version of the data filtering software (DPBO:0000023).” DPBO DPBO:0000024 @@ -1669,9 +1669,9 @@ - + - + The parameters of the data filtering software (DPBO:0000023).” DPBO DPBO:0000025 @@ -1681,9 +1681,9 @@ - + - + Name and version of the genome reference.” MS:1002644 NCIT:C16438 @@ -1695,9 +1695,9 @@ - + - + File format of the processed data file” DPBO DPBO:0000027 @@ -1707,9 +1707,9 @@ - + - + Name of the processed data file” DPBO DPBO:0000028 @@ -1719,9 +1719,9 @@ - + - + Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum DPBO DPBO:0000029 @@ -1730,9 +1730,9 @@ - + - + Publication reference for isolation and growth condition specifications of the organism/material DPBO DPBO:0000030 @@ -1742,9 +1742,9 @@ - + - + The haploid chromosome count of a eukaryote DPBO DPBO:0000031 @@ -1753,9 +1753,9 @@ - + - + The estimated size of the genome prior to sequencing DPBO DPBO:0000032 @@ -1765,9 +1765,9 @@ - + - + A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). DPBO DPBO:0000033 @@ -1777,9 +1777,9 @@ - + - + Health status of the plant at the time of sample collection DPBO DPBO:0000034 @@ -1788,10 +1788,10 @@ - + - - + + Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. DPBO DPBO:0000035 @@ -1801,10 +1801,10 @@ - + - - + + The method used to select for or against, enrich, or screen the material being sequenced. GENEPIO:0001940 DPBO @@ -1816,9 +1816,9 @@ - + - + Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line DPBO DPBO:0000037 @@ -1827,9 +1827,9 @@ - + - + pH measurement of the culture rooting medium DPBO DPBO:0000038 @@ -1839,9 +1839,9 @@ - + - + Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L) DPBO DPBO:0000039 @@ -1851,9 +1851,9 @@ - + - + Model name or number of next generation sequencing instrument EFO:0003739 DPBO @@ -1863,9 +1863,9 @@ - + - + The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day) PECO:0007078 ZECO:0000147 @@ -1879,9 +1879,9 @@ - + - + Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2') MS:1001809 DPBO @@ -1891,9 +1891,9 @@ - + - + Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection) DPBO DPBO:0000043 @@ -1902,9 +1902,9 @@ - + - + Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile) DPBO DPBO:0000044 @@ -1913,9 +1913,9 @@ - + - + Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control) DPBO DPBO:0000045 @@ -1924,9 +1924,9 @@ - + - + Company name, and instrument name or serial number of the chromatography instrument DPBO DPBO:0000046 @@ -1935,9 +1935,9 @@ - + - + Company name, and name or serial number of the chromatography autosampler model DPBO DPBO:0000047 @@ -1946,9 +1946,9 @@ - + - + Company name, and name or serial number of the chromatography column DPBO DPBO:0000048 @@ -1957,9 +1957,9 @@ - + - + Company name, and name or serial number of the chromatography guard column DPBO DPBO:0000049 @@ -1968,9 +1968,9 @@ - + - + Chemical buffer, solvent or solution used to extract a component from a biological sample. DPBO DPBO:0000050 @@ -1980,9 +1980,9 @@ - + - + Volume of the buffer (DPBO:0000050) used during extraction. DPBO DPBO:0000051 @@ -1992,9 +1992,9 @@ - + - + Derivatization for metabolomics mass spectrometry. CHMO:0001485 @@ -2005,9 +2005,9 @@ - + - + Type of chromatography column (DPBO:0000048) CHMO:0001000 DPBO @@ -2017,9 +2017,9 @@ - + - + Method or kit that was used to extract DNA or RNA DPBO DPBO:0000054 @@ -2029,9 +2029,9 @@ - + - + Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L) DPBO DPBO:0000055 @@ -2041,9 +2041,9 @@ - + - + Amount of DNA (microgram) used as starting material for library construction DPBO DPBO:0000056 @@ -2053,9 +2053,9 @@ - + - + Name of the company that produces next generation sequencing instruments GENEPIO:0000071 DPBO @@ -2065,9 +2065,9 @@ - + - + Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L) DPBO DPBO:0000058 @@ -2077,9 +2077,9 @@ - + - + Strategy that was used to assemble reads into contigs GENEPIO:0000090 DPBO @@ -2090,9 +2090,9 @@ - + - + The version of the sequence assembly algorithm (OBI_0001522) DPBO DPBO:0000060 @@ -2102,9 +2102,9 @@ - + - + Status of the genome sequence that is uploaded DPBO DPBO:0000061 @@ -2114,9 +2114,9 @@ - + - + Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis. DPBO DPBO:0000062 @@ -2125,9 +2125,9 @@ - + - + The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345. NCIT:C175890 DPBO @@ -2138,9 +2138,9 @@ - + - + Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly NCIT:C70713 DPBO @@ -2151,9 +2151,9 @@ - + - + Source of organic carbon in the culture rooting medium; e.g. sucrose DPBO DPBO:0000065 @@ -2163,9 +2163,9 @@ - + - + Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA DPBO DPBO:0000066 @@ -2175,9 +2175,9 @@ - + - + Specification of the solidifying agent in the culture rooting medium; e.g. agar DPBO DPBO:0000067 @@ -2187,10 +2187,10 @@ - + - - + + A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ] NCIT:C16403 DPBO @@ -2202,10 +2202,10 @@ - + - - + + The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI] DPBO DPBO:0000069 @@ -2216,9 +2216,9 @@ - + - + Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence. DPBO DPBO:0000070 @@ -2228,9 +2228,9 @@ - + - + Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence. DPBO DPBO:0000071 @@ -2240,9 +2240,9 @@ - + - + Stage of plant disease at the time of sampling. DPBO DPBO:0000072 @@ -2251,9 +2251,9 @@ - + - + Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601 NCIT:C16977 DPBO @@ -2264,9 +2264,9 @@ - + - + Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps' NCIT:C16632 DPBO @@ -2277,9 +2277,9 @@ - + - + Incomplete promoter with its 5' end upstream of the submitted sequence. DPBO DPBO:0000075 @@ -2289,9 +2289,9 @@ - + - + Incomplete promoter with its 3' end downstream of the submitted sequence. DPBO DPBO:0000076 @@ -2301,9 +2301,9 @@ - + - + metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title DPBO DPBO:0000077 @@ -2313,9 +2313,9 @@ - + - + BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]! NCIT:C175889 DPBO @@ -2326,9 +2326,9 @@ - + - + Coordinate of the 5' end of the promoter within the submitted sequence. DPBO DPBO:0000079 @@ -2338,9 +2338,9 @@ - + - + Coordinate of the 3' end of the promoter within the submitted sequence. DPBO DPBO:0000080 @@ -2350,9 +2350,9 @@ - + - + Settings of the gradient used during (e.g. liquid, gas or ion) chromatography DPBO DPBO:0000081 @@ -2361,9 +2361,9 @@ - + - + Method used for rRNA depletion during construction of the sequencing library. DPBO DPBO:0000082 @@ -2373,10 +2373,10 @@ - + - - + + Relative centrifugal force (RCF) is the amount of force applied to a sample when using a centrifuge. It is dependant on the speed of the centrifuge rotation as well as the distance of the sample from the center of rotation. RCF @@ -2388,9 +2388,9 @@ - + - + G-force is the force acting on an object as a result of acceleration or gravity. DPBO @@ -2400,9 +2400,9 @@ - + - + The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2. g0 @@ -2415,10 +2415,10 @@ - + - - + + A library layout which describes that only one end of the library fragment is sequenced GEO_RNASEQ RAW FILES_single or paired-end @@ -2430,9 +2430,9 @@ - + - + Short unique identifier for the sequencing library Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -2443,9 +2443,9 @@ - + - + A climatic chamber used for growing plants under controlled environmental conditions. DPBO @@ -2455,10 +2455,10 @@ - + - - + + Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. DPBO DPBO:0000089 @@ -2467,10 +2467,10 @@ - + - - + + The core tidyverse includes the packages that you’re likely to use in everyday data analyses. As of tidyverse 1.3.0, the following packages are included in the core tidyverse: ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats. DPBO DPBO:0000090 @@ -2479,10 +2479,10 @@ - + - - + + A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries. DPBO DPBO:0000091 @@ -2491,10 +2491,10 @@ - + - - + + Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. DPBO DPBO:0000092 @@ -2503,10 +2503,10 @@ - + - - + + Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization. DPBO DPBO:0000093 @@ -2515,10 +2515,10 @@ - + - - + + A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc. DPBO DPBO:0000094 @@ -2527,9 +2527,9 @@ - + - + Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality. DPBO DPBO:0000095 @@ -2538,9 +2538,9 @@ - + - + The version of the software package or library that was used in the analysis. DPBO DPBO:0000096 @@ -2549,9 +2549,9 @@ - + - + Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF). DPBO DPBO:0000097 @@ -2561,9 +2561,9 @@ - + - + Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis. DPBO DPBO:0000098 @@ -2573,9 +2573,9 @@ - + - + Concentration of an antibiotic that was added to a growth medium. DPBO DPBO:0000099 @@ -2584,9 +2584,9 @@ - + - + Duration of a bacterial cultivation. DPBO DPBO:0000100 @@ -2595,9 +2595,9 @@ - + - + The OD600 that was used to inoculate a bacterial culture. DPBO DPBO:0000101 @@ -2606,9 +2606,9 @@ - + - + Method that was used to harvest bacterial cells. DPBO DPBO:0000102 @@ -2617,9 +2617,9 @@ - + - + Constant percentage of dissolved oxygen in a culture medium. DPBO DPBO:0000103 @@ -2628,9 +2628,9 @@ - + - + An experiment that is used to grow bacterial cells under oxygen limitation conditions. DPBO @@ -2640,9 +2640,9 @@ - + - + Percent of oxygen that is added to a culture medium via gassing. DPBO DPBO:0000105 @@ -2651,9 +2651,9 @@ - + - + Percent of nitrogen that is added to a culture medium via gassing. DPBO DPBO:0000106 @@ -2662,9 +2662,9 @@ - + - + An experiment that is used to grow bacterial cells under oxygen excess conditions. DPBO @@ -2674,9 +2674,9 @@ - + - + A measurement that is used to identify transcriptional binding sites in a genome. DPBO DPBO:0000108 @@ -2685,9 +2685,9 @@ - + - + Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata. Stella Eggels DPBO @@ -2697,9 +2697,9 @@ - + - + Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation. Stella Eggels DPBO @@ -2709,9 +2709,9 @@ - + - + A word, term or short statement that clarifies the cause, context and/or consequence of another entity. DPBO DPBO:0000111 @@ -2720,9 +2720,9 @@ - + - + Multicellular structure comprising similar cells with some specific function. DPBO DPBO:0000112 @@ -2732,9 +2732,9 @@ - + - + The vertical distance below local surface at which the sample was taken. For sediment or soil samples depth is measured from sediment or soil surface, respectively. DPBO DPBO:0000113 @@ -2744,9 +2744,9 @@ - + - + Number of injections of a sample into a mass spectrometer or chromatograph. DPBO DPBO:0000114 @@ -2755,9 +2755,9 @@ - + - + Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. ENVO:01000813 DPBO @@ -2768,9 +2768,9 @@ - + - + Unique identificator for a study. This is used to link experiments to the study. DPBO DPBO:0002000 @@ -2779,9 +2779,9 @@ - + - + Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication. DPBO DPBO:0002001 @@ -2790,9 +2790,9 @@ - + - + Title of the study as would be used in a publication. DPBO DPBO:0002002 @@ -2801,9 +2801,9 @@ - + - + Name of the project within which the experiment was organized. DPBO DPBO:0002005 @@ -2812,9 +2812,9 @@ - + - + Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid. DPBO DPBO:0002006 @@ -2823,9 +2823,9 @@ - + - + Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium DPBO DPBO:0002007 @@ -2834,9 +2834,9 @@ - + - + The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. ENVO:00010483 DPBO @@ -2847,9 +2847,9 @@ - + - + MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported DPBO DPBO:0002010 @@ -2858,10 +2858,10 @@ - + - - + + The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. 2022-02-02T08:33:08Z @@ -2875,10 +2875,10 @@ - + - - + + The BioSample database contains descriptions of biological source materials used in experimental assays. 2022-02-02T08:33:08Z @@ -2891,10 +2891,10 @@ - + - - + + A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. 2022-02-02T08:58:37Z @@ -2908,10 +2908,10 @@ - + - - + + GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis. 2022-02-02T08:59:49Z @@ -2925,10 +2925,10 @@ - + - - + + Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. 2022-02-02T09:02:27Z @@ -2941,10 +2941,10 @@ - + - - + + Plant Genomics & Phenomics Research Data Repository 2022-02-02T09:03:35Z @@ -2957,10 +2957,10 @@ - + - - + + The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR. 2022-02-02T09:04:46Z @@ -2973,9 +2973,9 @@ - + - + The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay. Dominik Brilhaus @@ -2987,10 +2987,10 @@ - + - - + + Fresh (non-dry) biosource material Dominik Brilhaus @@ -3002,10 +3002,10 @@ - + - - + + Dry biosource material Dominik Brilhaus @@ -3017,9 +3017,9 @@ - + - + Internal standard added in known amount to an analytical sample Dominik Brilhaus @@ -3031,9 +3031,9 @@ - + - + Volume taken from the sample to be assayed (measured). Dominik Brilhaus @@ -3044,9 +3044,9 @@ - + - + Volume of the sample injected during chromatography Dominik Brilhaus @@ -3058,9 +3058,9 @@ - + - + This is to specify split / splitless runs during e.g. gas-chromatography. Dominik Brilhaus @@ -3072,10 +3072,10 @@ - + - - + + placeholder def of RNA-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3088,9 +3088,9 @@ - + - + A library strategy that can identify and quantify the microRNA sequences present in a biological sample. GEO_RNASEQ @@ -3103,9 +3103,9 @@ - + - + A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample. GEO_RNASEQ @@ -3118,9 +3118,9 @@ - + - + A library strategy with an additional size fractionation step after RNA-seq library preparation GEO_RNASEQ @@ -3133,9 +3133,9 @@ - + - + A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap. GEO_RNASEQ @@ -3148,9 +3148,9 @@ - + - + Rapid Amplification of cDNA Ends (RACE) is a library strategy for RNA-seq that is used to obtain the full length sequence of an RNA transcript found within a cell. RACE produces a cDNA copy of the RNA through reverse transcription which is amplified and sequenced. GEO_RNASEQ @@ -3163,10 +3163,10 @@ - + - - + + placeholder def of ssRNA-seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3179,10 +3179,10 @@ - + - - + + placeholder def of ChIP-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3195,10 +3195,10 @@ - + - - + + placeholder def of MNase-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3211,10 +3211,10 @@ - + - - + + placeholder def of MBD-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3227,10 +3227,10 @@ - + - - + + placeholder def of MRE-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3243,10 +3243,10 @@ - + - - + + placeholder def of Bisulfite-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3259,9 +3259,9 @@ - + - + A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation GEO_RNASEQ @@ -3276,10 +3276,10 @@ - + - - + + placeholder def of MeDIP-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3292,9 +3292,9 @@ - + - + A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation. GEO_RNASEQ @@ -3307,9 +3307,9 @@ - + - + A library strategy that is used to sequence transposons. GEO_RNASEQ @@ -3322,10 +3322,10 @@ - + - - + + placeholder def of FAIRE-seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3338,9 +3338,9 @@ - + - + A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment. GEO_RNASEQ @@ -3353,10 +3353,10 @@ - + - - + + placeholder def of RIP-Seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3369,10 +3369,10 @@ - + - - + + placeholder def of ATAC-seq GEO_RNASEQ PROTOCOLS_library strategy @@ -3386,10 +3386,10 @@ - + - - + + placeholder def of ChIA-PET GEO_RNASEQ PROTOCOLS_library strategy @@ -3402,10 +3402,10 @@ - + - - + + placeholder def of Hi-C GEO_RNASEQ PROTOCOLS_library strategy @@ -3418,9 +3418,9 @@ - + - + Any other possible library strategy that can be used for RNA-seq GEO_RNASEQ @@ -3433,10 +3433,10 @@ - + - - + + placeholder def of fastq GEO_RNASEQ RAW FILES_file type @@ -3449,10 +3449,10 @@ - + - - + + Binary format for storing of sequencing data GEO_RNASEQ RAW FILES_file type @@ -3464,10 +3464,10 @@ - + - - + + Illumina´s native QSEQ format GEO_RNASEQ RAW FILES_file type @@ -3478,10 +3478,10 @@ - + - - + + Illumina´s native sequencing format GEO_RNASEQ RAW FILES_file type @@ -3492,10 +3492,10 @@ - + - - + + SOLID´s native csfasta sequencing format GEO_RNASEQ RAW FILES_file type @@ -3506,10 +3506,10 @@ - + - - + + SOLI´s native quality sequencing format GEO_RNASEQ RAW FILES_file type @@ -3520,10 +3520,10 @@ - + - - + + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. GEO_RNASEQ RAW FILES_file type @@ -3535,10 +3535,10 @@ - + - - + + 454 pyrosequencing native sequencing file format GEO_RNASEQ RAW FILES_file type @@ -3549,10 +3549,10 @@ - + - - + + 454 pyrosequencing native quality sequencing file format GEO_RNASEQ RAW FILES_file type @@ -3563,10 +3563,10 @@ - + - - + + Helicos native file format GEO_RNASEQ RAW FILES_file type @@ -3577,10 +3577,10 @@ - + - - + + Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. GEO_RNASEQ RAW FILES_file type @@ -3592,10 +3592,10 @@ - + - - + + PacBio hierarchical, filesystem-like data format that can store metadata in the form of user-defined, named attributes, which are attached to groups and datasets, and representations of images and tables built up using datasets, groups and attributes. GEO_RNASEQ RAW FILES_file type @@ -3607,10 +3607,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3622,10 +3622,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3637,10 +3637,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3652,10 +3652,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3667,10 +3667,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3682,10 +3682,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3697,10 +3697,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3712,10 +3712,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3727,10 +3727,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3742,10 +3742,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3757,10 +3757,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3772,10 +3772,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3787,10 +3787,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3802,10 +3802,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3817,10 +3817,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3832,10 +3832,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3847,10 +3847,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3862,10 +3862,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3877,10 +3877,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3892,10 +3892,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3907,10 +3907,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3922,10 +3922,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3937,10 +3937,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3952,10 +3952,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3967,10 +3967,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3982,10 +3982,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -3997,10 +3997,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4012,10 +4012,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4027,10 +4027,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4042,10 +4042,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4057,10 +4057,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4072,10 +4072,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4087,10 +4087,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4102,10 +4102,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4117,10 +4117,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4130,10 +4130,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4143,10 +4143,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4156,10 +4156,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4171,10 +4171,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4186,10 +4186,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4201,10 +4201,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4214,10 +4214,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4229,10 +4229,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4244,10 +4244,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4259,10 +4259,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4274,10 +4274,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4289,10 +4289,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4304,10 +4304,10 @@ - + - - + + GEO_RNASEQ RAW FILES_instrument model DPBO @@ -4319,10 +4319,10 @@ - + - - + + placeholder def of single GEO_RNASEQ RAW FILES_single or paired-end @@ -4335,10 +4335,10 @@ - + - - + + A library layout which describes that both ends of the library fragment are sequenced GEO_RNASEQ RAW FILES_single or paired-end @@ -4350,10 +4350,10 @@ - + - - + + placeholder def of total RNA GEO_RNASEQ SAMPLES_molecule @@ -4366,10 +4366,10 @@ - + - - + + placeholder def of polyA RNA GEO_RNASEQ SAMPLES_molecule @@ -4381,10 +4381,10 @@ - + - - + + placeholder def of cytoplasmic RNA GEO_RNASEQ SAMPLES_molecule @@ -4397,10 +4397,10 @@ - + - - + + placeholder def of nuclear RNA GEO_RNASEQ SAMPLES_molecule @@ -4413,10 +4413,10 @@ - + - - + + placeholder def of genomic DNA GEO_RNASEQ SAMPLES_molecule @@ -4429,10 +4429,10 @@ - + - - + + placeholder def of protein GEO_RNASEQ SAMPLES_molecule @@ -4445,10 +4445,10 @@ - + - - + + Any other bio entity that can be characterized by