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srpAnalytics.yaml
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srpAnalytics.yaml
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id: http://w3id.org/linkml/examples/srpanalyics
name: srpanalytics
prefixes:
linkml: https://w3id.org/linkml
coderdata: https://w3id.org/linkml/examples/srpanalytics
schema: http://schema.org/
imports:
- linkml:types
default_range: string
default_prefix: srpanalytics
slots:
Chemical_ID:
description: Unique identifier for every chemical in the database
range: linkml:Any
identifier: true
slot_uri: schema:identifier
Sample_ID:
description: Unique identifier for every sample in the database
range: linkml:Any
identifier: true
slot_uri: schema:identifier
cas_number:
description: CAS identifier for a specific chemical
concentration:
description: Concentration at which chemical was administered in uM
range: float
concentration_unit:
description: Unit of concentration
Project:
description: name of project contributing the dataset
Model:
description: Model with best fit to data
BMD10:
description: Dose at which 10% of fish are affected
range: linkml:Any
BMD50:
description: Dose at which 50% of fish are affected
range: linkml:Any
Min_Dose:
description: Minimum dose administered
range: linkml:Any
Max_Dose:
description: Maximum dose administered
range: linkml:Any
AUC_Norm:
description: normalized area under the curve
range: linkml:Any
BMD_Analysis_Flag:
description: quality of curve fit
range: integer
IncludeInPortal:
description:
End_Point_Name:
description:
Description:
description: Name of endpoint
endPointLink:
description: Link to endpoint description
DataQC_Flag:
description: Quality of Data
Dose:
description: Dose of chemical
range: float
Response:
description: Response in terms of percentage of fish alive
range: float
CI_Lo:
description: Low range of confidence interval
range: float
CI_Hi:
description: High range of confidence interval
range: float
X_vals:
description: X coordinates of fitted curve
range: linkml:Any
Y_vals:
description: Y coordinates of fitted curve
range: linkml:Any
classes:
samples:
description: List of samples collected in the Superfund study
slots:
- Sample_ID
- projectName
attributes:
ClientName:
description:
SampleNumber:
description:
date_sampled:
description:
date_sample_start:
description:
range: linkml:Any
sample_matrix:
description:
technology:
description:
projectName:
description:
sampleName:
description:
LocationLat:
description:
range: float
LocationLon:
description:
range: float
projectLink:
description:
LocationAlternateDescription:
description:
LocationName:
description:
SampleName:
description:
AlternateName:
description:
chemicals:
description: List of chemicals measured in the Superfund study
slots:
- Chemical_ID
- cas_number
attributes:
DTXSID:
description:
PREFERRED_NAME:
description:
INCHIKEY:
description:
SMILES:
description:
MOLECULAR_FORMULA:
description:
AVERAGE_MASS:
description:
range: linkml:Any
PUBCHEM_DATA_SOURCES:
description: Number of data sources in pubchem citing this chemical
range: linkml:Any
chem_source:
description:
chemical_class:
description:
chemDescription:
description:
sampleToChemicals:
description: Measurements of chemicals in samples
slots:
- Chemical_ID
- cas_number
- Sample_ID
attributes:
measurement_value:
description:
range: linkml:Any
measurement_value_qualifier:
description:
measurement_value_unit:
description:
measurement_value_molar:
description:
range: linkml:Any
measurement_value_molar_unit:
description:
environment_concentration:
description:
range: linkml:Any
environment_concentration_qualifier:
description:
environment_concentration_unit:
description:
environment_concentration_molar:
description:
range: linkml:Any
environment_concentration_molar_unit:
description:
zebrafishSampBMDs:
description: Benchmark dose measurements of sample extracts in zebrafish
slots:
- Sample_ID
- Model
- BMD10
- BMD50
- Min_Dose
- Max_Dose
- AUC_Norm
- BMD_Analysis_Flag
- IncludeInPortal
- End_Point_Name
- Description
- endPointLink
- DataQC_Flag
zebrafishSampDoseResponse:
description: Dose response datapoints of sample extracts in zebrafish
slots:
- Sample_ID
- Dose
- Response
- CI_Lo
- CI_Hi
- IncludeInPortal
- End_Point_Name
- endPointLink
zebrafishSampXYCoords:
description: XY Coordinates of curve fit data for sample extracts in zebrafish
slots:
- Sample_ID
- X_vals
- Y_vals
- IncludeInPortal
- End_Point_Name
- endPointLink
zebrafishChemBMDs:
description: Benchmark dose measurements of chemicals in zebrafish
slots:
- Chemical_ID
- Model
- BMD10
- BMD50
- Min_Dose
- Max_Dose
- AUC_Norm
- BMD_Analysis_Flag
- IncludeInPortal
- End_Point_Name
- Description
- endPointLink
- DataQC_Flag
zebrafishChemDoseResponse:
description: Dose response datapoints of chemicals in zebrafish
slots:
- Chemical_ID
- Dose
- Response
- CI_Lo
- CI_Hi
- IncludeInPortal
- End_Point_Name
- endPointLink
zebrafishChemXYCoords:
description: XY Coordinates of curve fit data for chemicals in zebrafish
slots:
- Chemical_ID
- X_vals
- Y_vals
- IncludeInPortal
- End_Point_Name
- endPointLink
allGeneEx:
description: List of all experiments that measure gene expression changes in zebrafish upon chemical treatment changes
slots:
- Project
- cas_number
- Chemical_ID
- concentration
attributes:
Gene:
description:
range: linkml:Any
GeneID:
description:
adj_p_value:
description:
range: float
indication:
description:
range: integer
Log2FoldChange:
description: fold change
range: float
srpDEGStats:
description: Summary statistics
slots:
- Project
- cas_number
- Chemical_ID
- concentration
attributes:
link:
description: Link to experiment?
DownRegulatedGenes:
description: number of genes down-regulated upon chemical treatement
range: integer
UpRegulatedGenes:
description: number of genes up-regulated upon chemical treatement
range: integer
srpDEGPathways:
description: Pathways that are enriched in zebrafish genes that are differentially expressed upon treatment with a chemical
slots:
- Chemical_ID
- concentration
attributes:
term:
description:
adj_p_value:
description:
range: float
p_value:
description:
range: float
Genes:
description:
enrichment_score:
description:
range: float
z_score:
description:
range: float
overlap:
description:
toPlot:
description:
range: integer
exposomeGeneStats:
description: Summary and link to exposome measurements of human genes that are differentailly expressed upon chemical treatment
slots:
- Chemical_ID
- Project
- concentration
- cas_number
- concentration_unit
attributes:
nGenes:
description:
range: integer
Link:
description:
Condition:
description: