From 4aaf1e858c19663ac38da697b16dbab425de39fa Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 6 Dec 2023 10:08:42 -0600 Subject: [PATCH 1/7] add FISH --- modules/Assay/Assay.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/Assay/Assay.yaml b/modules/Assay/Assay.yaml index ebb3f207..eac55cd8 100644 --- a/modules/Assay/Assay.yaml +++ b/modules/Assay/Assay.yaml @@ -83,11 +83,16 @@ enums: An imaging-based system that allows measurement and analysis of peaks of human-derived induced pluripotent stem cells (hiPSCs), differentiated into cardiomyocytes and neurons, up to 100 times per second and quickly cherry pick events such as Early-After-Depolarization-like events (EAD-like events), fibrillation, and irregular beating. source: https://www.moleculardevices.com/products/flipr-penta-high-throughput-cellular-screening-system + Fluorescence In Situ Hybridization: + description: > + A physical mapping approach that uses fluorescent tags to detect hybridization of probes within metaphase chromosomes or less condensed somatic interphase chromatin. + This technique can be used for identification of chromosomal abnormalities and for gene mapping. + meaning: http://purl.obolibrary.org/obo/NCIT_C17563 Focus group: description: > A small, usually diverse group of people whose response to something is studied to determine the response that can be expected from a larger population. It is used especially in market research and political analysis. - source: http://purl.obolibrary.org/obo/NCIT_C154589 + meaning: http://purl.obolibrary.org/obo/NCIT_C154589 FTIR spectroscopy: description: > Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. From f8758be9fbca8cfa3dc95e60169a41e4938179e1 Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 6 Dec 2023 16:21:52 +0000 Subject: [PATCH 2/7] Build jsonld --- NF.jsonld | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/NF.jsonld b/NF.jsonld index dd77091a..29e7a858 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -4491,6 +4491,8 @@ "@id" : "bts:FIA-MSMS" }, { "@id" : "bts:FLIPRhigh-throughputcellularscreening" + }, { + "@id" : "bts:FluorescenceInSituHybridization" }, { "@id" : "bts:Focusgroup" }, { @@ -4828,6 +4830,8 @@ "@id" : "bts:FIA-MSMS" }, { "@id" : "bts:FLIPRhigh-throughputcellularscreening" + }, { + "@id" : "bts:FluorescenceInSituHybridization" }, { "@id" : "bts:Focusgroup" }, { @@ -12607,6 +12611,17 @@ }, "sms:displayName" : "University of Missouri, Saint Louis", "sms:required" : "sms:false" + }, { + "@id" : "bts:FluorescenceInSituHybridization", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "FluorescenceInSituHybridization", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Fluorescence In Situ Hybridization", + "sms:required" : "sms:false" }, { "@id" : "bts:noveltyresponsebehaviorassay", "@type" : "rdfs:Class", From d96f1f7f1d1d348bb5eab29bf46019509b23a716 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 6 Dec 2023 10:29:48 -0600 Subject: [PATCH 3/7] Update FileFormat.yaml --- modules/Data/FileFormat.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/modules/Data/FileFormat.yaml b/modules/Data/FileFormat.yaml index 6f69c6cd..cedf3e1e 100644 --- a/modules/Data/FileFormat.yaml +++ b/modules/Data/FileFormat.yaml @@ -164,9 +164,12 @@ enums: meaning: http://purl.obolibrary.org/obo/NCIT_C80220 hdf5: description: > - HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF. An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package. HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF). - + HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF. + An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. + Currently supported by the Python MDTraj package. HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF). meaning: http://edamontology.org/format_3590 + notes: + - This file format encompasses/includes the h5ad anndata format commonly used for scRNAseq data sharing. hdr: description: MRI Header file, as in the NIFTI-1 Analyze 7.5 format meaning: https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h From cc7629e753fa2c0dd1ec976d07c8d15e293eecba Mon Sep 17 00:00:00 2001 From: "nf-osi[bot]" Date: Wed, 6 Dec 2023 16:30:10 +0000 Subject: [PATCH 4/7] Build jsonld --- NF.jsonld | 1502 ++++++++++++++++++++++++++--------------------------- 1 file changed, 751 insertions(+), 751 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index 29e7a858..33e8ee12 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -9,569 +9,8 @@ }, "@id" : "http://schema.biothings.io/", "@graph" : [ { - "@id" : "bts:BodyPartEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BodyPartEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BodyPartEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:UnknownEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "UnknownEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "UnknownEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpecimenPreparationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SpecimenPreparationMethodEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SpecimenPreparationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:FileFormatEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "FileFormatEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "FileFormatEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SexEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SexEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SexEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MRISequenceEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MRISequenceEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "MRISequenceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:PlatformEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PlatformEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "PlatformEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:NF1Variant", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NF1Variant", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "NF1Variant", - "sms:required" : "sms:false" - }, { - "@id" : "bts:GenePerturbationEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GenePerturbationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:WorkflowEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "WorkflowEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "WorkflowEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BooleanEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "Boolean data as Yes/No enums", - "rdfs:label" : "BooleanEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BooleanEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:GenePerturbationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationMethodEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GenePerturbationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Data", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Data", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Data", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpeciesEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SpeciesEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SpeciesEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DiagnosisEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DiagnosisEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DiagnosisEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ProteinExtractSourceEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ProteinExtractSourceEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ProteinExtractSourceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:WorkingDistanceUnitEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "WorkingDistanceUnitEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "WorkingDistanceUnitEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:StrandednessEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "StrandednessEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "StrandednessEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:OrganismSubstance", - "@type" : "rdfs:Class", - "rdfs:comment" : "This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens.", - "rdfs:label" : "OrganismSubstance", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "OrganismSubstance", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BiologicalProcess", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BiologicalProcess", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BiologicalProcess", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ExpressionUnitEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "Quantification units for gene expression.", - "rdfs:label" : "ExpressionUnitEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ExpressionUnitEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:OrganEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OrganEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "OrganEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Tumor", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Tumor", "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Tumor", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ConcentrationUnit", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ConcentrationUnit", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ConcentrationUnit", - "sms:required" : "sms:false" - }, { - "@id" : "bts:NucleicAcidSourceEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NucleicAcidSourceEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "NucleicAcidSourceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReadPairOrientationEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReadPairOrientationEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ReadPairOrientationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:LibraryPrepEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryPrepEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "LibraryPrepEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Tissue", - "@type" : "rdfs:Class", - "rdfs:comment" : "Tissue is a group of cells that have similar structure and that function together as a unit.", - "rdfs:label" : "Tissue", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Tissue", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DataSubtype", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DataSubtype", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DataSubtype", - "sms:required" : "sms:false" - }, { - "@id" : "bts:LibraryPreparationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryPreparationMethodEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "LibraryPreparationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Metadata", - "@type" : "rdfs:Class", - "rdfs:comment" : "Data that provides information about other data", - "rdfs:label" : "Metadata", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Metadata", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ChannelEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ChannelEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ChannelEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Cell", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Cell", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Cell", - "sms:required" : "sms:false" - }, { - "@id" : "bts:GenomicReferenceEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenomicReferenceEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GenomicReferenceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Genotype", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Genotype", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Genotype", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DrugScreen", - "@type" : "rdfs:Class", - "rdfs:comment" : "This is a subset of Assay enum above.", - "rdfs:label" : "DrugScreen", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DrugScreen", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DissociationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DissociationMethodEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DissociationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TimeUnit", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TimeUnit", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TimeUnit", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Measurement", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Measurement", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Measurement", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Material", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Material", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Material", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TransplantationType", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TransplantationType", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TransplantationType", - "sms:required" : "sms:false" - }, { - "@id" : "bts:RunTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RunTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RunTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:NotApplicableEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NotApplicableEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "NotApplicableEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CellLineModel", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CellLineModel", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CellLineModel", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Resource", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Resource", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Resource", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MouseModel", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MouseModel", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "MouseModel", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AssayEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AssayEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AssayEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CuratedDataEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CuratedDataEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CuratedDataEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Institution", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Institution", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Institution", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReadStrandOriginEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReadStrandOriginEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ReadStrandOriginEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:GenePerturbationTechnologyEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationTechnologyEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GenePerturbationTechnologyEnum", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:institution", + "@id" : "bts:institution", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -5033,250 +4472,811 @@ }, { "@id" : "bts:oxygenconsumptionassay" }, { - 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"sms:displayName" : "GenePerturbationTechnologyEnum", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ { "@id" : "bts:ProteinAssayTemplate" From ef8d35cde1d979339d2ddb12082f9b85cef7da64 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 6 Dec 2023 14:16:12 -0600 Subject: [PATCH 5/7] fix test template ScRNASeqTemplate_1.csv --- tests/validate/ScRNASeqTemplate_1.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/validate/ScRNASeqTemplate_1.csv b/tests/validate/ScRNASeqTemplate_1.csv index 6733fdaa..139caa69 100644 --- a/tests/validate/ScRNASeqTemplate_1.csv +++ b/tests/validate/ScRNASeqTemplate_1.csv @@ -1,5 +1,5 @@ Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset -ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,, -ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,, -ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,, -ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,, \ No newline at end of file +ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,Not Applicable,10x,,,,,, +ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,Not Applicable,10x,,,,,, +ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably 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The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.\n", - "rdfs:label" : "slideID", + "rdfs:comment" : "TBD", + "rdfs:label" : "SpeciesEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "slideID", + "sms:displayName" : "SpeciesEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:sourceName", + "@id" : "bts:DiagnosisEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Intended for non-biological samples, tf the sample is a nanoparticle sample or some chemical substance not derived from a biological material, the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.\n", - "rdfs:label" : "sourceName", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "sourceName", + "sms:displayName" : "DiagnosisEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:ProteinExtractSourceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ProteinExtractSourceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readPairOrientation", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:fr-firststrand" - }, { - "@id" : "bts:inward" - }, { - "@id" : "bts:matching" - }, { - "@id" : "bts:outward" - } ], - "rdfs:label" : "readPairOrientation", - "rdfs:comment" : "The relative orientation of the reads in a paired-end protocol", + "sms:displayName" : "ProteinExtractSourceEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:WorkingDistanceUnitEnum", "@type" : "rdfs:Class", - "sms:displayName" : "readPairOrientation" + "rdfs:comment" : "TBD", + "rdfs:label" : "WorkingDistanceUnitEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "WorkingDistanceUnitEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:fileSize", + "@id" : "bts:StrandednessEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Size of file in bytes.", - "rdfs:label" : "fileSize", + "rdfs:comment" : "TBD", + "rdfs:label" : "StrandednessEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "fileSize", + "sms:displayName" : "StrandednessEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:benefactorId", + "@id" : "bts:OrganismSubstance", "@type" : "rdfs:Class", - "rdfs:comment" : "The id of the resource from which access control is inherited.", - "rdfs:label" : "benefactorId", + "rdfs:comment" : "This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens.", + "rdfs:label" : "OrganismSubstance", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "benefactorId", + "sms:displayName" : "OrganismSubstance", "sms:required" : "sms:false" }, { - "@id" : "bts:createdOn", + "@id" : "bts:BiologicalProcess", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to when the resource was created.", - "rdfs:label" : "createdOn", + "rdfs:comment" : "TBD", + "rdfs:label" : "BiologicalProcess", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdOn", + "sms:displayName" : "BiologicalProcess", "sms:required" : "sms:false" }, { - "@id" : "bts:protocolPurpose", + "@id" : "bts:ExpressionUnitEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Brief description of the protocol purpose.", - "rdfs:label" : "protocolPurpose", + "rdfs:comment" : "Quantification units for gene expression.", + "rdfs:label" : "ExpressionUnitEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ExpressionUnitEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:OrganEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OrganEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OrganEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Tumor", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Tumor", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Tumor", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ConcentrationUnit", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ConcentrationUnit", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ConcentrationUnit", + "sms:required" : "sms:false" + }, { + "@id" : "bts:NucleicAcidSourceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NucleicAcidSourceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "NucleicAcidSourceEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ReadPairOrientationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReadPairOrientationEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "protocolPurpose", + "sms:displayName" : "ReadPairOrientationEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:reporterSubstance", + "@id" : "bts:LibraryPrepEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.", - "rdfs:label" : "reporterSubstance", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryPrepEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterSubstance", + "sms:displayName" : "LibraryPrepEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:Tissue", + "@type" : "rdfs:Class", + "rdfs:comment" : "Tissue is a group of cells that have similar structure and that function together as a unit.", + "rdfs:label" : "Tissue", "rdfs:subClassOf" : [ ], - "@id" : "bts:slideVersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:V1" - }, { - "@id" : "bts:V2" - }, { - "@id" : "bts:V3" - }, { - "@id" : "bts:V4" - } ], - "rdfs:label" : "slideVersion", - "rdfs:comment" : "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "@type" : "rdfs:Class", - "sms:displayName" : "slideVersion" + "sms:displayName" : "Tissue", + "sms:required" : "sms:false" }, { - "@id" : "bts:reporterGene", + "@id" : "bts:DataSubtype", "@type" : "rdfs:Class", - "rdfs:comment" : "A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.", - "rdfs:label" : "reporterGene", + "rdfs:comment" : "TBD", + "rdfs:label" : "DataSubtype", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterGene", + "sms:displayName" : "DataSubtype", "sms:required" : "sms:false" }, { + "@id" : "bts:LibraryPreparationMethodEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryPreparationMethodEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:nf1Genotype", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:-/-" - }, { - "@id" : "bts:+/-" - }, { - "@id" : "bts:+/+" - }, { - "@id" : "bts:Unknown" - }, { - "@id" : "bts:Unknown" - } ], - "rdfs:label" : "nf1Genotype", - "rdfs:comment" : "Genotype of NF1 gene in the biospecimen from which the data were derived, if known.", - "@type" : "rdfs:Class", - "sms:displayName" : "nf1Genotype" + "sms:displayName" : "LibraryPreparationMethodEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Metadata", + "@type" : "rdfs:Class", + "rdfs:comment" : "Data that provides information about other data", + "rdfs:label" : "Metadata", "rdfs:subClassOf" : [ ], - "@id" : "bts:diagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Neurofibromatosistype1" - }, { - "@id" : "bts:Neurofibromatosistype2" - }, { - "@id" : "bts:Schwannomatosis" - }, { - "@id" : "bts:SporadicSchwannoma" - } ], - "rdfs:label" : "diagnosis", - "rdfs:comment" : "A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.", - "@type" : "rdfs:Class", - "sms:displayName" : "diagnosis" + "sms:displayName" : "Metadata", + "sms:required" : "sms:false" }, { - "@id" : "bts:targetDepth", + "@id" : "bts:ChannelEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "The targeted read depth prior to sequencing.", - "rdfs:label" : "targetDepth", + "rdfs:comment" : "TBD", + "rdfs:label" : "ChannelEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "targetDepth", + "sms:displayName" : "ChannelEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:creator", + "@id" : "bts:Cell", "@type" : "rdfs:Class", - "rdfs:comment" : "An entity responsible for making the resource.", - "rdfs:label" : "creator", + "rdfs:comment" : "TBD", + "rdfs:label" : "Cell", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "creator", - "sms:required" : "sms:true" + "sms:displayName" : "Cell", + "sms:required" : "sms:false" }, { + "@id" : "bts:GenomicReferenceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GenomicReferenceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:age", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "age", - "rdfs:comment" : "A numeric value representing age of the individual. Use with `ageUnit`.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:ageUnit" - } ], - "sms:displayName" : "age" + "sms:displayName" : "GenomicReferenceEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Genotype", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Genotype", "rdfs:subClassOf" : [ ], - "@id" : "bts:isCellLine", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isCellLine", - "rdfs:comment" : "Whether or not sample source is a cell line (Yes; No)", - "@type" : "rdfs:Class", - "sms:displayName" : "isCellLine" + "sms:displayName" : "Genotype", + "sms:required" : "sms:false" }, { + "@id" : "bts:DrugScreen", + "@type" : "rdfs:Class", + "rdfs:comment" : "This is a subset of Assay enum above.", + "rdfs:label" : "DrugScreen", "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryPreparationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:10x" - }, { - "@id" : "bts:CEL-seq" - }, { - "@id" : "bts:Drop-Seq" - }, { - "@id" : "bts:GTAC@WUSTLin-houseprep" - }, { - "@id" : "bts:IDTxGenExomeResearchPanel" - }, { - "@id" : "bts:IlluminaTruSeqDNANano" - }, { - "@id" : "bts:KAPAHyperPrepKitPCR-free" - }, { - "@id" : "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)" - }, { - "@id" : "bts:KAPAmRNAHyperPrepKit" - }, { - "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" - }, { - "@id" : "bts:Omni-ATAC" - }, { - "@id" : "bts:QuantSeqFWDV2withUDI" - }, { - "@id" : "bts:Smart-seq2" - }, { - "@id" : "bts:Smart-seq4" - }, { - "@id" : "bts:TruSeq" - }, { - "@id" : "bts:TruSeqstandardtotalRNAlibrarykit" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "libraryPreparationMethod", - "rdfs:comment" : "Method by which library was prepared", - "@type" : "rdfs:Class", - "sms:displayName" : "libraryPreparationMethod" + "sms:displayName" : "DrugScreen", + "sms:required" : "sms:false" }, { - "@id" : "bts:publisher", + "@id" : "bts:DissociationMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "An entity responsible for making the resource available.", - "rdfs:label" : "publisher", + "rdfs:comment" : "TBD", + "rdfs:label" : "DissociationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "publisher", + "sms:displayName" : "DissociationMethodEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:averageBaseQuality", + "@id" : "bts:TimeUnit", "@type" : "rdfs:Class", - "rdfs:comment" : "Average base quality collected from samtools", - "rdfs:label" : "averageBaseQuality", + "rdfs:comment" : "TBD", + "rdfs:label" : "TimeUnit", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "averageBaseQuality", + "sms:displayName" : "TimeUnit", "sms:required" : "sms:false" }, { + "@id" : "bts:Measurement", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Measurement", "rdfs:subClassOf" : [ ], - "@id" : "bts:sex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Male" - }, { - "@id" : "bts:Female" - }, { - "@id" : "bts:Unknown" - }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "sex", - "rdfs:comment" : "Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.", - "@type" : "rdfs:Class", - "sms:displayName" : "sex" + "sms:displayName" : "Measurement", + "sms:required" : "sms:false" }, { - "@id" : "bts:createdBy", + "@id" : "bts:Material", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to the user who created the resource.", - "rdfs:label" : "createdBy", + "rdfs:comment" : "TBD", + "rdfs:label" : "Material", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdBy", + "sms:displayName" : "Material", "sms:required" : "sms:false" }, { + "@id" : "bts:TransplantationType", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TransplantationType", "rdfs:subClassOf" : [ ], - "@id" : "bts:genePerturbationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "genePerturbationType", - "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", - "@type" : "rdfs:Class", - "sms:displayName" : "genePerturbationType" + "sms:displayName" : "TransplantationType", + "sms:required" : "sms:false" }, { + "@id" : "bts:RunTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RunTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:compoundDose", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "rdfs:label" : "compoundDose", - "rdfs:comment" : "A dose quantity for the treatment compound. To be used with compoundDoseUnit.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:compoundDoseUnit" - } ], - "sms:displayName" : "compoundDose" + }, + "sms:displayName" : "RunTypeEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:NotApplicableEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NotApplicableEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readDepth", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "readDepth", - "rdfs:comment" : "If available, the coverage statistic as output from bedtools coverage or samtools stats.", - "@type" : "rdfs:Class", - "sms:displayName" : "readDepth" + "sms:displayName" : "NotApplicableEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:InChIKey", + "@id" : "bts:CellLineModel", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). This is a more reliable identifier than the compound name and should be used if available.