high-throuput sequencing. GEO_RNASEQ SAMPLES_molecule @@ -4459,9 +4459,9 @@ - + - + Parent term to collect endpoint repositories (ER). DPBO DPBO:1000095 @@ -4471,11 +4471,11 @@ - + - - - + + + GEO (Gene Expression Omnibus) is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. DPBO DPBO:1000096 @@ -4485,10 +4485,10 @@ - + - - + + MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals. DPBO DPBO:1000097 @@ -4498,10 +4498,10 @@ - + - - + + The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets. DPBO DPBO:1000098 @@ -4511,11 +4511,11 @@ - + - - - + + + Parent term to collect terms required for RNASeq submission to GEO DPBO DPBO:1000099 @@ -4524,10 +4524,10 @@ - + - - + + Parent term to collect terms required for microarray submission to GEO DPBO DPBO:1000100 @@ -4536,10 +4536,10 @@ - + - - + + A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. OME:Well DPBO @@ -4551,9 +4551,9 @@ - + - + The number of a well in a well plate. DPBO DPBO:1000102 @@ -4562,9 +4562,9 @@ - + - + The identifier of a siRNA from a reagent library. DPBO DPBO:1000103 @@ -4573,10 +4573,10 @@ - + - - + + Unique name of a chemical compound. EDAM:data_0990 DPBO @@ -4588,10 +4588,10 @@ - + - - + + Identifier of an entry from a database of chemicals. data:1086 DPBO @@ -4603,9 +4603,9 @@ - + - + The class a compound belongs to, defined by its biological function or the chemical property. DPBO DPBO:1000106 @@ -4615,10 +4615,10 @@ - + - - + + A unique gene name within a specific repository, database, or collection. NCIT:C48664 DPBO @@ -4629,9 +4629,9 @@ - + - + The sequence of the sense strand. DPBO DPBO:1000109 @@ -4641,9 +4641,9 @@ - + - + The sequence of the antisense strand. DPBO DPBO:1000110 @@ -4653,10 +4653,10 @@ - + - - + + A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated. NCIT:C49647 DPBO @@ -4668,9 +4668,9 @@ - + - + Result of quality control. This can be: pass/fail, or other information such as: no cells DPBO DPBO:1000112 @@ -4680,9 +4680,9 @@ - + - + The label used in a microscopy assay and what it targets, separated by a colon. Each pair of labels and visualized object is separated by a semi-colon. E.g. DAPI:nuclei;TRITC:HA_Flag tagged protein. DPBO DPBO:1000113 @@ -4692,9 +4692,9 @@ - + - + The type of a high content screening experiment like RNAi screen or antibody screen. DPBO DPBO:1000114 @@ -4704,9 +4704,9 @@ - + - + Version of a reagent library used e.g. in high content screening. DPBO DPBO:1000116 @@ -4716,10 +4716,10 @@ - + - - + + A type of protein made by B lymphocytes in response to a foreign substance (antigen). Each antibody only binds to a specific antigen, helping to destroy the antigen directly or by assisting white blood cells to destroy the antigen. NCIT:C16295 DPBO @@ -4731,10 +4731,10 @@ - + - - + + A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope. NCIT:C126370 DPBO @@ -4746,9 +4746,9 @@ - + - + DPBO DPBO:1000120 "Needed for imaging templates" @@ -4757,9 +4757,9 @@ - + - + Compartment of interest in the prepared sample DPBO DPBO:1000121 @@ -4769,10 +4769,10 @@ - + - - + + The name of the software program to capture and/or process imaging data. NCIT:C175898 DPBO @@ -4784,9 +4784,9 @@ - + - + The version of the software program to capture and/or process imaging data. DPBO DPBO:1000123 @@ -4796,9 +4796,9 @@ - + - + The used settings in the software program to capture and/or process imaging data. DPBO DPBO:1000124 @@ -4808,9 +4808,9 @@ - + - + Channel the image was taken with. DPBO DPBO:1000125 @@ -4820,9 +4820,9 @@ - + - + dwc:datasetName DPBO DPBO:1000126 @@ -4832,10 +4832,10 @@ - + - - + + The name of the assay. NCIT:C178857 DPBO @@ -4846,9 +4846,9 @@ - + - + Software used for the processing of microscopy images like for adaption of contrast or stacking. DPBO DPBO:1000128 @@ -4858,9 +4858,9 @@ - + - + Software used to analyze data extracted from microscopy images. DPBO DPBO:1000129 @@ -4870,9 +4870,9 @@ - + - + Applied settings of the software used for the processing of microscopy images DPBO DPBO:1000130 @@ -4882,9 +4882,9 @@ - + - + Software used for the extraction of features from microscopy images. DPBO DPBO:1000131 @@ -4894,9 +4894,9 @@ - + - + Description of the approach to extract features from microscopy images. DPBO DPBO:1000133 @@ -4906,9 +4906,9 @@ - + - + Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it. DPBO DPBO:1000135 @@ -4918,9 +4918,9 @@ - + - + The gene annotation build the siRNAs for a high content screen library were mapped to. DPBO DPBO:1000136 @@ -4930,9 +4930,9 @@ - + - + additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype' DPBO DPBO:1000137 @@ -4942,9 +4942,9 @@ - + - + additional information why a quality control passed or failed' DPBO DPBO:1000138 @@ -4954,9 +4954,9 @@ - + - + Type of an imaging study. DPBO DPBO:1000139 @@ -4966,9 +4966,9 @@ - + - + The magnification of a microscopy image DPBO DPBO:1000140 @@ -4978,9 +4978,9 @@ - + - + The sizes along the axis of the XYZCT dimensions in a microscopy image. DPBO DPBO:1000141 @@ -4990,10 +4990,10 @@ - + - - + + The microscope's objective lens. OME:Objective DPBO @@ -5005,9 +5005,9 @@ - + - + How a sample was further prepared for microscopy. MS:1000831 DPBO @@ -5017,9 +5017,9 @@ - + - + Plant material fixation on a microscopy slide. DPBO DPBO:1000144 @@ -5029,9 +5029,9 @@ - + - + The part of an organism that has been prepared for an experiment DPBO DPBO:1000145 @@ -5041,10 +5041,10 @@ - + - - + + A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. "Fabian Haas | ORCID:0000-0002-7711-5282" EFO:0005135 @@ -5057,10 +5057,10 @@ - + - - + + A device that can be used to restrict the location of material entities over time "Fabian Haas | ORCID:0000-0002-7711-5282" OBI:0000967 @@ -5073,9 +5073,9 @@ - + - + A wide-mouthed cylindrical container made of glass or pottery and typically having a lid "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5086,9 +5086,9 @@ - + - + A flat dish, typically circular "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5099,10 +5099,10 @@ - + - - + + The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. [database_cross_reference: https://en.wikipedia.org/wiki/Contamination][database_cross_reference: https://github.com/pato-ontology/pato/issues/420] "Fabian Haas | ORCID:0000-0002-7711-5282" PATO:0015031 @@ -5114,9 +5114,9 @@ - + - + Free from other living organisms "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5127,9 +5127,9 @@ - + - + Latest laboratory cultivated the strain. Who sent the strain to your laboratory "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5140,9 +5140,9 @@ - + - + The day of the month or year as specified by a number. According to ISO 8601-1 [ISO 8601-1] please use the format YYYY-MM-DD. "Fabian Haas | ORCID:0000-0002-7711-5282" dc:date @@ -5153,10 +5153,10 @@ - + - - + + A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. [database_cross_reference: PATOC:GVG] "Fabian Haas | ORCID:0000-0002-7711-5282" PATO:0000918 @@ -5169,9 +5169,9 @@ - + - + Volume of culture medium used to grow the organism "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5182,10 +5182,10 @@ - + - - + + The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. "Fabian