\n", - "rdfs:label" : "InChIKey", + "rdfs:comment" : "TBD", + "rdfs:label" : "CellLineModel", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "InChIKey", + "sms:displayName" : "CellLineModel", "sms:required" : "sms:false" }, { + "@id" : "bts:Resource", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Resource", "rdfs:subClassOf" : [ ], - "@id" : "bts:concentrationMaterial", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "concentrationMaterial", - "rdfs:comment" : "Numeric value for concentration of the material", - "@type" : "rdfs:Class", - "sms:displayName" : "concentrationMaterial" + "sms:displayName" : "Resource", + "sms:required" : "sms:false" }, { - "@id" : "bts:fileCount", + "@id" : "bts:MouseModel", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of files in the resource collection.", - "rdfs:label" : "fileCount", + "rdfs:comment" : "TBD", + "rdfs:label" : "MouseModel", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "fileCount", + "sms:displayName" : "MouseModel", "sms:required" : "sms:false" }, { - "@id" : "bts:assayTarget", + "@id" : "bts:AssayEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.", - "rdfs:label" : "assayTarget", + "rdfs:comment" : "TBD", + "rdfs:label" : "AssayEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "assayTarget", + "sms:displayName" : "AssayEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:license", + "@id" : "bts:CuratedDataEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Link to a license or name of license applicable for the resource.", - "rdfs:label" : "license", + "rdfs:comment" : "TBD", + "rdfs:label" : "CuratedDataEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "license", + "sms:displayName" : "CuratedDataEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:Institution", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Institution", "rdfs:subClassOf" : [ ], - "@id" : "bts:readLength", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "readLength", - "rdfs:comment" : "Number of base pairs (bp) sequenced for a read", - "@type" : "rdfs:Class", - "sms:displayName" : "readLength" + "sms:displayName" : "Institution", + "sms:required" : "sms:false" }, { - "@id" : "bts:studyId", + "@id" : "bts:ReadStrandOriginEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Id of study.", - "rdfs:label" : "studyId", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReadStrandOriginEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - 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Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1", - "@type" : "rdfs:Class", - "sms:displayName" : "progressReportNumber" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:specimenPreparationMethod", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:Freshcollected" + "@id" : "bts:UniversityofNorthCarolina,Charlotte" }, { - "@id" : "bts:Flashfrozen" + "@id" : "bts:MedicalUniversityofSouthCarolina" }, { - "@id" : "bts:FFPE" + "@id" : "bts:NewYorkMedicalCollege" }, { - "@id" : "bts:Cryopreserved" + "@id" : "bts:RushUniversity" }, { - "@id" : "bts:OCT" + "@id" : "bts:UniversityofTexas,SanAntonio" }, { - "@id" : "bts:RNAlater" + "@id" : "bts:UniversityofOklahoma" }, { - "@id" : "bts:formalin-fixed" + "@id" : "bts:VirginiaCommonwealthUniversity" }, { - "@id" : "bts:ethanol" + "@id" : "bts:UniversityofHouston" }, { - "@id" : "bts:Viablyfrozen" - } ], - "rdfs:label" : "specimenPreparationMethod", - "rdfs:comment" : "Term that represents preservation of the sample before usage in, e.g. sequencing", - "@type" : "rdfs:Class", - "sms:displayName" : "specimenPreparationMethod" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:isMultiIndividual", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:GeorgiaInstituteofTechnology" }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isMultiIndividual", - "rdfs:comment" : "Whether or not a file has data for multiple individuals (Yes; No)", - "@type" : "rdfs:Class", - "sms:displayName" : "isMultiIndividual" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryStrand", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:FirstStranded" + "@id" : "bts:FordhamUniversity" }, { - "@id" : "bts:SecondStranded" + "@id" : "bts:UniversityofMassachusetts,Amherst" }, { - "@id" : "bts:Unstranded" + "@id" : "bts:SaintLouisUniversity" }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "libraryStrand", - "rdfs:comment" : "Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.", - "@type" : "rdfs:Class", - "sms:displayName" : "libraryStrand" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:immersion", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:air" + "@id" : "bts:RensselaerPolytechnicInstitute" }, { - "@id" : "bts:oil" + "@id" : "bts:JAX" }, { - "@id" : "bts:water" + "@id" : "bts:UniversityofNewMexico" }, { - "@id" : "bts:other" - } ], - "rdfs:label" : "immersion", - "rdfs:comment" : "Immersion medium", - "@type" : "rdfs:Class", - "sms:displayName" : "immersion" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:captureArea", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:A" + "@id" : "bts:UniversityofMissouri,SaintLouis" + }, { + "@id" : "bts:VirginiaPolytechnicInstituteandStateUniversity" + }, { + "@id" : "bts:UniversityofMinnesota,Duluth" + }, { + "@id" : "bts:FloridaInstituteofTechnology" + }, { + "@id" : "bts:SUNY,DownstateHealthSciencesUniversity" + }, { + "@id" : "bts:UniversityofKansas" + }, { + "@id" : "bts:UniversityofRhodeIsland" + }, { + "@id" : "bts:CentralMichiganUniversity" + }, { + "@id" : "bts:UniversityofRochester" + }, { + "@id" : "bts:UniversityofCalifornia,Davis" + }, { + "@id" : "bts:UniversityofMontana,Missoula" + }, { + "@id" : "bts:KansasStateUniversity" + }, { + "@id" : "bts:UniversityofCalifornia,Riverside" + }, { + "@id" : "bts:LouisianaTechUniversity" + }, { + "@id" : "bts:UniversityofFlorida" + }, { + "@id" : "bts:BostonCollege" + }, { + "@id" : "bts:ChapmanUniversity" + }, { + "@id" : "bts:LouisianaStateUniversity,HealthSciencesCenter,Shreveport" + }, { + "@id" : "bts:UniversityofNorthCarolina,Wilmington" + }, { + "@id" : "bts:MiamiUniversity" + }, { + "@id" : "bts:EmoryUniversity" + }, { + "@id" : "bts:PortlandStateUniversity" + }, { + "@id" : "bts:CaliforniaInstituteofTechnology" + }, { + "@id" : "bts:UniversityofGeorgia" + }, { + "@id" : "bts:DelawareStateUniversity" + }, { + "@id" : "bts:UniversityofTexasHealthScienceCenter,SanAntonio" + }, { + "@id" : "bts:GeorgeMasonUniversity" + }, { + "@id" : "bts:BoiseStateUniversity" + }, { + "@id" : "bts:UniversityofSouthFlorida,SaintPetersburg" + }, { + "@id" : "bts:UniversityofNorthTexas,Denton" + }, { + "@id" : "bts:DuquesneUniversity" + }, { + "@id" : "bts:OregonHealthandScienceUniversity" + }, { + "@id" : "bts:OhioUniversity" + }, { + "@id" : "bts:VanderbiltUniversity" + }, { + "@id" : "bts:SouthernIllinoisUniversity,Carbondale" + }, { + "@id" : "bts:UniversityofPittsburgh,Pittsburgh" + }, { + "@id" : "bts:UniversityofCalifornia,SantaBarbara" }, { - "@id" : "bts:B" + "@id" : "bts:GeorgetownUniversity" }, { - "@id" : "bts:C" + "@id" : "bts:MercerUniversity" }, { - "@id" : "bts:D" + "@id" : "bts:UniversityofNotreDame" }, { - "@id" : "bts:A1" + "@id" : "bts:IllinoisStateUniversity" }, { - "@id" : "bts:B1" + "@id" : "bts:UniversityofAlabama" }, { - "@id" : "bts:C1" + "@id" : "bts:UniversityofSouthDakota" }, { - "@id" : "bts:D1" - } ], - "rdfs:label" : "captureArea", - "rdfs:comment" : "One of the either four or two active regions where tissue can be placed on a Visium slide. 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This is a low-level field set by the platform and is not a user annotation.", - "rdfs:label" : "concreteType", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "concreteType", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:transplantationType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:allograft" + "@id" : "bts:UniversityofWestFlorida" }, { - "@id" : "bts:xenograft" + "@id" : "bts:HowardUniversity" }, { - "@id" : "bts:autograft" + "@id" : "bts:AugustaUniversity" }, { - "@id" : "bts:isograft" - } ], - "rdfs:label" : "transplantationType", - "rdfs:comment" : "Type of transplantation involved in the experiment, derived from MESH", - "@type" : "rdfs:Class", - "sms:displayName" : "transplantationType" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:yearPublished", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "yearPublished", - "rdfs:comment" : "Year in which the resource was published.", - "@type" : "rdfs:Class", - "sms:displayName" : "yearPublished" - }, { - "@id" : "bts:fundingAgency", - "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to the funding organization for the generated resource. This annotation is handled by the DCC.", - "rdfs:label" : "fundingAgency", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "fundingAgency", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:nucleicAcidSource", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:bulkcell" + "@id" : "bts:UniversityofCalifornia,SanDiego" }, { - "@id" : "bts:bulknuclei" + "@id" : "bts:UniversityofCalifornia,Merced" }, { - "@id" : "bts:mitochondria" + "@id" : "bts:UniversityofNebraska,MedicalCenter" }, { - "@id" : "bts:singlecell" + "@id" : "bts:WichitaStateUniversity" }, { - "@id" : "bts:singlenucleus" + "@id" : "bts:UniversityofCalifornia,SanFrancisco" + }, { + "@id" : "bts:SouthDakotaStateUniversity" + }, { + "@id" : "bts:UniversityofWyoming" + }, { + "@id" : "bts:UniformedServicesUniversityoftheHealthSciences" + }, { + "@id" : "bts:SouthernIllinoisUniversity,Edwardsville" + }, { + "@id" : "bts:UniversityofArizona" + }, { + "@id" : "bts:AmericanUniversity" + }, { + "@id" : "bts:UniversityofIllinois,Urbana-Champaign" + }, { + "@id" : "bts:UniversityofNebraska,Omaha" + }, { + "@id" : "bts:MorehouseSchoolofMedicine" + }, { + "@id" : "bts:VillanovaUniversity" } ], - "rdfs:label" : "nucleicAcidSource", - "rdfs:comment" : "Source of the extracted nucleic acid used in the experiment", + "rdfs:label" : "institution", + "rdfs:comment" : "Institution (organization)", "@type" : "rdfs:Class", - "sms:displayName" : "nucleicAcidSource" + "sms:displayName" : "institution" }, { - "@id" : "bts:meanCoverage", - "@type" : "rdfs:Class", - "rdfs:comment" : "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools", - "rdfs:label" : "meanCoverage", "rdfs:subClassOf" : [ ], + "@id" : "bts:proportionCoverage30x", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "meanCoverage", - "sms:required" : "sms:false" - }, { - "@id" : "bts:genePerturbed", + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "proportionCoverage30x", + "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", "@type" : "rdfs:Class", - "rdfs:comment" : "The HUGO gene symbol for the gene that is perturbed.", - "rdfs:label" : "genePerturbed", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "genePerturbed", - "sms:required" : "sms:false" + "sms:displayName" : "proportionCoverage30x" }, { - "@id" : "bts:type", + "@id" : "bts:description", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to the type of the resource on the platform, e.g. “file”.", - "rdfs:label" : "type", + "rdfs:comment" : "Text describing a resource.", + "rdfs:label" : "description", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "type", + "sms:displayName" : "description", "sms:required" : "sms:false" }, { - "@id" : "bts:etag", + "@id" : "bts:compoundDoseUnit", "@type" : "rdfs:Class", - "rdfs:comment" : "Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. The E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date.", - "rdfs:label" : "etag", + "rdfs:comment" : "A unit associated with the value(s) in compoundDose.", + "rdfs:label" : "compoundDoseUnit", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "etag", + "sms:displayName" : "compoundDoseUnit", "sms:required" : "sms:false" }, { - "@id" : "bts:runtimePlatform", - "@type" : "rdfs:Class", - "rdfs:comment" : "Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).", - "rdfs:label" : "runtimePlatform", "rdfs:subClassOf" : [ ], + "@id" : "bts:isStranded", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "runtimePlatform", - "sms:required" : "sms:false" - }, { - "@id" : "bts:manifestation", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + } ], + "rdfs:label" : "isStranded", + "rdfs:comment" : "Whether or not the library is stranded (Yes; No)", "@type" : "rdfs:Class", - "rdfs:comment" : "An associated phenotype characteristic.", - "rdfs:label" : "manifestation", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "manifestation", - "sms:required" : "sms:false" + "sms:displayName" : "isStranded" }, { - "@id" : "bts:concentrationNaCl", + "@id" : "bts:genomicReferenceLink", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value for NaCl concentration", - "rdfs:label" : "concentrationNaCl", + "rdfs:comment" : "Link to genome reference data file used for alignment in processing workflow", + "rdfs:label" : "genomicReferenceLink", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "concentrationNaCl", + "sms:displayName" : "genomicReferenceLink", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:resourceType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:experimentalData" - }, { - "@id" : "bts:result" - }, { - "@id" : "bts:tool" - }, { - "@id" : "bts:workflowreport" - }, { - "@id" : "bts:report" - }, { - "@id" : "bts:metadata" - }, { - "@id" : "bts:protocol" - }, { - "@id" : "bts:weblink" - } ], - "rdfs:label" : "resourceType", - "rdfs:comment" : "The type of resource being stored and annotated", - "@type" : "rdfs:Class", - "sms:displayName" : "resourceType" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:dissociationMethod", + "@id" : "bts:programmingLanguage", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:10x_v2" - }, { - "@id" : "bts:FACS" - }, { - "@id" : "bts:FluidigmC1" + "@id" : "bts:Python" }, { - "@id" : "bts:drop-seq" + "@id" : "bts:R" }, { - "@id" : "bts:inDrop" + "@id" : "bts:MATLAB" }, { - "@id" : "bts:mouthpipette" + "@id" : "bts:Java" }, { - "@id" : "bts:enzymatic" + "@id" : "bts:C" }, { - "@id" : "bts:mechanical" - } ], - "rdfs:label" : "dissociationMethod", - "rdfs:comment" : "Procedure by which a biological specimen is dissociated into individual cells or a cell suspension", - "@type" : "rdfs:Class", - "sms:displayName" : "dissociationMethod" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:materialType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:nanoparticles" + "@id" : "bts:C++" }, { - "@id" : "bts:polymericnanoparticles" + "@id" : "bts:C#" }, { - "@id" : "bts:smallmolecule" + "@id" : "bts:Javascript" }, { - "@id" : "bts:DNA" + "@id" : "bts:bash" } ], - "rdfs:label" : "materialType", - "rdfs:comment" : "Type of material in the characterization", - "@type" : "rdfs:Class", - "sms:displayName" : "materialType" - }, { - "@id" : "bts:auxiliaryAsset", + "rdfs:label" : "programmingLanguage", + "rdfs:comment" : "A computer programming language", "@type" : "rdfs:Class", - "rdfs:comment" : "URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity.\n", - "rdfs:label" : "auxiliaryAsset", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "auxiliaryAsset", - "sms:required" : "sms:false" + "sms:displayName" : "programmingLanguage" }, { - "@id" : "bts:doi", + "@id" : "bts:slideID", "@type" : "rdfs:Class", - "rdfs:comment" : "Digital object identifier of the resource.", - "rdfs:label" : "doi", + "rdfs:comment" : "Unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.\n", + "rdfs:label" : "slideID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "doi", + "sms:displayName" : "slideID", "sms:required" : "sms:false" }, { - "@id" : "bts:readsDuplicatedPercent", + "@id" : "bts:sourceName", "@type" : "rdfs:Class", - "rdfs:comment" : "Percent of duplicated reads collected from samtools", - "rdfs:label" : "readsDuplicatedPercent", + "rdfs:comment" : "Intended for non-biological samples, tf the sample is a nanoparticle sample or some chemical substance not derived from a biological material, the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.\n", + "rdfs:label" : "sourceName", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "readsDuplicatedPercent", + "sms:displayName" : "sourceName", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:isMultiSpecimen", + "@id" : "bts:readPairOrientation", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:fr-firststrand" }, { - "@id" : "bts:No" + "@id" : "bts:inward" + }, { + "@id" : "bts:matching" + }, { + "@id" : "bts:outward" } ], - "rdfs:label" : "isMultiSpecimen", - "rdfs:comment" : "Whether or not a file has data for multiple specimens (Yes; No)", + "rdfs:label" : "readPairOrientation", + "rdfs:comment" : "The relative orientation of the reads in a paired-end protocol", "@type" : "rdfs:Class", - "sms:displayName" : "isMultiSpecimen" + "sms:displayName" : "readPairOrientation" }, { + "@id" : "bts:fileSize", + "@type" : "rdfs:Class", + "rdfs:comment" : "Size of file in bytes.", + "rdfs:label" : "fileSize", "rdfs:subClassOf" : [ ], - "@id" : "bts:MRISequence", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:PD-weighted" - }, { - "@id" : "bts:ShortTauInversionRecovery" - }, { - "@id" : "bts:T1-weighted" - }, { - "@id" : "bts:T2-weighted" - } ], - "rdfs:label" : "MRISequence", - "rdfs:comment" : "A mode used in MRI imaging", - "@type" : "rdfs:Class", - "sms:displayName" : "MRISequence" + "sms:displayName" : "fileSize", + "sms:required" : "sms:false" }, { - "@id" : "bts:datasetSizeInBytes", + "@id" : "bts:benefactorId", "@type" : "rdfs:Class", - "rdfs:comment" : "Size of dataset entity in bytes. Auto-calculated by Synapse.", - "rdfs:label" : "datasetSizeInBytes", + "rdfs:comment" : "The id of the resource from which access control is inherited.", + "rdfs:label" : "benefactorId", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "datasetSizeInBytes", + "sms:displayName" : "benefactorId", "sms:required" : "sms:false" }, { + "@id" : "bts:createdOn", + "@type" : "rdfs:Class", + "rdfs:comment" : "Refers to when the resource was created.", + "rdfs:label" : "createdOn", "rdfs:subClassOf" : [ ], - "@id" : "bts:yearProcessed", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "yearProcessed", - "rdfs:comment" : "Year in which the resource was processed/derived.", - "@type" : "rdfs:Class", - "sms:displayName" : "yearProcessed" + "sms:displayName" : "createdOn", + "sms:required" : "sms:false" }, { - "@id" : "bts:referenceSequence", + "@id" : "bts:protocolPurpose", "@type" : "rdfs:Class", - "rdfs:comment" : "Syntactic sequences that has a role as reference of an annotation.", - "rdfs:label" : "referenceSequence", + "rdfs:comment" : "Brief description of the protocol purpose.", + "rdfs:label" : "protocolPurpose", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "referenceSequence", + "sms:displayName" : "protocolPurpose", "sms:required" : "sms:false" }, { - "@id" : "bts:title", + "@id" : "bts:reporterSubstance", "@type" : "rdfs:Class", - "rdfs:comment" : "Title of a resource.", - "rdfs:label" : "title", + "rdfs:comment" : "A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.", + "rdfs:label" : "reporterSubstance", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "title", - "sms:required" : "sms:true" + "sms:displayName" : "reporterSubstance", + "sms:required" : "sms:false" }, { - "@id" : "bts:documentation", - "@type" : "rdfs:Class", - "rdfs:comment" : "URL to any documentation describing the resource and its use.", - "rdfs:label" : "documentation", "rdfs:subClassOf" : [ ], + "@id" : "bts:slideVersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "documentation", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:V1" + }, { + "@id" : "bts:V2" + }, { + "@id" : "bts:V3" + }, { + "@id" : "bts:V4" + } ], + "rdfs:label" : "slideVersion", + "rdfs:comment" : "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "@type" : "rdfs:Class", + "sms:displayName" : "slideVersion" }, { - "@id" : "bts:relatedDataset", + "@id" : "bts:reporterGene", "@type" : "rdfs:Class", - "rdfs:comment" : "Reference to a relevant dataset entity.", - "rdfs:label" : "relatedDataset", + "rdfs:comment" : "A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.", + "rdfs:label" : "reporterGene", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "relatedDataset", + "sms:displayName" : "reporterGene", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:concentrationMaterialUnit", + "@id" : "bts:nf1Genotype", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:mg/mL" + "@id" : "bts:-/-" }, { - "@id" : "bts:mM" + "@id" : "bts:+/-" }, { - "@id" : "bts:particles/mL" + "@id" : "bts:+/+" + }, { + "@id" : "bts:Unknown" + }, { + "@id" : "bts:Unknown" } ], - "rdfs:label" : "concentrationMaterialUnit", - "rdfs:comment" : "Unit used for the material concentration, e.g. mg/mL", + "rdfs:label" : "nf1Genotype", + "rdfs:comment" : "Genotype of NF1 gene in the biospecimen from which the data were derived, if known.", "@type" : "rdfs:Class", - "sms:displayName" : "concentrationMaterialUnit" + "sms:displayName" : "nf1Genotype" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:proportionCoverage10x", + "@id" : "bts:diagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "proportionCoverage10x", - "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", + "schema:rangeIncludes" : [ { + "@id" : "bts:Neurofibromatosistype1" + }, { + "@id" : "bts:Neurofibromatosistype2" + }, { + "@id" : "bts:Schwannomatosis" + }, { + "@id" : "bts:SporadicSchwannoma" + } ], + "rdfs:label" : "diagnosis", + "rdfs:comment" : "A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.", "@type" : "rdfs:Class", - "sms:displayName" : "proportionCoverage10x" + "sms:displayName" : "diagnosis" }, { - "@id" : "bts:studyName", + "@id" : "bts:targetDepth", "@type" : "rdfs:Class", - "rdfs:comment" : "Name of a study.", - "rdfs:label" : "studyName", + "rdfs:comment" : "The targeted read depth prior to sequencing.", + "rdfs:label" : "targetDepth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "studyName", - "sms:required" : "sms:true" + "sms:displayName" : "targetDepth", + "sms:required" : "sms:false" }, { - "@id" : "bts:libraryID", + "@id" : "bts:creator", "@type" : "rdfs:Class", - "rdfs:comment" : "", - "rdfs:label" : "libraryID", + "rdfs:comment" : "An entity responsible for making the resource.", + "rdfs:label" : "creator", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "libraryID", - "sms:required" : "sms:false" + "sms:displayName" : "creator", + "sms:required" : "sms:true" }, { - "@id" : "bts:author", - "@type" : "rdfs:Class", - "rdfs:comment" : "The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.", - "rdfs:label" : "author", "rdfs:subClassOf" : [ ], + "@id" : "bts:age", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "author", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "age", + "rdfs:comment" : "A numeric value representing age of the individual. Use with `ageUnit`.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:ageUnit" + } ], + "sms:displayName" : "age" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:isPrimaryCell", + "@id" : "bts:isCellLine", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -2341,2942 +1509,3774 @@ "schema:rangeIncludes" : [ { "@id" : "bts:Yes" }, { - "@id" : "bts:No" + "@id" : "bts:No" + } ], + "rdfs:label" : "isCellLine", + "rdfs:comment" : "Whether or not sample source is a cell line (Yes; No)", + "@type" : "rdfs:Class", + "sms:displayName" : "isCellLine" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:libraryPreparationMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:10x" + }, { + "@id" : "bts:CEL-seq" + }, { + "@id" : "bts:Drop-Seq" + }, { + "@id" : "bts:GTAC@WUSTLin-houseprep" + }, { + "@id" : "bts:IDTxGenExomeResearchPanel" + }, { + "@id" : "bts:IlluminaTruSeqDNANano" + }, { + "@id" : "bts:KAPAHyperPrepKitPCR-free" + }, { + "@id" : "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)" + }, { + "@id" : "bts:KAPAmRNAHyperPrepKit" + }, { + "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" + }, { + "@id" : "bts:Omni-ATAC" + }, { + "@id" : "bts:QuantSeqFWDV2withUDI" + }, { + "@id" : "bts:Smart-seq2" + }, { + "@id" : "bts:Smart-seq4" + }, { + "@id" : "bts:TruSeq" + }, { + "@id" : "bts:TruSeqstandardtotalRNAlibrarykit" + }, { + "@id" : "bts:unknown" } ], - "rdfs:label" : "isPrimaryCell", - "rdfs:comment" : "Whether or not cellType is primary (Yes; No)", + "rdfs:label" : "libraryPreparationMethod", + "rdfs:comment" : "Method by which library was prepared", "@type" : "rdfs:Class", - "sms:displayName" : "isPrimaryCell" + "sms:displayName" : "libraryPreparationMethod" }, { - "@id" : "bts:citation", + "@id" : "bts:publisher", "@type" : "rdfs:Class", - "rdfs:comment" : "Citation (e.g. doi) that usage of data or resource should be cited with.", - "rdfs:label" : "citation", + "rdfs:comment" : "An entity responsible for making the resource available.", + "rdfs:label" : "publisher", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "citation", + "sms:displayName" : "publisher", "sms:required" : "sms:false" }, { - "@id" : "bts:sampleType", + "@id" : "bts:averageBaseQuality", "@type" : "rdfs:Class", - "rdfs:comment" : "Type of sample used", - "rdfs:label" : "sampleType", + "rdfs:comment" : "Average base quality collected from samtools", + "rdfs:label" : "averageBaseQuality", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "sampleType", + "sms:displayName" : "averageBaseQuality", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:recordingSource", + "@id" : "bts:sex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:electrode" - }, { - "@id" : "bts:tetrode" + "@id" : "bts:Male" }, { - "@id" : "bts:shank" + "@id" : "bts:Female" }, { - "@id" : "bts:Utaharray" + "@id" : "bts:Unknown" }, { - "@id" : "bts:otherelectrodearray" + "@id" : "bts:NotApplicable" } ], - "rdfs:label" : "recordingSource", - "rdfs:comment" : "Source of electrophysiology recording.", + "rdfs:label" : "sex", + "rdfs:comment" : "Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.", "@type" : "rdfs:Class", - "sms:displayName" : "recordingSource" + "sms:displayName" : "sex" }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:workflow", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:CNVkit" - }, { - "@id" : "bts:DeepVariant" - }, { - "@id" : "bts:DESeq2" - }, { - "@id" : "bts:FastQC" - }, { - "@id" : "bts:FreeBayes" - }, { - "@id" : "bts:GATKBaseRecalibration" - }, { - "@id" : "bts:GATKMarkDuplicates" - }, { - "@id" : "bts:MultiQC" - }, { - "@id" : "bts:Mutect2" - }, { - "@id" : "bts:Sarek" - }, { - "@id" : "bts:STARandSalmon" - }, { - "@id" : "bts:Strelka2" - }, { - "@id" : "bts:StringTie" - }, { - "@id" : "bts:TrimGalore" - } ], - "rdfs:label" : "workflow", - "rdfs:comment" : "Name and version of the workflow used to generate/analyze the data", + "@id" : "bts:createdBy", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:workflowLink" - } ], - "sms:displayName" : "workflow" - }, { + "rdfs:comment" : "Refers to the user who created the resource.", + "rdfs:label" : "createdBy", "rdfs:subClassOf" : [ ], - "@id" : "bts:pH", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "pH", - "rdfs:comment" : "Numeric value for pH (range 0-14)", - "@type" : "rdfs:Class", - "sms:displayName" : "pH" + "sms:displayName" : "createdBy", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:pairsOnDifferentChr", + "@id" : "bts:genePerturbationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "pairsOnDifferentChr", - "rdfs:comment" : "Pairs on different chromosomes collected from samtools", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "genePerturbationType", + "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", "@type" : "rdfs:Class", - "sms:displayName" : "pairsOnDifferentChr" + "sms:displayName" : "genePerturbationType" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:concentrationNaClUnit", + "@id" : "bts:compoundDose", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:mg/mL" - }, { - "@id" : "bts:mM" - }, { - "@id" : "bts:particles/mL" - } ], - "rdfs:label" : "concentrationNaClUnit", - "rdfs:comment" : "Unit used for the NaCl concentration, e.g. mM", + "rdfs:label" : "compoundDose", + "rdfs:comment" : "A dose quantity for the treatment compound. To be used with compoundDoseUnit.", "@type" : "rdfs:Class", - "sms:displayName" : "concentrationNaClUnit" + "sms:requiresDependency" : [ { + "@id" : "bts:compoundDoseUnit" + } ], + "sms:displayName" : "compoundDose" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:transplantationRecipientTissue", + "@id" : "bts:readDepth", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cerebralcortex" - }, { - "@id" : "bts:bonemarrow" - }, { - "@id" : "bts:plasma" - }, { - "@id" : "bts:DorsalRootGanglion" - }, { - "@id" : "bts:opticnerve" - }, { - "@id" : "bts:tumor-adjacentnormal" - }, { - "@id" : "bts:serum" - }, { - "@id" : "bts:spheroid" - }, { - "@id" : "bts:sciaticnerve" - }, { - "@id" : "bts:meninges" - }, { - "@id" : "bts:nervetissue" - }, { - "@id" : "bts:BuccalMucosa" - }, { - "@id" : "bts:embryonictissue" - }, { - "@id" : "bts:wholebrain" - }, { - "@id" : "bts:microtissue" - }, { - "@id" : "bts:retina" - }, { - "@id" : "bts:CDXtissue" - }, { - "@id" : "bts:organoid" - }, { - "@id" : "bts:splenocyte" - }, { - "@id" : "bts:blood" - }, { - "@id" : "bts:connectivetissue" - }, { - "@id" : "bts:primarytumor" - }, { - "@id" : "bts:PDXtissue" - }, { - "@id" : "bts:BuffyCoat" - } ], - "rdfs:label" : "transplantationRecipientTissue", - "rdfs:comment" : "Tissue into which a xenograph sample is transplanted", + "sms:validationRules" : [ "int" ], + "rdfs:label" : "readDepth", + "rdfs:comment" : "If available, the coverage statistic as output from bedtools coverage or samtools stats.", "@type" : "rdfs:Class", - "sms:displayName" : "transplantationRecipientTissue" + "sms:displayName" : "readDepth" }, { + "@id" : "bts:InChIKey", + "@type" : "rdfs:Class", + "rdfs:comment" : "A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). This is a more reliable identifier than the compound name and should be used if available.