Haas | ORCID:0000-0002-7711-5282" EFO:0000568 @@ -5198,9 +5198,9 @@ - + - + The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source) "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5212,10 +5212,10 @@ - + - - + + A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. "Fabian Haas | ORCID:0000-0002-7711-5282" DPBO @@ -5225,7 +5225,7 @@ true - + A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. UOB:LKSR @@ -5233,9 +5233,9 @@ - + - + Nucleic acids have absorbance maxima at 260 nm. Historically, the ratio of this absorbance maximum to the absorbance at 280 nm has been used as a measure of purity in both DNA and RNA extractions. A 260/280 ratio of ~1.8 is generally accepted as pure for DNA; a ratio of ~2.0 is generally accepted as pure for RNA. "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5247,9 +5247,9 @@ - + - + The 260/230 values for pure nucleic acid are often higher than the respective 260/280 values. Expected 260/230 values are commonly in the range of 2.0–2.2 "Fabian Haas | ORCID:0000-0002-7711-5282" @@ -5261,9 +5261,9 @@ - + - + ISA-related term to identify the type of protocol (the set of procedures and rules that must be performed and when) used during the study or assay. Dominik Brilhaus DPBO @@ -5274,10 +5274,10 @@ - + - - + + A protocol that provides instructions for the growth of a biological sample. Describes the conditions, materials and procedure used to grow and/or maintain the sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0003789 @@ -5290,9 +5290,9 @@ - + - + A protocol that provides instructions for growing algae. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5303,9 +5303,9 @@ - + - + A protocol that provides instructions for growing a plant cultivar. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5316,9 +5316,9 @@ - + - + A protocol that provides instructions for growing a microbial sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5329,10 +5329,10 @@ - + - - + + A protocol that provides instructions for growing a bacterial sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5342,10 +5342,10 @@ - + - - + + A protocol that provides instructions for growing yeast. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5355,10 +5355,10 @@ - + - - + + A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0003969 @@ -5371,10 +5371,10 @@ - + - - + + A protocol that provides instructions on how a biological sample for an experiment was collected. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0005518 @@ -5387,10 +5387,10 @@ - + - - + + A protocol that details how a sample is processed or changed to prepare it for analysis. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5400,10 +5400,10 @@ - + - - + + A protocol used to obtain something of experimental interest from a sample via chemical, physical or mechanical means. Often tailored to match the starting material as well as the end goals (resulting material, quality level, etc.) of the procedure required by the following assay Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0000490 @@ -5416,10 +5416,10 @@ - + - - + + A protocol that describes how to remove and purify DNA from a sample. This requires physical and/or chemical methods in order to separate the DNA from cell membranes, proteins and other cellular components. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5431,10 +5431,10 @@ - + - - + + A protocol that describes the steps for removing and purifying DNA from a biological sample Kathryn Dumschott | ORCID: 0000-0002-9905-4011 EFO:0010959 @@ -5447,10 +5447,10 @@ - + - - + + A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5462,9 +5462,9 @@ - + - + A protocol that describes the step by step process for removing metabolites from a biological sample. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5475,10 +5475,10 @@ - + - - + + A protocol that describes the steps to be taken to transform a sample before an assay can be performed Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5488,10 +5488,10 @@ - + - - + + A protocol that describes how to perform an assay. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5501,10 +5501,10 @@ - + - - + + A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5515,10 +5515,10 @@ - + - - + + A protocol that describes the operations performed to filter or select a smaller part of the dataset to be used for or rejected from subsequent analysis steps Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5528,10 +5528,10 @@ - + - - + + A protocol that describes the operations performed to convert data from one format, structure, or value into another. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5541,10 +5541,10 @@ - + - - + + A protocol that describes the operations performed to take a specific data set out of a larger data set and present it in a useable format. Kathryn Dumschott | ORCID: 0000-0002-9905-401 DPBO @@ -5554,9 +5554,9 @@ - + - + An unique identifier for grouping experminental replicates - replication of an experiment to assess biological or technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, replicate groups must be the same for each replicate in the group (e.g. 'group 1' for each replicate in the group). This adds the possibility to aggregate the replicates without additional annotations. Kevin Schneider | ORCID: 0000-0002-2198-5262 DPBO @@ -5566,10 +5566,10 @@ - + - - + + An unique identifier for grouping biological replicates - replicates made from different individual biosamples to assess biological variation in an experiment. In contrast to other ways of annotating replicates in experimental design, biological replicate groups must be the same for each replicate in the group (e.g. 'b_1' for each biological replicate in the group). This adds the possibility to aggregate the biological replicates without additional annotations. Kevin Schneider | ORCID: 0000-0002-2198-5262 DPBO @@ -5579,10 +5579,10 @@ - + - - + + An unique identifier for grouping technical replicates - replicates made from different individual biosamples to assess technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, technical replicate groups must be the same for each replicate in the group (e.g. 't_1' for each technical replicate in the group). This adds the possibility to aggregate the technical replicates without additional annotations. Kevin Schneider | ORCID: 0000-0002-2198-526 DPBO @@ -5592,9 +5592,9 @@ - + - + The time that a sample should incubate (keep at a suitable temperature) during a experimental protocol to allow for a reaction or proces to occur. Kathryn Dumschott | ORCID: 0000-0002-9905-401 BAO:0002833 @@ -5605,9 +5605,9 @@ - + - + Axiovert series, inverse microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5618,9 +5618,9 @@ - + - + binocular, stereo microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5631,9 +5631,9 @@ - + - + camera Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5644,10 +5644,10 @@ - + - - + + white Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5657,10 +5657,10 @@ - + - - + + white Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5670,10 +5670,10 @@ - + - - + + differential interference contrast Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5683,10 +5683,10 @@ - + - - + + yellow Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5696,10 +5696,10 @@ - + - - + + green Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5709,10 +5709,10 @@ - + - - + + red Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5722,9 +5722,9 @@ - + - + software controlling imaging systems from ZEISS. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5735,9 +5735,9 @@ - + - + microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5748,9 +5748,9 @@ - + - + microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5761,9 +5761,9 @@ - + - + microscope slide Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5774,9 +5774,9 @@ - + - + cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5787,9 +5787,9 @@ - + - + cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5800,9 +5800,9 @@ - + - + cover slip Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5813,10 +5813,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5826,10 +5826,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5839,10 +5839,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5852,10 +5852,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5865,10 +5865,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5878,10 +5878,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5891,10 +5891,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5904,10 +5904,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5917,10 +5917,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5930,10 +5930,10 @@ - + - - + + magnification of Olympus SZX7 (Bino) Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -5943,9 +5943,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5956,9 +5956,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5969,9 +5969,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5982,9 +5982,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -5995,9 +5995,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6008,9 +6008,9 @@ - + - + objective lens of Zeiss Axioplan 2 Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6021,9 +6021,9 @@ - + - + objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6034,9 +6034,9 @@ - + - + objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6047,9 +6047,9 @@ - + - + objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6060,9 +6060,9 @@ - + - + objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6073,9 +6073,9 @@ - + - + objective lens of Zeiss Axiovert Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6086,9 +6086,9 @@ - + - + A solution designed for the growth of plant cell, tissue and organ culture. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6101,9 +6101,9 @@ - + - + The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype. Kathryn Dumschott | ORCID: 0000-0002-9905-4011 DPBO @@ -6114,9 +6114,9 @@ - + - + Axioplan series, imaging fluorescence microscope Kathryn Dumschott | ORCID: 0000-0002-9905-4011 @@ -6128,9 +6128,9 @@ - + - + A role of a student in a research project which is acknowledged in papers. Andrea Schrader | 0000-0002-3879-7057 DPBO @@ -6140,9 +6140,9 @@ - + - + A person that helps at various steps of the plant growth cycle e.g. sowing seeds, separating plants at the correct age or collecting seeds. DPBO DPBO:1000227 @@ -6152,9 +6152,9 @@ - + - + A method for physical delivery of DNA (likely also RNA) into cells. Gold or tungsten particles are coated with DNA and shot with a gene gun / particle gun on tissue like leaves, seedlings, callus or other types of tissue and cells. Often, in plant sciences, this method is used as a transient transformation method in protein or protein-protein interaction localization studies using binary vectors. Co-transformation of multiple vectors is possible. particle bombardment DPBO @@ -6165,9 +6165,9 @@ - + - + A protocol describing the method of a bioimaging technique. Bioimaging is a biological imaging method causing as minimal interference to living processes as possible or getting a 3-D structure from the outside without physical interference e.g. of cells, tissues or other living matter. Usually, the method is non-invasive but also fixed biological material is covered by a wider definition. (adapted from https://cab.ku.dk/what_is_bioimaging/) DPBO DPBO:1000229 @@ -6177,9 +6177,9 @@ - + - + A protocol describing a transformation method of cell, tissues or organisms. DPBO DPBO:1000230 @@ -6189,9 +6189,9 @@ - + - + Inverted fluorescence microscope suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 @@ -6203,9 +6203,9 @@ - + - + Upright fluorescence microscope suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 @@ -6217,9 +6217,9 @@ - + - + A data field which describes the MG-RAST identifier linking raw read data, methodological metadata and quality control metrics submitted to the MG-RAST metagenomics analysis server. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6230,9 +6230,9 @@ - + - + Tool/Software used for assembly. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6243,9 +6243,9 @@ - + - + Parameters used for assembly. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6256,9 +6256,9 @@ - + - + The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6269,9 +6269,9 @@ - + - + Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6282,9 +6282,9 @@ - + - + The parameters that have been applied during the extraction of genomes from metagenomic datasets. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6295,9 +6295,9 @@ - + - + The phylogenetic marker(s) used to assign an organism name to the SAG or MAG. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6308,9 +6308,9 @@ - + - + Tools used for completion estimate, i.e. checkm, anvi'o, busco. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6321,9 +6321,9 @@ - + - + Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores. Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6334,9 +6334,9 @@ - + - + The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases Angela Kranz | ORCID: 0000-0002-8000-0400 DPBO @@ -6370,7 +6370,7 @@ - + FASTQ short read format ignoring quality scores. DPBO EDAM:1930 @@ -6382,7 +6382,7 @@ - + DPBO EFO:0000490 extraction protocol @@ -6490,7 +6490,7 @@ - + DPBO EFO:0003789 growth protocol @@ -6501,7 +6501,7 @@ - + DPBO EFO:0003969 treatment protocol @@ -6512,7 +6512,7 @@ - + A DNA sequencer developed by Illumina. DPBO EFO:0004202 @@ -6524,7 +6524,7 @@ - + The Illumina HiSeq 2000 is a sequencing machine developed by Illumina. DPBO EFO:0004203 @@ -6536,7 +6536,7 @@ - + The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions and 16S metagenomic sequencing. DPBO EFO:0004205 @@ -6548,7 +6548,7 @@ - + The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004206 @@ -6573,7 +6573,7 @@ - + The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004431 @@ -6585,7 +6585,7 @@ - + DPBO EFO:0004432 454 GS FLX sequencer @@ -6596,7 +6596,7 @@ - + The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004433 @@ -6608,7 +6608,7 @@ - + The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences. DPBO EFO:0004434 @@ -6620,7 +6620,7 @@ - + DPBO EFO:0004437 AB SOLiD PI System @@ -6631,7 +6631,7 @@ - + DPBO EFO:0004438 AB SOLiD 4 System @@ -6642,7 +6642,7 @@ - + DPBO EFO:0004439 AB SOLiD System 3.0 @@ -6653,7 +6653,7 @@ - + DPBO EFO:0004441 AB SOLiD 4hq System @@ -6664,7 +6664,7 @@ - + DPBO EFO:0004442 AB SOLiD System 2.0 @@ -6675,7 +6675,7 @@ - + An RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimen. DPBO EFO:0004964 @@ -6710,7 +6710,7 @@ - + DPBO EFO:0005518 sample collection protocol @@ -6746,7 +6746,7 @@ - + The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008563 @@ -6758,7 +6758,7 @@ - + The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008564 @@ -6770,7 +6770,7 @@ - + The Illumina HiSeq 2500 is a sequencing machine developed by Illumina. DPBO EFO:0008565 @@ -6782,7 +6782,7 @@ - + The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina. Its primary applications include exome sequencing, targeted gene sequencing (amplicon, gene panel), whole-transcriptome sequencing and cytogenomic arrays. DPBO EFO:0008566 @@ -6794,7 +6794,7 @@ - + The PacBio RS II is a high-throughput sequencing machine developed by PacBio. Its primary applications are whole genome sequencing of smaller organisms and targeted sequencing of DNA and RNA. DPBO EFO:0008631 @@ -6806,7 +6806,7 @@ - + The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies. DPBO EFO:0008632 @@ -6818,7 +6818,7 @@ - + The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. DPBO EFO:0008635 @@ -6830,7 +6830,7 @@ - + The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina. DPBO EFO:0008636 @@ -6842,7 +6842,7 @@ - + The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina. DPBO EFO:0008637 @@ -6910,7 +6910,7 @@ - + The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina. DPBO EFO:0009173 @@ -6933,7 +6933,7 @@ - + The Illumina HiSeq 1500 is a sequencing machine developed by Illumina. DPBO EFO:0011027 @@ -6967,7 +6967,7 @@ - + DPBO EFO:0030052 nuclear RNA @@ -6978,7 +6978,7 @@ - + A hot spring that erupts periodically, ejecting a column of hot water and steam into the air. DPBO ENVO:00000050 @@ -6990,7 +6990,7 @@ - + A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor. DPBO ENVO:01000263 @@ -7002,7 +7002,7 @@ - + This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified. DPBO ENVO:01000403 @@ -7137,7 +7137,7 @@ - + Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: 'Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).' DPBO GENEPIO:0001924 @@ -7149,7 +7149,7 @@ - + DPBO GENEPIO:0001928 SOLiD 4hq System @@ -7160,7 +7160,7 @@ - + DPBO GENEPIO:0001931 SOLiD PI System @@ -7171,7 +7171,7 @@ - + DPBO GENEPIO:0001932 SOLiD System 2.0 @@ -7182,7 +7182,7 @@ - + DPBO GENEPIO:0001933 SOLiD System 3.0 @@ -7193,7 +7193,7 @@ - + DPBO GENEPIO:0001936 454 Genome Sequencer FLX Titanium @@ -7204,7 +7204,7 @@ - + DPBO GENEPIO:0001938 454 Genome Sequencer Junior @@ -7542,6 +7542,7 @@ + The library source specifies the type of source material that is being sequenced. DPBO GENEPIO:0001965 @@ -7550,6 +7551,104 @@ + + + + + Genomic DNA (includes PCR products from genomic DNA). + Damion Dooley + NCBI SRA: GENOMIC + DPBO + GENEPIO:0001966 + genomic source + + + + + + + + + Mixed material from metagenome. + Damion Dooley + NCBI SRA: METAGENOMIC + DPBO + GENEPIO:0001967 + metagenomic source + + + + + + + + + Transcription products from community targets + Damion Dooley + NCBI SRA: METATRANSCRIPTOMIC + DPBO + GENEPIO:0001968 + metatranscriptomic source + + + + + + + + + Other, unspecified, or unknown library source material. + Damion Dooley + NCBI SRA: OTHER + DPBO + GENEPIO:0001969 + other library source + + + + + + + + + Synthetic DNA. + Damion Dooley + NCBI SRA: SYNTHETIC + DPBO + GENEPIO:0001970 + synthetic source + + + + + + + + + Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). + Damion Dooley + NCBI SRA: TRANSCRIPTOMIC + DPBO + GENEPIO:0001971 + transcriptomic source + + + + + + + + + Viral RNA. + Damion Dooley + NCBI SRA: VIRAL RNA + DPBO + GENEPIO:0001972 + viral RNA source + + + + @@ -7567,7 +7666,7 @@ - + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an 'SQ Module' to support microfluidics. DPBO GENEPIO:0100109 @@ -7579,7 +7678,7 @@ - + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. DPBO GENEPIO:0100112 @@ -7591,7 +7690,7 @@ - + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. DPBO GENEPIO:0100113 @@ -7603,7 +7702,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. DPBO GENEPIO:0100115 @@ -7615,7 +7714,7 @@ - + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. DPBO GENEPIO:0100121 @@ -7627,7 +7726,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. DPBO GENEPIO:0100123 @@ -7639,7 +7738,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. DPBO GENEPIO:0100124 @@ -7651,7 +7750,7 @@ - + A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. DPBO GENEPIO:0100128 @@ -7663,7 +7762,7 @@ - + A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes 'SMRT Cells' for single-molecule real-time sequencing. The RS was the first model made by the company. DPBO GENEPIO:0100131 @@ -7675,7 +7774,7 @@ - + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation DPBO GENEPIO:0100133 @@ -7687,7 +7786,7 @@ - + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. DPBO GENEPIO:0100134 @@ -7699,7 +7798,7 @@ - + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. DPBO GENEPIO:0100136 @@ -7711,7 +7810,7 @@ - + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. DPBO GENEPIO:0100137 @@ -7723,7 +7822,7 @@ - + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. DPBO GENEPIO:0100138 @@ -7735,7 +7834,7 @@ - + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. DPBO GENEPIO:0100139 @@ -7747,7 +7846,7 @@ - + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual DPBO GENEPIO:0100141 @@ -7759,7 +7858,7 @@ - + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. DPBO GENEPIO:0100142 @@ -7771,7 +7870,7 @@ - + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. DPBO GENEPIO:0100143 @@ -7783,7 +7882,7 @@ - + A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'. DPBO GENEPIO:0100145 @@ -7795,7 +7894,7 @@ - + A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. DPBO GENEPIO:0100147 @@ -7807,7 +7906,7 @@ - + A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. DPBO GENEPIO:0100148 @@ -7819,7 +7918,7 @@ - + A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. DPBO GENEPIO:0100150 @@ -7926,7 +8025,7 @@ - + A proprietary next-generation DNA sequencing system from BGI Genomics using combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB) technology. The cPAS chemistry works by incorporating a fluorescent probe to a DNA anchor on the DNB, followed by high-resolution digital imaging. DPBO NCIT:C146812 @@ -7938,7 +8037,7 @@ - + A next-generation DNA sequencing service offered by Complete Genomics. Unamplified human genomic DNA is sheared into 500bp fragments and then amplified to create DNA nano-balls (DNBs). The DNBs are arrayed on a substrate and their sequence is determined by Combinatorial Probe-Anchor Ligation (cPAL) sequencing. DPBO NCIT:C146815 @@ -7989,7 +8088,7 @@ - + RNA present in the cytoplasm. It is involved in the protein