\n", + "rdfs:label" : "InChIKey", "rdfs:subClassOf" : [ ], - "@id" : "bts:specimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cerebralcortex" - }, { - "@id" : "bts:bonemarrow" - }, { - "@id" : "bts:plasma" - }, { - "@id" : "bts:DorsalRootGanglion" - }, { - "@id" : "bts:opticnerve" - }, { - "@id" : "bts:tumor-adjacentnormal" - }, { - "@id" : "bts:serum" - }, { - "@id" : "bts:spheroid" - }, { - "@id" : "bts:sciaticnerve" - }, { - "@id" : "bts:meninges" - }, { - "@id" : "bts:nervetissue" - }, { - "@id" : "bts:BuccalMucosa" - }, { - "@id" : "bts:embryonictissue" - }, { - "@id" : "bts:wholebrain" - }, { - "@id" : "bts:microtissue" - }, { - "@id" : "bts:retina" - }, { - "@id" : "bts:CDXtissue" - }, { - "@id" : "bts:organoid" - }, { - "@id" : "bts:splenocyte" - }, { - "@id" : "bts:blood" - }, { - "@id" : "bts:connectivetissue" - }, { - "@id" : "bts:primarytumor" - }, { - "@id" : "bts:PDXtissue" - }, { - "@id" : "bts:BuffyCoat" - }, { - "@id" : "bts:saliva" - }, { - "@id" : "bts:mucus" - }, { - "@id" : "bts:urine" - }, { - "@id" : "bts:stool" - }, { - "@id" : "bts:sweat" - } ], - "rdfs:label" : "specimenType", - "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", + "sms:displayName" : "InChIKey", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:concentrationMaterial", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "concentrationMaterial", + "rdfs:comment" : "Numeric value for concentration of the material", "@type" : "rdfs:Class", - "sms:displayName" : "specimenType" + "sms:displayName" : "concentrationMaterial" }, { - "@id" : "bts:datasetItemCount", + "@id" : "bts:fileCount", "@type" : "rdfs:Class", - "rdfs:comment" : "Count of files in dataset. Auto-calculated by Synapse.", - "rdfs:label" : "datasetItemCount", + "rdfs:comment" : "Number of files in the resource collection.", + "rdfs:label" : "fileCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "datasetItemCount", + "sms:displayName" : "fileCount", "sms:required" : "sms:false" }, { - "@id" : "bts:workflowLink", + "@id" : "bts:assayTarget", "@type" : "rdfs:Class", - "rdfs:comment" : "Workflow URL reference", - "rdfs:label" : "workflowLink", + "rdfs:comment" : "Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.", + "rdfs:label" : "assayTarget", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "workflowLink", + "sms:displayName" : "assayTarget", "sms:required" : "sms:false" }, { - "@id" : "bts:dataFileHandleId", + "@id" : "bts:license", "@type" : "rdfs:Class", - "rdfs:comment" : "(Files only) Refers to the id of the file.", - "rdfs:label" : "dataFileHandleId", + "rdfs:comment" : "Link to a license or name of license applicable for the resource.", + "rdfs:label" : "license", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "dataFileHandleId", + "sms:displayName" : "license", "sms:required" : "sms:false" }, { - "@id" : "bts:individualIdSource", + "rdfs:subClassOf" : [ ], + "@id" : "bts:readLength", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "int" ], + "rdfs:label" : "readLength", + "rdfs:comment" : "Number of base pairs (bp) sequenced for a read", "@type" : "rdfs:Class", - "rdfs:comment" : "Database or repository to which individual ID maps", - "rdfs:label" : "individualIdSource", + "sms:displayName" : "readLength" + }, { + "@id" : "bts:studyId", + "@type" : "rdfs:Class", + "rdfs:comment" : "Id of study.", + "rdfs:label" : "studyId", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "individualIdSource", + "sms:displayName" : "studyId", + "sms:required" : "sms:true" + }, { + "@id" : "bts:Filename", + "@type" : "rdfs:Class", + "rdfs:comment" : "The name of the file.", + "rdfs:label" : "Filename", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Filename", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:totalReads", + "@id" : "bts:readStrandOrigin", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "totalReads", - "rdfs:comment" : "If available, the total number of reads collected from samtools.", + "schema:rangeIncludes" : [ { + "@id" : "bts:forward" + }, { + "@id" : "bts:reverse" + } ], + "rdfs:label" : "readStrandOrigin", + "rdfs:comment" : "The strand from which the read originates in a strand-specific protocol", "@type" : "rdfs:Class", - "sms:displayName" : "totalReads" + "sms:displayName" : "readStrandOrigin" }, { - "@id" : "bts:contributor", + "@id" : "bts:series", "@type" : "rdfs:Class", - "rdfs:comment" : "An entity responsible for making contributions to the resource.", - "rdfs:label" : "contributor", + "rdfs:comment" : "Which series this resource belongs to, can be a name or link.", + "rdfs:label" : "series", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "contributor", + "sms:displayName" : "series", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:dataType", + "@id" : "bts:nf1Variant", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "nf1Variant", + "rdfs:comment" : "Named variant (mutation) in the NF1 gene/protein in the biospecimen from which the data were derived, if known/applicable.", + "@type" : "rdfs:Class", + "sms:displayName" : "nf1Variant" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ageUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:immunoassay" + "@id" : "bts:seconds" }, { - "@id" : "bts:behaviorprocess" + "@id" : "bts:minutes" }, { - "@id" : "bts:clinical" + "@id" : "bts:hours" }, { - "@id" : "bts:demographics" + "@id" : "bts:days" }, { - "@id" : "bts:particlecharacterization" + "@id" : "bts:weeks" }, { - "@id" : "bts:drugCombinationScreen" + "@id" : "bts:months" }, { - "@id" : "bts:isoformExpression" + "@id" : "bts:years" + } ], + "rdfs:label" : "ageUnit", + "rdfs:comment" : "A time unit that can be used with a given age value, e.g. years.", + "@type" : "rdfs:Class", + "sms:displayName" : "ageUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:progressReportNumber", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:1" }, { - "@id" : "bts:proteomics" + "@id" : "bts:2" }, { - "@id" : "bts:surveyData" + "@id" : "bts:3" }, { - "@id" : "bts:kinomics" + "@id" : "bts:4" }, { - "@id" : "bts:SomaticVariants" + "@id" : "bts:5" }, { - "@id" : "bts:Volume" + "@id" : "bts:6" }, { - "@id" : "bts:characteristic" + "@id" : "bts:7" }, { - "@id" : "bts:drugScreen" + "@id" : "bts:8" }, { - "@id" : "bts:geneExpression" + "@id" : "bts:9" }, { - "@id" : "bts:AlignedReads" + "@id" : "bts:10" }, { - "@id" : "bts:genomicFeatures" + "@id" : "bts:NotApplicable" + } ], + "rdfs:label" : "progressReportNumber", + "rdfs:comment" : "Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1", + "@type" : "rdfs:Class", + "sms:displayName" : "progressReportNumber" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:specimenPreparationMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Freshcollected" }, { - "@id" : "bts:genomicVariants" + "@id" : "bts:Flashfrozen" }, { - "@id" : "bts:rawcounts" + "@id" : "bts:FFPE" }, { - "@id" : "bts:PharmacokineticStudy" + "@id" : "bts:Cryopreserved" }, { - "@id" : "bts:maskimage" + "@id" : "bts:OCT" }, { - "@id" : "bts:chromatinActivity" + "@id" : "bts:RNAlater" }, { - "@id" : "bts:StructuralVariants" + "@id" : "bts:formalin-fixed" }, { - "@id" : "bts:GermlineVariants" + "@id" : "bts:ethanol" }, { - "@id" : "bts:CopyNumberVariants" + "@id" : "bts:Viablyfrozen" + } ], + "rdfs:label" : "specimenPreparationMethod", + "rdfs:comment" : "Term that represents preservation of the sample before usage in, e.g. sequencing", + "@type" : "rdfs:Class", + "sms:displayName" : "specimenPreparationMethod" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:isMultiIndividual", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" }, { - "@id" : "bts:image" + "@id" : "bts:No" + } ], + "rdfs:label" : "isMultiIndividual", + "rdfs:comment" : "Whether or not a file has data for multiple individuals (Yes; No)", + "@type" : "rdfs:Class", + "sms:displayName" : "isMultiIndividual" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:libraryStrand", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:FirstStranded" }, { - "@id" : "bts:network" + "@id" : "bts:SecondStranded" }, { - "@id" : "bts:cellularPhysiology" + "@id" : "bts:Unstranded" }, { - "@id" : "bts:metabolomics" + "@id" : "bts:NotApplicable" + } ], + "rdfs:label" : "libraryStrand", + "rdfs:comment" : "Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.", + "@type" : "rdfs:Class", + "sms:displayName" : "libraryStrand" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:immersion", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:air" + }, { + "@id" : "bts:oil" + }, { + "@id" : "bts:water" + }, { + "@id" : "bts:other" + } ], + "rdfs:label" : "immersion", + "rdfs:comment" : "Immersion medium", + "@type" : "rdfs:Class", + "sms:displayName" : "immersion" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:captureArea", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:A" + }, { + "@id" : "bts:B" }, { - "@id" : "bts:AnnotatedSomaticVariants" + "@id" : "bts:C" }, { - "@id" : "bts:AnnotatedGermlineVariants" + "@id" : "bts:D" }, { - "@id" : "bts:Weight" + "@id" : "bts:A1" }, { - "@id" : "bts:electrophysiology" + "@id" : "bts:B1" }, { - "@id" : "bts:audiotranscript" + "@id" : "bts:C1" }, { - "@id" : "bts:dataIndex" + "@id" : "bts:D1" + } ], + "rdfs:label" : "captureArea", + "rdfs:comment" : "One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.\n", + "@type" : "rdfs:Class", + "sms:displayName" : "captureArea" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:experimentalFactor", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:braingrowthmeasurement" }, { - "@id" : "bts:DescriptiveMetadata" + "@id" : "bts:brainvolumemeasurement" }, { - "@id" : "bts:StructuralMetadata" + "@id" : "bts:bodyweight" }, { - "@id" : "bts:AdministrativeMetadata" + "@id" : "bts:clinicallaboratorymeasurement" }, { - "@id" : "bts:ReferenceMetadata" + "@id" : "bts:cognitivefunctionmeasurement" }, { - "@id" : "bts:StatisticalMetadata" + "@id" : "bts:gaitmeasurement" }, { - "@id" : "bts:LegalMetadata" + "@id" : "bts:motordevelopmentmeasurement" }, { - "@id" : "bts:WorkflowMetadata" + "@id" : "bts:painmeasurement" } ], - "rdfs:label" : "dataType", - "rdfs:comment" : "A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.\n", + "rdfs:label" : "experimentalFactor", + "rdfs:comment" : "An ontology concept for experimental factor measured with this data.", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:dataSubtype" - } ], - "sms:displayName" : "dataType" + "sms:displayName" : "experimentalFactor" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:timepointUnit", + "@id" : "bts:readPair", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "inRange 1 2" ], + "rdfs:label" : "readPair", + "rdfs:comment" : "The read of origin, Read 1 or Read 2", + "@type" : "rdfs:Class", + "sms:displayName" : "readPair" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:workingDistanceUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:seconds" - }, { - "@id" : "bts:minutes" - }, { - "@id" : "bts:hours" + "@id" : "bts:angstrom" }, { - "@id" : "bts:days" + "@id" : "bts:nanometer" }, { - "@id" : "bts:weeks" + "@id" : "bts:micrometer" }, { - "@id" : "bts:months" + "@id" : "bts:millimeter" }, { - "@id" : "bts:years" + "@id" : "bts:centimeter" } ], - "rdfs:label" : "timepointUnit", - "rdfs:comment" : "For timed experiments this represents the unit of time measured", + "rdfs:label" : "workingDistanceUnit", + "rdfs:comment" : "Unit for working distance.", "@type" : "rdfs:Class", - "sms:displayName" : "timepointUnit" + "sms:displayName" : "workingDistanceUnit" }, { - "@id" : "bts:currentVersion", + "@id" : "bts:antibodyID", "@type" : "rdfs:Class", - "rdfs:comment" : "(Versionable entities only) The current version number of the resource.", - "rdfs:label" : "currentVersion", + "rdfs:comment" : "Antibody ID such as RRID if available, otherwise use vendor ID.", + "rdfs:label" : "antibodyID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "currentVersion", + "sms:displayName" : "antibodyID", "sms:required" : "sms:false" }, { - "@id" : "bts:genomicReference", + "@id" : "bts:specimenIDSource", "@type" : "rdfs:Class", - "rdfs:comment" : "Version of genome reference used for alignment in processing workflow", - "rdfs:label" : "genomicReference", + "rdfs:comment" : "Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.", + "rdfs:label" : "specimenIDSource", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "genomicReference", - "sms:required" : "sms:true" + "sms:displayName" : "specimenIDSource", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:dataSubtype", + "@id" : "bts:isPairedEnd", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:normalized" - }, { - "@id" : "bts:dataMatrix" - }, { - "@id" : "bts:raw" - }, { - "@id" : "bts:processed" - }, { - "@id" : "bts:metadata" + "@id" : "bts:Yes" }, { - "@id" : "bts:representative" + "@id" : "bts:No" } ], - "rdfs:label" : "dataSubtype", - "rdfs:comment" : "Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.", + "rdfs:label" : "isPairedEnd", + "rdfs:comment" : "(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).", "@type" : "rdfs:Class", - "sms:displayName" : "dataSubtype" + "sms:displayName" : "isPairedEnd" }, { + "@id" : "bts:dataStatus", + "@type" : "rdfs:Class", + "rdfs:comment" : "Status of data in a study.", + "rdfs:label" : "dataStatus", "rdfs:subClassOf" : [ ], - "@id" : "bts:organ", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:kidney" - }, { - "@id" : "bts:ovary" - }, { - "@id" : "bts:lung" - }, { - "@id" : "bts:bonemarrow" - }, { - "@id" : "bts:prostate" - }, { - "@id" : "bts:breast" - }, { - "@id" : "bts:mesentery" - }, { - "@id" : "bts:mammarygland" - }, { - "@id" : "bts:colon" - }, { - "@id" : "bts:spleen" - }, { - "@id" : "bts:BursaOfFabricius" - }, { - "@id" : "bts:nose" - }, { - "@id" : "bts:brain" - }, { - "@id" : "bts:pancreas" - }, { - "@id" : "bts:liver" - }, { - "@id" : "bts:blood" - }, { - "@id" : "bts:lymphnode" - }, { - "@id" : "bts:nerves" - }, { - "@id" : "bts:skin" - }, { - "@id" : "bts:eye" - } ], - "rdfs:label" : "organ", - "rdfs:comment" : "A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.", - "@type" : "rdfs:Class", - "sms:displayName" : "organ" + "sms:displayName" : "dataStatus", + "sms:required" : "sms:true" }, { - "@id" : "bts:id", + "@id" : "bts:contentSize", "@type" : "rdfs:Class", - "rdfs:comment" : "The entity id for the resource automatically assigned by the platform.", - "rdfs:label" : "id", + "rdfs:comment" : "(Files only) File size, usually calculated by the backend.", + "rdfs:label" : "contentSize", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "id", + "sms:displayName" : "contentSize", "sms:required" : "sms:false" }, { + "@id" : "bts:targetCaptureKitID", + "@type" : "rdfs:Class", + "rdfs:comment" : "A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.\n", + "rdfs:label" : "targetCaptureKitID", "rdfs:subClassOf" : [ ], - "@id" : "bts:isXenograft", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isXenograft", - "rdfs:comment" : "Whether or not sample source is a xenograft (Yes; No)", + "sms:displayName" : "targetCaptureKitID", + "sms:required" : "sms:false" + }, { + "@id" : "bts:aliquotID", "@type" : "rdfs:Class", - "sms:displayName" : "isXenograft" + "rdfs:comment" : "A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.", + "rdfs:label" : "aliquotID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "aliquotID", + "sms:required" : "sms:false" }, { - "@id" : "bts:Resource_id", + "@id" : "bts:initiative", "@type" : "rdfs:Class", - "rdfs:comment" : "A UUID for a Resource from the NF Research Tools Database", - "rdfs:label" : "Resource_id", + "rdfs:comment" : "Refers to a funding initiative. This annotation is usually handled by the DCC or funder, not the researcher.", + "rdfs:label" : "initiative", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Resource_id", + "sms:displayName" : "initiative", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:drugScreenType", + "@id" : "bts:nominalMagnification", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "nominalMagnification", + "rdfs:comment" : "magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens.", + "@type" : "rdfs:Class", + "sms:displayName" : "nominalMagnification" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:genePerturbationTechnology", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:combinationlibraryscreen" - 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"@id" : "bts:HeLaSilenciXNF1" + "@id" : "bts:gct" }, { - "@id" : "bts:hTERTNF1ipNF95.11bC/T" + "@id" : "bts:gff3" }, { - "@id" : "bts:HEK293NF1-/-Exon47insT#14" + "@id" : "bts:gtf" }, { - "@id" : "bts:HS-PSS" + "@id" : "bts:gzip" }, { - "@id" : "bts:YST-1" + "@id" : "bts:hdf5" }, { - "@id" : "bts:M3MPNST" + "@id" : "bts:hdr" }, { - "@id" : "bts:S462.TY" + "@id" : "bts:hic" }, { - "@id" : "bts:S462" + "@id" : "bts:html" }, { - "@id" : "bts:HEK293NF1-/-Exon17#B48G629Rcrypticsplice" + "@id" : "bts:hyperlink" }, { - "@id" : "bts:GM11602" + "@id" : "bts:idat" }, { - "@id" : "bts:Lis47_NF1_2N" + "@id" : "bts:idx" }, { - "@id" : "bts:hTERTNF1sipnNF95.12B" + "@id" : "bts:img" }, { - "@id" : "bts:KCL025" + "@id" : "bts:jpg" }, { - "@id" : "bts:SchwanncellNF1-/-withR816XmNf1cDNA" + "@id" : "bts:js" }, { - "@id" : "bts:hiPSC-SCP" + "@id" : "bts:json" }, { - "@id" : "bts:sNF96.2" + "@id" : "bts:locs" }, { - "@id" : "bts:cNF98.4c" + "@id" : "bts:maf" }, { - "@id" : "bts:NF1-R68XEmbryoniccells" + "@id" : "bts:md" }, { - "@id" : "bts:BJFF.6" + "@id" : "bts:mov" }, { - "@id" : "bts:Ben-Men-1" + "@id" : "bts:msf" }, { - "@id" : "bts:HEK293NF1-/-withR816XmNf1cDNA" + "@id" : "bts:mtx" }, { - "@id" : "bts:hTERTNF1ipNF05.5" + "@id" : "bts:mzML" }, { - "@id" : "bts:i18cNF" + "@id" : "bts:nii" }, { - "@id" : "bts:hTERTSCipn97.4" + "@id" : "bts:ome-tiff" }, { - "@id" : "bts:i21cNF" + "@id" : "bts:pdf" }, { - "@id" : "bts:cNF98.4d" + "@id" : "bts:plink" }, { - "@id" : "bts:28cNF" + "@id" : "bts:png" }, { - "@id" : "bts:SC4[Mouseschwannoma]" + "@id" : "bts:powerpoint" }, { - "@id" : "bts:cNF18.1a" + "@id" : "bts:pzfx" }, { - "@id" : "bts:Nf1Arg681*/Arg681*ES" + "@id" : "bts:raw" }, { - "@id" : "bts:GM11601" + "@id" : "bts:rds" }, { - "@id" : "bts:HEK293NF1-/-withR2550XmNf1cDNA" + "@id" : "bts:recal" }, { - "@id" : "bts:JH-2-103-CL" + "@id" : "bts:rmd" }, { - "@id" : "bts:HS-Sch-2" + "@id" : "bts:sam" }, { - "@id" : "bts:hTERTNF1ipn02.32λ" + "@id" : "bts:sav" }, { - "@id" : "bts:ELK-TADLuciferaseReporterHEK293Stable" + "@id" : "bts:sdf" }, { - "@id" : "bts:6PNF_SiPSrv_PM_2" + "@id" : "bts:seg" }, { - "@id" : "bts:hTERTNF1ipNF03.3" + "@id" : "bts:sf" }, { - "@id" : "bts:JH-2-079-CL" + "@id" : "bts:sif" }, { - "@id" : "bts:hTERTNF1ipNF04.4" + "@id" : "bts:sqlite" }, { - "@id" : "bts:Nf1Arg681*/Arg681*MEFs" + "@id" : "bts:sra" }, { - "@id" : "bts:Nf1Arg681*/+ES" + "@id" : "bts:svg" }, { - "@id" : "bts:cNF97.2a" + "@id" : "bts:svs" }, { - "@id" : "bts:Schwanncelli28cNFNF1-/-(#14)" + "@id" : "bts:tagAlign" }, { - "@id" : "bts:hTERTNF1ipNF00.6" + "@id" : "bts:tar" }, { - "@id" : "bts:NCC-MPNST3-X2-C1" + "@id" : "bts:tbi" }, { - "@id" : "bts:JHU2-002-PDX" + "@id" : "bts:tif" }, { - "@id" : "bts:hTERTNF1ipNF95.11bC" + "@id" : "bts:tom" }, { - "@id" : "bts:5PNF_TDiPSsv_MM_4" + "@id" : "bts:tranches" }, { - "@id" : "bts:hTERTNF1ipn06.2A" + "@id" : "bts:tsv" }, { - "@id" : "bts:hTERTSCipn02.8" + "@id" : "bts:txt" }, { - "@id" : "bts:SZ-NF2" + "@id" : "bts:vcf" }, { - "@id" : "bts:B6;129S2-Trp53tm1TyjNf1tm1Tyj/J" + "@id" : "bts:wiggle" }, { - "@id" : "bts:Prss56Cre;R26mT" + "@id" : "bts:xml" }, { - "@id" : "bts:B6.129S1-Nf1tm1Cbr/J" + "@id" : "bts:yaml" }, { - "@id" : "bts:Nf1-OPG" + "@id" : "bts:zip" + } ], + "rdfs:label" : "fileFormat", + "rdfs:comment" : "Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software", + "@type" : "rdfs:Class", + "sms:displayName" : "fileFormat" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nf2Genotype", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:-/-" }, { - "@id" : "bts:C57BL/6J" + "@id" : "bts:+/-" }, { - "@id" : "bts:NRG" + "@id" : "bts:+/+" }, { - "@id" : "bts:Nf1-OPG-Arg816" + "@id" : "bts:Unknown" }, { - "@id" : "bts:NODscidgamma" + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "nf2Genotype", + "rdfs:comment" : "Genotype of NF2 gene in the biospecimen from which the data were derived, if known", + "@type" : "rdfs:Class", + "sms:displayName" : "nf2Genotype" + }, { + "@id" : "bts:Component", + "@type" : "rdfs:Class", + "rdfs:comment" : "Type of metadata template; provide the same one for all items/rows.", + "rdfs:label" : "Component", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Component", + "sms:required" : "sms:true" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:species", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Rattusnorvegicus" }, { - "@id" : "bts:B6.129S2-Nf1tm1Tyj/J" + "@id" : "bts:Gallusgallus" }, { - "@id" : "bts:B6;129-Trp53tm1TyjNf1tm1TyjSuz12Gt(Betageo)1Khe/KcichJ" + "@id" : "bts:Pantroglodytes" }, { - "@id" : "bts:B6.129(Cg)-Nf1tm1Par/J" + "@id" : "bts:Musmusculus(humanized)" }, { - "@id" : "bts:GFAP-Cre;Nf1-G848R/Flox" + "@id" : "bts:Homosapiens" }, { - "@id" : "bts:GFAP-Cre;Nf1-R681X/Flox" + "@id" : "bts:Daniorerio" }, { - "@id" : "bts:GFAP-Cre;Nf1-C383X/Flox" + "@id" : "bts:Drosophilamelanogaster" }, { - "@id" : "bts:Nf1-C848R/Flox" + "@id" : "bts:Rhesusmacaque" }, { - "@id" : "bts:Nf1-R681X/Flox" + "@id" : "bts:Susscrofa" }, { - "@id" : "bts:Nf1-C383X/Flox" + "@id" : "bts:Oryctolaguscuniculus" }, { - "@id" : "bts:Nf1flox/flox" + "@id" : "bts:Musmusculus" } ], - "rdfs:label" : "modelSystemName", - "rdfs:comment" : "A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)", + "rdfs:label" : "species", + "rdfs:comment" : "The name of a species (typically a taxonomic group) of organism.", "@type" : "rdfs:Class", - "sms:displayName" : "modelSystemName" + "sms:displayName" : "species" + }, { + "@id" : "bts:concreteType", + "@type" : "rdfs:Class", + "rdfs:comment" : "Refers to the class model the data platform uses for representing the resource. This is a low-level field set by the platform and is not a user annotation.", + "rdfs:label" : "concreteType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "concreteType", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:proteinExtractSource", + "@id" : "bts:transplantationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:celllysate" + "@id" : "bts:allograft" }, { - "@id" : "bts:cytoplasm" + "@id" : "bts:xenograft" }, { - "@id" : "bts:mitochondria" + "@id" : "bts:autograft" }, { - "@id" : "bts:nuclearextract" + "@id" : "bts:isograft" } ], - "rdfs:label" : "proteinExtractSource", - "rdfs:comment" : "Source of the extracted protein used in the experiment", + "rdfs:label" : "transplantationType", + "rdfs:comment" : "Type of transplantation involved in the experiment, derived from MESH", "@type" : "rdfs:Class", - "sms:displayName" : "proteinExtractSource" + "sms:displayName" : "transplantationType" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:dataCollectionMode", + "@id" : "bts:yearPublished", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", + "sms:validationRules" : [ "int" ], + "rdfs:label" : "yearPublished", + "rdfs:comment" : "Year in which the resource was published.", + "@type" : "rdfs:Class", + "sms:displayName" : "yearPublished" + }, { + "@id" : "bts:fundingAgency", + "@type" : "rdfs:Class", + "rdfs:comment" : "Refers to the funding organization for the generated resource. This annotation is handled by the DCC.", + "rdfs:label" : "fundingAgency", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "fundingAgency", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nucleicAcidSource", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:DDA" + "@id" : "bts:bulkcell" }, { - "@id" : "bts:DIA" + "@id" : "bts:bulknuclei" }, { - "@id" : "bts:Other" + "@id" : "bts:mitochondria" + }, { + "@id" : "bts:singlecell" + }, { + "@id" : "bts:singlenucleus" } ], - "rdfs:label" : "dataCollectionMode", - "rdfs:comment" : "Mode of data collection in tandem MS assays. Either DDA (data-dependent acquisition) or DIA (data-independent) acquisition.", + "rdfs:label" : "nucleicAcidSource", + "rdfs:comment" : "Source of the extracted nucleic acid used in the experiment", "@type" : "rdfs:Class", - "sms:displayName" : "dataCollectionMode" + "sms:displayName" : "nucleicAcidSource" + }, { + "@id" : "bts:meanCoverage", + "@type" : "rdfs:Class", + "rdfs:comment" : "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools", + "rdfs:label" : "meanCoverage", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "meanCoverage", + "sms:required" : "sms:false" + }, { + "@id" : "bts:genePerturbed", + "@type" : "rdfs:Class", + "rdfs:comment" : "The HUGO gene symbol for the gene that is perturbed.", + "rdfs:label" : "genePerturbed", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "genePerturbed", + "sms:required" : "sms:false" + }, { + "@id" : "bts:type", + "@type" : "rdfs:Class", + "rdfs:comment" : "Refers to the type of the resource on the platform, e.g. “file”.", + "rdfs:label" : "type", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "type", + "sms:required" : "sms:false" + }, { + "@id" : "bts:etag", + "@type" : "rdfs:Class", + "rdfs:comment" : "Synapse employs an Optimistic Concurrency Control (OCC) scheme to handle concurrent updates. The E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date.", + "rdfs:label" : "etag", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "etag", + "sms:required" : "sms:false" + }, { + "@id" : "bts:runtimePlatform", + "@type" : "rdfs:Class", + "rdfs:comment" : "Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).", + "rdfs:label" : "runtimePlatform", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "runtimePlatform", + "sms:required" : "sms:false" + }, { + "@id" : "bts:manifestation", + "@type" : "rdfs:Class", + "rdfs:comment" : "An associated phenotype characteristic.", + "rdfs:label" : "manifestation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "manifestation", + "sms:required" : "sms:false" + }, { + "@id" : "bts:concentrationNaCl", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value for NaCl concentration", + "rdfs:label" : "concentrationNaCl", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "concentrationNaCl", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:bodySite", + "@id" : "bts:resourceType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:axilla" - }, { - "@id" : "bts:groin" - }, { - "@id" : "bts:leg" - }, { - "@id" : "bts:thoracicspine" - }, { - "@id" : "bts:forearm" - }, { - "@id" : "bts:acetabulum" - }, { - "@id" : "bts:muscle" - }, { - "@id" : "bts:finger" - }, { - "@id" : "bts:iliacspine" - }, { - "@id" : "bts:head" - }, { - "@id" : "bts:neck" - }, { - "@id" : "bts:shoulder" + "@id" : "bts:experimentalData" }, { - "@id" : "bts:back" + "@id" : "bts:result" }, { - "@id" : "bts:spine" + "@id" : "bts:tool" }, { - "@id" : "bts:scalp" + "@id" : "bts:workflowreport" }, { - "@id" : "bts:scapula" + "@id" : "bts:report" }, { - "@id" : "bts:pelvis" + "@id" : "bts:metadata" }, { - "@id" : "bts:dorsolateralprefrontalcortex" + "@id" : "bts:protocol" }, { - "@id" : "bts:occcipitallobe" + "@id" : "bts:weblink" } ], - "rdfs:label" : "bodySite", - "rdfs:comment" : "Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.", + "rdfs:label" : "resourceType", + "rdfs:comment" : "The type of resource being stored and annotated", "@type" : "rdfs:Class", - "sms:displayName" : "bodySite" + "sms:displayName" : "resourceType" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryPrep", + "@id" : "bts:dissociationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:lncRNAenrichment" - }, { - "@id" : "bts:miRNAenrichment" - }, { - "@id" : "bts:polyAselection" - }, { - "@id" : "bts:rRNAdepletion" - } ], - "rdfs:label" : "libraryPrep", - "rdfs:comment" : "The general strategy by which the library was prepared", - "@type" : "rdfs:Class", - "sms:displayName" : "libraryPrep" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:tumorType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:DiffuseAstrocytoma" - }, { - "@id" : "bts:SubcutaneousNeurofibroma" - }, { - "@id" : "bts:PilomyxoidAstrocytoma" - }, { - "@id" : "bts:JuvenileMyelomonocyticLeukemia" - }, { - "@id" : "bts:AnaplasticAstrocytoma" - }, { - "@id" : "bts:MalignantPeripheralNerveSheathTumor" - }, { - "@id" : "bts:LocalizedNeurofibroma" - }, { - "@id" : "bts:CutaneousNeurofibroma" - }, { - "@id" : "bts:ColorectalAdenocarcinoma" - }, { - "@id" : "bts:AnaplasticPilocyticAstrocytoma" - }, { - "@id" : "bts:Schwannoma" - }, { - "@id" : "bts:HemorrhagicNeoplasm" - }, { - "@id" : "bts:NotApplicable" - }, { - "@id" : "bts:PilocyticAstrocytoma" - }, { - "@id" : "bts:Ganglioglioma" - }, { - "@id" : "bts:PlexiformNeurofibroma" - }, { - "@id" : "bts:NF2-AssociatedTumor" - }, { - "@id" : "bts:Fibrosarcoma" - }, { - "@id" : "bts:Low-GradeGliomaNOS" - }, { - "@id" : "bts:Glioblastoma" - }, { - "@id" : "bts:AnaplasticPleomorphicXanthoastrocytoma" - 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This could be a patient or animal ID.", - "rdfs:label" : "individualID", + "rdfs:comment" : "Title of a resource.", + "rdfs:label" : "title", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "individualID", + "sms:displayName" : "title", "sms:required" : "sms:true" }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:failedQC", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "failedQC", - "rdfs:comment" : "Whether the sample or data failed QC checks (Yes, No)", - "@type" : "rdfs:Class", - "sms:displayName" : "failedQC" - }, { - "@id" : "bts:compoundName", + "@id" : "bts:documentation", "@type" : "rdfs:Class", - "rdfs:comment" : "Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)", - "rdfs:label" : "compoundName", + "rdfs:comment" : "URL to any documentation describing the resource and its use.", + "rdfs:label" : "documentation", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "compoundName", + "sms:displayName" : "documentation", "sms:required" : "sms:false" }, { - "@id" : "bts:isFilteredReads", + "@id" : "bts:relatedDataset", "@type" : "rdfs:Class", - "rdfs:comment" : "Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator", - "rdfs:label" : "isFilteredReads", + "rdfs:comment" : "Reference to a relevant dataset entity.", + "rdfs:label" : "relatedDataset", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "isFilteredReads", + "sms:displayName" : "relatedDataset", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:runType", + "@id" : "bts:concentrationMaterialUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:pairedEnd" + "@id" : "bts:mg/mL" }, { - "@id" : "bts:singleEnd" + "@id" : "bts:mM" + }, { + "@id" : "bts:particles/mL" } ], - "rdfs:label" : "runType", - "rdfs:comment" : "Sequencing run type.", + "rdfs:label" : "concentrationMaterialUnit", + "rdfs:comment" : "Unit used for the material concentration, e.g. mg/mL", "@type" : "rdfs:Class", - "sms:displayName" : "runType" + "sms:displayName" : "concentrationMaterialUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:lensAperture", + "@id" : "bts:proportionCoverage10x", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:validationRules" : [ "num" ], - "rdfs:label" : "lensAperture", - "rdfs:comment" : "Numerical aperture of the lens. 