export process from the cells. DPBO NCIT:C84512 @@ -8090,7 +8189,7 @@ - + Is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. DPBO OBI:0000702 @@ -8102,7 +8201,7 @@ - + Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry DPBO OBI:0000717 @@ -8135,7 +8234,7 @@ - + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. DPBO OBI:0002000 @@ -8147,7 +8246,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. DPBO OBI:0002001 @@ -8159,7 +8258,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. DPBO OBI:0002002 @@ -8171,7 +8270,7 @@ - + A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. DPBO OBI:0002007 @@ -8183,7 +8282,7 @@ - + A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. DPBO OBI:0002012 @@ -8195,7 +8294,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. DPBO OBI:0002022 @@ -8207,7 +8306,7 @@ - + A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. DPBO OBI:0002048 @@ -8219,7 +8318,7 @@ - + A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. DPBO OBI:0002049 @@ -8231,7 +8330,7 @@ - + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. DPBO OBI:0002129 @@ -8243,7 +8342,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. DPBO OBI:0002630 @@ -8255,7 +8354,7 @@ - + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation DPBO OBI:0002632 @@ -8267,7 +8366,7 @@ - + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. DPBO OBI:0002633 @@ -8279,7 +8378,7 @@ - + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. DPBO OBI:0002750 @@ -8291,7 +8390,7 @@ - + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. DPBO OBI:0002752 @@ -8303,7 +8402,7 @@ - + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. DPBO OBI:0003114 @@ -8315,7 +8414,7 @@ - + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. DPBO OBI:0003386 @@ -8363,7 +8462,7 @@ - + DPBO OME:Objective Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective @@ -8416,7 +8515,7 @@ - + DPBO PO:0009001 fruit @@ -8427,7 +8526,7 @@ - + DPBO PO:0009008 plant organ @@ -8438,7 +8537,7 @@ - + DPBO PO:0009010 seed @@ -8449,7 +8548,7 @@ - + DPBO PO:0025498 cardinal part of multi-tissue plant structure @@ -9083,7 +9182,7 @@ - + Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. DPBO:0000035 DPBO @@ -9111,7 +9210,7 @@ george gkoutos unit.ontology UO:0000048 - + acceleration unit @@ -9173,9 +9272,9 @@ Chemical name DPBO data:0990 - - - + + + Compound name @@ -9199,9 +9298,9 @@ Small molecule identifier DPBO data:1086 - - - + + + Compound identifier @@ -9221,7 +9320,7 @@ - + Sequencing technique intended for a next generation sequencing library. GENEPIO:0001973 DPBO @@ -9249,8 +9348,8 @@ Short sequence read mapping DPBO operation:3198 - - + + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. Read mapping @@ -9278,17 +9377,17 @@ Small RNA DPBO topic:0099 - - + + RNA - + - - + + A mutant in which a gene ore genes are expressed at higher levels than the wild type. DPBO MCO_0000041 @@ -9297,10 +9396,10 @@ - + - - + + A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality. DPBO MCO_0000042 @@ -9309,10 +9408,10 @@ - + - - + + A mutant in which the function of a target gene has been disrupted within its normal biological context. Utilized to examine the involvement of a gene in a complex biological process. DPBO MCO_0000051 @@ -9321,10 +9420,10 @@ - + - - + + a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication. DPBO MCO_0000052 @@ -9333,10 +9432,10 @@ - + - - + + An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit. DPBO MCO_0000059 @@ -9345,9 +9444,9 @@ - + - + A physical quality that inheres in a bearer by virtue of the amount of light that the bearer of the quality is able to transmit. DPBO MCO_0000077 @@ -9356,10 +9455,10 @@ - + - - + + DPBO MCO_0000173 @@ -9368,10 +9467,10 @@ - + - - + + DPBO MCO_0000174 @@ -9380,10 +9479,10 @@ - + - - + + DPBO MCO_0000177 @@ -9392,10 +9491,10 @@ - + - - + + DPBO MCO_0000178 @@ -9404,10 +9503,10 @@ - + - - + + DPBO MCO_0000179 @@ -9416,10 +9515,10 @@ - + - - + + DPBO MCO_0000180 @@ -9428,9 +9527,9 @@ - + - + A biological quality that inheres in specific organisms and that describes its total genetic content DPBO MCO_0000851 @@ -9439,9 +9538,9 @@ - + - + A process in which the act is intended to modify or alter some other material entity. DPBO MCO_0000866 @@ -9450,10 +9549,10 @@ - + - - + + A proprietary next-generation DNA sequencing system from Solexa that uses reversible terminator nucleotides. The genomic DNA to be sequenced is fragmented and ligated to adapter molecules on both ends to construct an Illumina-specific adapter library. PCR amplification of the DNA fragments is then performed using the adapter sequence as primer. Sequencing is carried out by repeated cycles of adding reversible fluorescent-labelled nucleotide and incorporation of the nucleotides to the complementary strand. The fluorescence of the incorporated nucleotides is detected. DPBO NCIT_C146817 @@ -9462,10 +9561,10 @@ - + - - + + A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis. DPBO NCIT_C146818 @@ -9474,10 +9573,10 @@ - + - - + + An altered form of an individual, organism, population, or genetic character that differs from the corresponding wild type due to one or more alterations (mutations). DPBO NCIT_C25360 @@ -9486,10 +9585,10 @@ - + - - + + The naturally-occurring, normal, non-mutated version of a gene or genome. DPBO NCIT_C62195 @@ -9498,10 +9597,10 @@ - + - - + + A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. DPBO OBI_0000869 @@ -9510,9 +9609,9 @@ - + - + DPBO ObsoleteClass Obsolete Class diff --git a/dpbo.obo b/dpbo.obo index 4fd8a5b..d407b19 100644 --- a/dpbo.obo +++ b/dpbo.obo @@ -3821,6 +3821,63 @@ is_a: GENEPIO:0001940 ! library selection id: GENEPIO:0001965 name: library source def: "The library source specifies the type of source material that is being sequenced." [] +is_a: GENEPIO:0001681 ! laboratory sequencing datum + +[Term] +id: GENEPIO:0001966 +name: genomic source +def: "Genomic DNA (includes PCR products from genomic DNA)." [] +xref: NCBI SRA: GENOMIC +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001967 +name: metagenomic source +def: "Mixed material from metagenome." [] +xref: NCBI SRA: METAGENOMIC +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001968 +name: metatranscriptomic source +def: "Transcription products from community targets" [] +xref: NCBI SRA: METATRANSCRIPTOMIC +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001969 +name: other library source +def: "Other, unspecified, or unknown library source material." [] +xref: NCBI SRA: OTHER +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001970 +name: synthetic source +def: "Synthetic DNA." [] +xref: NCBI SRA: SYNTHETIC +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001971 +name: transcriptomic source +def: "Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries)." [] +xref: NCBI SRA: TRANSCRIPTOMIC +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string + +[Term] +id: GENEPIO:0001972 +name: viral RNA source +def: "Viral RNA." [] +xref: NCBI SRA: VIRAL RNA +is_a: GENEPIO:0001965 ! library source +property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: GENEPIO:0001973