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The parentSpecimenID can be the same as specimenID when there is no subsectioning.\n", - "rdfs:label" : "parentSpecimenID", + "sms:displayName" : "pH" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:pairsOnDifferentChr", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "parentSpecimenID", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:validationRules" : [ "int" ], + "rdfs:label" : "pairsOnDifferentChr", + "rdfs:comment" : "Pairs on different chromosomes collected from samtools", + "@type" : "rdfs:Class", + "sms:displayName" : "pairsOnDifferentChr" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:experimentalTimepoint", + "@id" : "bts:concentrationNaClUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "experimentalTimepoint", - "rdfs:comment" : "The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:timepointUnit" + "schema:rangeIncludes" : [ { + "@id" : "bts:mg/mL" + }, { + "@id" : "bts:mM" + }, { + "@id" : "bts:particles/mL" } ], - "sms:displayName" : "experimentalTimepoint" + "rdfs:label" : "concentrationNaClUnit", + "rdfs:comment" : "Unit used for the NaCl concentration, e.g. mM", + "@type" : "rdfs:Class", + "sms:displayName" : "concentrationNaClUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:protocolAssay", + "@id" : "bts:transplantationRecipientTissue", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:2DAlamarBlueabsorbance" - }, { - "@id" : "bts:2DAlamarBluefluorescence" - }, { - "@id" : "bts:2DCellTiter-Glo" - }, { - "@id" : "bts:2DIncucyte" - }, { - "@id" : "bts:3Dconfocalimaging" - }, { - "@id" : "bts:3Delectronmicroscopy" - }, { - "@id" : "bts:3Dimaging" - }, { - "@id" : "bts:3Dmicrotissueviability" - }, { - "@id" : "bts:ATAC-seq" - }, { - "@id" : "bts:ATPaseactivityassay" - }, { - "@id" : "bts:BrdUproliferationassay" - }, { - "@id" : "bts:CAPP-seq" - }, { - "@id" : "bts:CUT&RUN" - }, { - "@id" : "bts:ChIP-seq" - }, { - "@id" : "bts:ChildBehaviorChecklistforAges1.5-5" - }, { - "@id" : "bts:ChildBehaviorChecklistforAges6-18" - }, { - "@id" : "bts:Corsiblocks" - }, { - "@id" : "bts:DNAopticalmapping" - }, { - "@id" : "bts:ELISA" - }, { - "@id" : "bts:ERRbisulfitesequencing" - }, { - "@id" : "bts:EdUproliferationassay" - }, { - "@id" : "bts:FIA-MSMS" - }, { - "@id" : "bts:FLIPRhigh-throughputcellularscreening" - }, { - "@id" : "bts:FluorescenceInSituHybridization" - }, { - "@id" : "bts:Focusgroup" - }, { - "@id" : "bts:FTIRspectroscopy" - }, { - "@id" : "bts:HI-C" - }, { - "@id" : "bts:HPLC" - }, { - "@id" : "bts:Interview" - }, { - "@id" : "bts:ISO-seq" - }, { - "@id" : "bts:MIB/MS" - }, { - "@id" : "bts:Matrigel-basedtumorigenesisassay" - }, { - "@id" : "bts:MudPIT" - }, { - "@id" : "bts:NIHToolbox" - }, { - "@id" : "bts:NOMe-seq" - }, { - "@id" : "bts:RNAarray" + "@id" : "bts:cerebralcortex" }, { - "@id" : "bts:RNA-seq" + "@id" : "bts:bonemarrow" }, { - "@id" : "bts:RPPA" + "@id" : "bts:plasma" }, { - "@id" : "bts:RiccardiandAblonscales" + "@id" : "bts:DorsalRootGanglion" }, { - "@id" : "bts:SNParray" + "@id" : "bts:opticnerve" }, { - "@id" : "bts:SUSHI" + "@id" : "bts:tumor-adjacentnormal" }, { - "@id" : "bts:Sangersequencing" + "@id" : "bts:serum" }, { - "@id" : "bts:SocialResponsivenessScale" + "@id" : "bts:spheroid" }, { - "@id" : "bts:SocialResponsivenessScale,SecondEdition" + "@id" : "bts:sciaticnerve" }, { - "@id" : "bts:Tcellreceptorrepertoiresequencing" + "@id" : "bts:meninges" }, { - "@id" : "bts:TIDE" + "@id" : "bts:nervetissue" }, { - "@id" : "bts:TMTquantitation" + "@id" : "bts:BuccalMucosa" }, { - "@id" : "bts:VonFreytest" + "@id" : "bts:embryonictissue" }, { - "@id" : "bts:activeavoidancelearningbehaviorassay" + "@id" : "bts:wholebrain" }, { - "@id" : "bts:array" + "@id" : "bts:microtissue" }, { - "@id" : "bts:atomicforcemicroscopy" + "@id" : "bts:retina" }, { - "@id" : "bts:autoradiography" + "@id" : "bts:CDXtissue" }, { - "@id" : "bts:bisulfitesequencing" + "@id" : "bts:organoid" }, { - "@id" : "bts:bloodchemistrymeasurement" + "@id" : "bts:splenocyte" }, { - "@id" : "bts:bluenativePAGE" + "@id" : "bts:blood" }, { - "@id" : "bts:bodysizetraitmeasurement" + "@id" : "bts:connectivetissue" }, { - "@id" : "bts:brightfieldmicroscopy" + "@id" : "bts:primarytumor" }, { - "@id" : "bts:cAMP-GloMaxAssay" + "@id" : "bts:PDXtissue" }, { - "@id" : "bts:calciumretentioncapacityassay" + "@id" : "bts:BuffyCoat" + } ], + "rdfs:label" : "transplantationRecipientTissue", + "rdfs:comment" : "Tissue into which a xenograph sample is transplanted", + "@type" : "rdfs:Class", + "sms:displayName" : "transplantationRecipientTissue" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:specimenType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cerebralcortex" }, { - "@id" : "bts:cellcompetition" + "@id" : "bts:bonemarrow" }, { - "@id" : "bts:cellcount" + "@id" : "bts:plasma" }, { - "@id" : "bts:cellproliferation" + "@id" : "bts:DorsalRootGanglion" }, { - "@id" : "bts:cellviabilityassay" + "@id" : "bts:opticnerve" }, { - "@id" : "bts:clinicaldata" + "@id" : "bts:tumor-adjacentnormal" }, { - "@id" : "bts:cNF-Skindex" + "@id" : "bts:serum" }, { - "@id" : "bts:combinationlibraryscreen" + "@id" : "bts:spheroid" }, { - "@id" : "bts:combinationscreen" + "@id" : "bts:sciaticnerve" }, { - "@id" : "bts:complexIIenzymeactivityassay" + "@id" : "bts:meninges" }, { - "@id" : "bts:compoundscreen" + "@id" : "bts:nervetissue" }, { - "@id" : "bts:contextualconditioningbehaviorassay" + "@id" : "bts:BuccalMucosa" }, { - "@id" : "bts:conventionalMRI" + "@id" : "bts:embryonictissue" }, { - "@id" : "bts:Children'sDermatologyLifeQualityIndexQuestionnaire" + "@id" : "bts:wholebrain" }, { - "@id" : "bts:differentialscanningcalorimetry" + "@id" : "bts:microtissue" }, { - "@id" : "bts:dynamiclightscattering" + "@id" : "bts:retina" }, { - "@id" : "bts:electrochemiluminescence" + "@id" : "bts:CDXtissue" }, { - "@id" : "bts:elevatedplusmazetest" + "@id" : "bts:organoid" }, { - "@id" : "bts:FACE-QAppearance-relatedDistress" + "@id" : "bts:splenocyte" }, { - "@id" : "bts:flowcytometry" + "@id" : "bts:blood" }, { - "@id" : "bts:focusformingassay" + "@id" : "bts:connectivetissue" }, { - "@id" : "bts:functionalMRI" + "@id" : "bts:primarytumor" }, { - "@id" : "bts:gaitmeasurement" + "@id" : "bts:PDXtissue" }, { - "@id" : "bts:gelfiltrationchromatography" + "@id" : "bts:BuffyCoat" }, { - "@id" : "bts:genotyping" + "@id" : "bts:saliva" }, { - "@id" : "bts:highcontentscreen" + "@id" : "bts:mucus" }, { - "@id" : "bts:highfrequencyultrasound" + "@id" : "bts:urine" }, { - "@id" : "bts:high-performanceliquidchromatography/tandemmassspectrometry" + "@id" : "bts:stool" }, { + "@id" : "bts:sweat" + } ], + "rdfs:label" : "specimenType", + "rdfs:comment" : "The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances.\n", + "@type" : "rdfs:Class", + "sms:displayName" : "specimenType" + }, { + "@id" : "bts:datasetItemCount", + "@type" : "rdfs:Class", + "rdfs:comment" : "Count of files in dataset. Auto-calculated by Synapse.", + "rdfs:label" : "datasetItemCount", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "datasetItemCount", + "sms:required" : "sms:false" + }, { + "@id" : "bts:workflowLink", + "@type" : "rdfs:Class", + "rdfs:comment" : "Workflow URL reference", + "rdfs:label" : "workflowLink", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "workflowLink", + "sms:required" : "sms:false" + }, { + "@id" : "bts:dataFileHandleId", + "@type" : "rdfs:Class", + "rdfs:comment" : "(Files only) Refers to the id of the file.", + "rdfs:label" : "dataFileHandleId", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "dataFileHandleId", + "sms:required" : "sms:false" + }, { + "@id" : "bts:individualIdSource", + "@type" : "rdfs:Class", + "rdfs:comment" : "Database or repository to which individual ID maps", + "rdfs:label" : "individualIdSource", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "individualIdSource", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:totalReads", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "int" ], + "rdfs:label" : "totalReads", + "rdfs:comment" : "If available, the total number of reads collected from samtools.", + "@type" : "rdfs:Class", + "sms:displayName" : "totalReads" + }, { + "@id" : "bts:contributor", + "@type" : "rdfs:Class", + "rdfs:comment" : "An entity responsible for making contributions to the resource.", + "rdfs:label" : "contributor", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "contributor", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:dataType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { "@id" : "bts:immunoassay" }, { - "@id" : "bts:immunocytochemistry" + "@id" : "bts:behaviorprocess" }, { - "@id" : "bts:immunofluorescence" + "@id" : "bts:clinical" }, { - "@id" : "bts:immunohistochemistry" + "@id" : "bts:demographics" }, { - "@id" : "bts:invitrotumorigenesis" + "@id" : "bts:particlecharacterization" }, { - "@id" : "bts:invivoPDXviability" + "@id" : "bts:drugCombinationScreen" }, { - "@id" : "bts:invivobioluminescence" + "@id" : "bts:isoformExpression" }, { - "@id" : "bts:invivotumorgrowth" + "@id" : "bts:proteomics" }, { - "@id" : "bts:jumpinglibrary" + "@id" : "bts:surveyData" }, { - "@id" : "bts:labelfreemassspectrometry" + "@id" : "bts:kinomics" }, { - "@id" : "bts:laserspeckleimaging" + "@id" : "bts:SomaticVariants" }, { - "@id" : "bts:lightscatteringassay" + "@id" : "bts:Volume" }, { - "@id" : "bts:liquidchromatography-electrochemicaldetection" + "@id" : "bts:characteristic" }, { - "@id" : "bts:liquidchromatography/massspectrometry" + "@id" : "bts:drugScreen" }, { - "@id" : "bts:liquidchromatography/tandemmassspectrometry" + "@id" : "bts:geneExpression" }, { - "@id" : "bts:lncRNA-seq" + "@id" : "bts:AlignedReads" }, { - "@id" : "bts:localfieldpotentialrecording" + "@id" : "bts:genomicFeatures" }, { - "@id" : "bts:longtermpotentiationassay" + "@id" : "bts:genomicVariants" }, { - "@id" : "bts:mRNAcounts" + "@id" : "bts:rawcounts" }, { - "@id" : "bts:magneticresonancespectroscopy" + "@id" : "bts:PharmacokineticStudy" }, { - "@id" : "bts:massspectrometry" + "@id" : "bts:maskimage" }, { - "@id" : "bts:massivelyparallelreporterassay" + "@id" : "bts:chromatinActivity" }, { - "@id" : "bts:methylationarray" + "@id" : "bts:StructuralVariants" }, { - "@id" : "bts:miRNAarray" + "@id" : "bts:GermlineVariants" }, { - "@id" : "bts:miRNA-seq" + "@id" : "bts:CopyNumberVariants" }, { - "@id" : "bts:microrheology" + "@id" : "bts:image" }, { - "@id" : "bts:Skindex-16" + "@id" : "bts:network" }, { - "@id" : "bts:multi-electrodearray" + "@id" : "bts:cellularPhysiology" }, { - "@id" : "bts:nanoparticletrackinganalysis" + "@id" : "bts:metabolomics" }, { - "@id" : "bts:n-backtask" + "@id" : "bts:AnnotatedSomaticVariants" }, { - "@id" : "bts:nextgenerationtargetedsequencing" + "@id" : "bts:AnnotatedGermlineVariants" }, { - "@id" : "bts:noveltyresponsebehaviorassay" + "@id" : "bts:Weight" }, { - "@id" : "bts:openfieldtest" + "@id" : "bts:electrophysiology" }, { - "@id" : "bts:opticalcoherencetomography" + "@id" : "bts:audiotranscript" }, { - "@id" : "bts:optokineticreflexassay" + "@id" : "bts:dataIndex" }, { - "@id" : "bts:oscillatoryrheology" + "@id" : "bts:DescriptiveMetadata" }, { - "@id" : "bts:oxBS-seq" + "@id" : "bts:StructuralMetadata" }, { - "@id" : "bts:oxygenconsumptionassay" + "@id" : "bts:AdministrativeMetadata" }, { - "@id" : "bts:patternelectroretinogram" + "@id" : "bts:ReferenceMetadata" }, { - "@id" : "bts:perineurialcellthickness" + "@id" : "bts:StatisticalMetadata" }, { - "@id" : "bts:phase-contrastmicroscopy" + "@id" : "bts:LegalMetadata" }, { - "@id" : "bts:photograph" + "@id" : "bts:WorkflowMetadata" + } ], + "rdfs:label" : "dataType", + "rdfs:comment" : "A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.\n", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:dataSubtype" + } ], + "sms:displayName" : "dataType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:timepointUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:seconds" }, { - "@id" : "bts:polymerasechainreaction" + "@id" : "bts:minutes" }, { - "@id" : "bts:positronemissiontomography" + "@id" : "bts:hours" }, { - "@id" : "bts:PROMISCognitiveFunction" + "@id" : "bts:days" }, { - "@id" : "bts:quantitativePCR" + "@id" : "bts:weeks" }, { - "@id" : "bts:questionnaire" + "@id" : "bts:months" }, { - "@id" : "bts:reactiveoxygenspeciesassay" + "@id" : "bts:years" + } ], + "rdfs:label" : "timepointUnit", + "rdfs:comment" : "For timed experiments this represents the unit of time measured", + "@type" : "rdfs:Class", + "sms:displayName" : "timepointUnit" + }, { + "@id" : "bts:currentVersion", + "@type" : "rdfs:Class", + "rdfs:comment" : "(Versionable entities only) The current version number of the resource.", + "rdfs:label" : "currentVersion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "currentVersion", + "sms:required" : "sms:false" + }, { + "@id" : "bts:genomicReference", + "@type" : "rdfs:Class", + "rdfs:comment" : "Version of genome reference used for alignment in processing workflow", + "rdfs:label" : "genomicReference", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "genomicReference", + "sms:required" : "sms:true" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:dataSubtype", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:normalized" }, { - "@id" : "bts:reportergeneassay" + "@id" : "bts:dataMatrix" }, { - "@id" : "bts:rheometry" + "@id" : "bts:raw" }, { - "@id" : "bts:ribo-seq" + "@id" : "bts:processed" }, { - "@id" : "bts:rotarodperformancetest" + "@id" : "bts:metadata" }, { - "@id" : "bts:sandwichELISA" + "@id" : "bts:representative" + } ], + "rdfs:label" : "dataSubtype", + "rdfs:comment" : "Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.", + "@type" : "rdfs:Class", + "sms:displayName" : "dataSubtype" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:organ", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:kidney" }, { - "@id" : "bts:scCGI-seq" + "@id" : "bts:ovary" }, { - "@id" : "bts:scale" + "@id" : "bts:lung" }, { - "@id" : "bts:singlemoleculedrugscreenassay" + "@id" : "bts:bonemarrow" }, { - "@id" : "bts:single-cellRNA-seq" + "@id" : "bts:prostate" }, { - "@id" : "bts:smallmoleculelibraryscreen" + "@id" : "bts:breast" }, { - "@id" : "bts:sorbitoldehydrogenaseactivitylevelassay" + "@id" : "bts:mesentery" }, { - "@id" : "bts:spatialfrequencydomainimaging" + "@id" : "bts:mammarygland" }, { - "@id" : "bts:spatialtranscriptomics" + "@id" : "bts:colon" }, { - "@id" : "bts:staticlightscattering" + "@id" : "bts:spleen" }, { - "@id" : "bts:survival" + "@id" : "bts:BursaOfFabricius" }, { - "@id" : "bts:targetedexomesequencing" + "@id" : "bts:nose" }, { - "@id" : "bts:tractionforcemicroscopy" + "@id" : "bts:brain" }, { - "@id" : "bts:twinspotassay" + "@id" : "bts:pancreas" }, { - "@id" : "bts:ultrahigh-performanceliquidchromatography/tandemmassspectrometry" + "@id" : "bts:liver" }, { - "@id" : "bts:westernblot" + "@id" : "bts:blood" }, { - "@id" : "bts:wholeexomesequencing" + "@id" : "bts:lymphnode" }, { - "@id" : "bts:wholegenomesequencing" + "@id" : "bts:nerves" }, { - "@id" : "bts:whole-cellpatchclamp" + "@id" : "bts:skin" }, { - "@id" : "bts:STRprofile" + "@id" : "bts:eye" } ], - "rdfs:label" : "protocolAssay", - "rdfs:comment" : "Main assay type that this protocol is related to, e.g. this is a prep protocol for single-cell RNA-seq assay. This is especially helpful for newly-developed or in-house assays.\n", + "rdfs:label" : "organ", + "rdfs:comment" : "A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. 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This could be a patient or animal ID.", + "rdfs:label" : "individualID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NucleicAcidSourceEnum", - "sms:required" : "sms:false" + "sms:displayName" : "individualID", + "sms:required" : "sms:true" }, { - "@id" : "bts:ReadPairOrientationEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReadPairOrientationEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:failedQC", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReadPairOrientationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:LibraryPrepEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + } ], + "rdfs:label" : "failedQC", + "rdfs:comment" : "Whether the sample or data failed QC checks (Yes, No)", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryPrepEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "LibraryPrepEnum", - "sms:required" : "sms:false" + "sms:displayName" : "failedQC" }, { - "@id" : "bts:Tissue", + "@id" : "bts:compoundName", "@type" : "rdfs:Class", - "rdfs:comment" : "Tissue is a group of cells that have similar structure and that function together as a unit.", - "rdfs:label" : "Tissue", + "rdfs:comment" : "Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)", + "rdfs:label" : "compoundName", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Tissue", + "sms:displayName" : "compoundName", "sms:required" : "sms:false" }, { - "@id" : "bts:DataSubtype", + "@id" : "bts:isFilteredReads", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DataSubtype", + "rdfs:comment" : "Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator", + "rdfs:label" : "isFilteredReads", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DataSubtype", + "sms:displayName" : "isFilteredReads", "sms:required" : "sms:false" }, { - "@id" : "bts:LibraryPreparationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryPreparationMethodEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:runType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryPreparationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Metadata", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:pairedEnd" + }, { + "@id" : "bts:singleEnd" + } ], + "rdfs:label" : "runType", + "rdfs:comment" : "Sequencing run type.", "@type" : "rdfs:Class", - "rdfs:comment" : "Data that provides information about other data", - "rdfs:label" : "Metadata", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Metadata", - "sms:required" : "sms:false" + "sms:displayName" : "runType" }, { - "@id" : "bts:ChannelEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ChannelEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:lensAperture", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ChannelEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Cell", + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "lensAperture", + "rdfs:comment" : "Numerical aperture of the lens. Floating point value > 0.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Cell", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Cell", - "sms:required" : "sms:false" + "sms:displayName" : "lensAperture" }, { - "@id" : "bts:GenomicReferenceEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenomicReferenceEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:referenceSet", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "GenomicReferenceEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "referenceSet", + "rdfs:comment" : "A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data.", + "@type" : "rdfs:Class", + "sms:displayName" : "referenceSet" }, { - "@id" : "bts:Genotype", + "@id" : "bts:parentId", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Genotype", + "rdfs:comment" : "The id of the parent resource, i.e. the parent folder on the platform. ", + "rdfs:label" : "parentId", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Genotype", + "sms:displayName" : "parentId", "sms:required" : "sms:false" }, { - "@id" : "bts:DrugScreen", + "@id" : "bts:diseaseFocus", "@type" : "rdfs:Class", - "rdfs:comment" : "This is a subset of Assay enum above.", - "rdfs:label" : "DrugScreen", + "rdfs:comment" : "Disease that acts as the main topic.", + "rdfs:label" : "diseaseFocus", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DrugScreen", + "sms:displayName" : "diseaseFocus", "sms:required" : "sms:false" }, { - "@id" : "bts:DissociationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DissociationMethodEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:transplantationRecipientSpecies", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DissociationMethodEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Human" + }, { + "@id" : "bts:Mouse" + } ], + "rdfs:label" : "transplantationRecipientSpecies", + "rdfs:comment" : "Species into which donor was grown", + "@type" : "rdfs:Class", + "sms:displayName" : "transplantationRecipientSpecies" }, { - "@id" : "bts:TimeUnit", + "@id" : "bts:experimentId", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TimeUnit", + "rdfs:comment" : "When applicable, an optional identifier that can be used to distinguish or group the experiments that generated the data; also can be used to denote internal batch reference if needed.", + "rdfs:label" : "experimentId", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TimeUnit", + "sms:displayName" : "experimentId", "sms:required" : "sms:false" }, { - "@id" : "bts:Measurement", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Measurement", "rdfs:subClassOf" : [ ], + "@id" : "bts:cellType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Measurement", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:validationRules" : [ "list like" ], + "schema:rangeIncludes" : [ { + "@id" : "bts:monocytes" + }, { + "@id" : "bts:macrophages" + }, { + "@id" : "bts:iPSC-derivedneuron" + }, { + "@id" : "bts:lymphoblast" + }, { + "@id" : "bts:iPSC" + }, { + "@id" : "bts:DRG/nerverootneurospherecell" + }, { + "@id" : "bts:CD138+" + }, { + "@id" : "bts:schwannoma" + }, { + "@id" : "bts:iPSC-derivedtelencephalicorganoids" + }, { + "@id" : "bts:monocyte-derivedmicroglia" + }, { + "@id" : "bts:microglia" + }, { + "@id" : "bts:SH-SY5Y" + }, { + "@id" : "bts:CNON" + }, { + "@id" : "bts:NeuN+" + }, { + "@id" : "bts:culturedMullerglia" + }, { + "@id" : "bts:B-lymphocytes" + }, { + "@id" : "bts:round" + }, { + "@id" : "bts:epithelial" + }, { + "@id" : "bts:epithelial-like" + }, { + "@id" : "bts:CD8+T-Cells" + }, { + "@id" : "bts:GLUtamatergicneurons" + }, { + "@id" : "bts:arachnoid" + }, { + "@id" : "bts:GABAergicneurons" + }, { + "@id" : "bts:schwann" + }, { + "@id" : "bts:iPSC-derivedglia" + }, { + "@id" : "bts:iPSC-derivedastrocytes" + }, { + "@id" : "bts:iPSC-derivedneuronalprogenitorcell" + }, { + "@id" : "bts:oligodendrocyte" + }, { + "@id" : "bts:fibroblast" + }, { + "@id" : "bts:astrocytes" + }, { + "@id" : "bts:Schwanncellprecursor" + }, { + "@id" : "bts:NeuN-" + }, { + "@id" : "bts:Embryonicstemcells" + }, { + "@id" : "bts:teratoma" + }, { + "@id" : "bts:meningioma" + } ], + "rdfs:label" : "cellType", + "rdfs:comment" : "A cell type is a distinct morphological or functional form of cell.", + "@type" : "rdfs:Class", + "sms:displayName" : "cellType" }, { - "@id" : "bts:Material", + "@id" : "bts:modifiedBy", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Material", + "rdfs:comment" : "Refers to a user who last modified the resource on the platform.", + "rdfs:label" : "modifiedBy", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Material", + "sms:displayName" : "modifiedBy", "sms:required" : "sms:false" }, { - "@id" : "bts:TransplantationType", + "@id" : "bts:parentSpecimenID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TransplantationType", + "rdfs:comment" : "A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning.\n", + "rdfs:label" : "parentSpecimenID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TransplantationType", + "sms:displayName" : "parentSpecimenID", "sms:required" : "sms:false" }, { - "@id" : "bts:RunTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RunTypeEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:experimentalTimepoint", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RunTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:NotApplicableEnum", + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "experimentalTimepoint", + "rdfs:comment" : "The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NotApplicableEnum", + "sms:requiresDependency" : [ { + "@id" : "bts:timepointUnit" + } ], + "sms:displayName" : "experimentalTimepoint" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:protocolAssay", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NotApplicableEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CellLineModel", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:2DAlamarBlueabsorbance" + }, { + "@id" : "bts:2DAlamarBluefluorescence" + }, { + "@id" : "bts:2DCellTiter-Glo" + }, { + "@id" : "bts:2DIncucyte" + }, { + "@id" : "bts:3Dconfocalimaging" + }, { + "@id" : "bts:3Delectronmicroscopy" + }, { + "@id" : "bts:3Dimaging" + }, { + "@id" : "bts:3Dmicrotissueviability" + }, { + "@id" : "bts:ATAC-seq" + }, { + "@id" : "bts:ATPaseactivityassay" + }, { + "@id" : "bts:BrdUproliferationassay" + }, { + "@id" : "bts:CAPP-seq" + }, { + "@id" : "bts:CUT&RUN" + }, { + "@id" : "bts:ChIP-seq" + }, { + "@id" : "bts:ChildBehaviorChecklistforAges1.5-5" + }, { + "@id" : "bts:ChildBehaviorChecklistforAges6-18" + }, { + "@id" : "bts:Corsiblocks" + }, { + "@id" : "bts:DNAopticalmapping" + }, { + "@id" : "bts:ELISA" + }, { + "@id" : "bts:ERRbisulfitesequencing" + }, { + "@id" : "bts:EdUproliferationassay" + }, { + "@id" : "bts:FIA-MSMS" + }, { + "@id" : "bts:FLIPRhigh-throughputcellularscreening" + }, { + "@id" : "bts:FluorescenceInSituHybridization" + }, { + "@id" : "bts:Focusgroup" + }, { + "@id" : "bts:FTIRspectroscopy" + }, { + "@id" : "bts:HI-C" + }, { + "@id" : "bts:HPLC" + }, { + "@id" : "bts:Interview" + }, { + "@id" : "bts:ISO-seq" + }, { + "@id" : "bts:MIB/MS" + }, { + "@id" : "bts:Matrigel-basedtumorigenesisassay" + }, { + "@id" : "bts:MudPIT" + }, { + "@id" : "bts:NIHToolbox" + }, { + "@id" : "bts:NOMe-seq" + }, { + "@id" : "bts:RNAarray" + }, { + "@id" : "bts:RNA-seq" + }, { + "@id" : "bts:RPPA" + }, { + "@id" : "bts:RiccardiandAblonscales" + }, { + "@id" : "bts:SNParray" + }, { + "@id" : "bts:SUSHI" + }, { + "@id" : "bts:Sangersequencing" + }, { + "@id" : "bts:SocialResponsivenessScale" + }, { + "@id" : "bts:SocialResponsivenessScale,SecondEdition" + }, { + "@id" : "bts:Tcellreceptorrepertoiresequencing" + }, { + "@id" : "bts:TIDE" + }, { + "@id" : "bts:TMTquantitation" + }, { + "@id" : "bts:VonFreytest" + }, { + "@id" : "bts:activeavoidancelearningbehaviorassay" + }, { + "@id" : "bts:array" + }, { + "@id" : "bts:atomicforcemicroscopy" + }, { + "@id" : "bts:autoradiography" + }, { + "@id" : "bts:bisulfitesequencing" + }, { + "@id" : "bts:bloodchemistrymeasurement" + }, { + "@id" : "bts:bluenativePAGE" + }, { + "@id" : "bts:bodysizetraitmeasurement" + }, { + "@id" : "bts:brightfieldmicroscopy" + }, { + "@id" : "bts:cAMP-GloMaxAssay" + }, { + "@id" : "bts:calciumretentioncapacityassay" + }, { + "@id" : "bts:cellcompetition" + }, { + "@id" : "bts:cellcount" + }, { + "@id" : "bts:cellproliferation" + }, { + "@id" : "bts:cellviabilityassay" + }, { + "@id" : "bts:clinicaldata" + }, { + "@id" : "bts:cNF-Skindex" + }, { + "@id" : "bts:combinationlibraryscreen" + }, { + "@id" : "bts:combinationscreen" + }, { + "@id" : "bts:complexIIenzymeactivityassay" + }, { + "@id" : "bts:compoundscreen" + }, { + "@id" : "bts:contextualconditioningbehaviorassay" + }, { + "@id" : "bts:conventionalMRI" + }, { + "@id" : "bts:Children'sDermatologyLifeQualityIndexQuestionnaire" + }, { + "@id" : "bts:differentialscanningcalorimetry" + }, { + "@id" : "bts:dynamiclightscattering" + }, { + "@id" : "bts:electrochemiluminescence" + }, { + "@id" : "bts:elevatedplusmazetest" + }, { + "@id" : "bts:FACE-QAppearance-relatedDistress" + }, { + "@id" : "bts:flowcytometry" + }, { + "@id" : "bts:focusformingassay" + }, { + "@id" : "bts:functionalMRI" + }, { + "@id" : "bts:gaitmeasurement" + }, { + "@id" : "bts:gelfiltrationchromatography" + }, { + "@id" : "bts:genotyping" + }, { + "@id" : 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{ + "@id" : "bts:mRNAcounts" + }, { + "@id" : "bts:magneticresonancespectroscopy" + }, { + "@id" : "bts:massspectrometry" + }, { + "@id" : "bts:massivelyparallelreporterassay" + }, { + "@id" : "bts:methylationarray" + }, { + "@id" : "bts:miRNAarray" + }, { + "@id" : "bts:miRNA-seq" + }, { + "@id" : "bts:microrheology" + }, { + "@id" : "bts:Skindex-16" + }, { + "@id" : "bts:multi-electrodearray" + }, { + "@id" : "bts:nanoparticletrackinganalysis" + }, { + "@id" : "bts:n-backtask" + }, { + "@id" : "bts:nextgenerationtargetedsequencing" + }, { + "@id" : "bts:noveltyresponsebehaviorassay" + }, { + "@id" : "bts:openfieldtest" + }, { + "@id" : "bts:opticalcoherencetomography" + }, { + "@id" : "bts:optokineticreflexassay" + }, { + "@id" : "bts:oscillatoryrheology" + }, { + "@id" : "bts:oxBS-seq" + }, { + "@id" : "bts:oxygenconsumptionassay" + }, { + "@id" : "bts:patternelectroretinogram" + }, { + "@id" : "bts:perineurialcellthickness" + }, { + "@id" : "bts:phase-contrastmicroscopy" + }, { + 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"rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationTechnologyEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GenePerturbationTechnologyEnum", - "sms:required" : "sms:false" + "sms:displayName" : "platform" }, { "rdfs:subClassOf" : [ { "@id" : "bts:ProteinAssayTemplate" From 0973a0c0546deb5092d76d9245ddc2a104dbf27f Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Wed, 6 Dec 2023 14:17:03 -0600 Subject: [PATCH 7/7] revert :facepalm emoji: --- tests/validate/ScRNASeqTemplate_1.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/validate/ScRNASeqTemplate_1.csv b/tests/validate/ScRNASeqTemplate_1.csv index 139caa69..6a810157 100644 --- a/tests/validate/ScRNASeqTemplate_1.csv +++ b/tests/validate/ScRNASeqTemplate_1.csv @@ -1,5 +1,5 @@ Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset -ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,Not Applicable,10x,,,,,, -ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,Not Applicable,10x,,,,,, -ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,Not Applicable,10x,,,,,, -ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,Not Applicable,10x,,,,,, +ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,, +ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,, +ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,, +ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,