From 7d92c509abf982cf84fa4c4d252cc9464fd58488 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com> Date: Fri, 2 Dec 2022 15:27:13 -0700 Subject: [PATCH] Patch/light scattering assays (#222) * Add new data type * Patch template * Build jsonld Co-authored-by: nf-osi[bot] --- NF.csv | 5 ++-- NF.jsonld | 39 ++++++++++++++++++++++++++--- modules/Data/Data_Class.csv | 1 + modules/Data/annotationProperty.csv | 2 +- modules/Template/Template.csv | 2 +- 5 files changed, 41 insertions(+), 8 deletions(-) diff --git a/NF.csv b/NF.csv index 64e7d799..aa9fd5f2 100644 --- a/NF.csv +++ b/NF.csv @@ -258,6 +258,7 @@ immunoassay,Laboratory test involving interaction of antigens with specific anti electrophysiology,Data generated from an electrophysiology assay.,"","",FALSE,http://purl.obolibrary.org/obo/ERO_0000564,dataType,,"","",Electrophysiology,Class,Data,Data_Class,"","","","" mask image,"Image used as the mask for an image processing operation, such as subtraction.","","",FALSE,http://dicom.nema.org/resources/ontology/DCM/121321,dataType,,"","",Mask_Image,Class,Data,Data_Class,"","","","" curatedData,"Any file derived from or pertaining a manually or programatically curated data resource. Examples include: reference sequences, drug information databases, identifier maps""""","","",FALSE,"","",,"","",Curated_Data,Class,Data,Data_Class,"","","","" +characteristic,"Broad data type for measures that can encompass volume, weight, brightness, color, capacity, etc.","",assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25447,dataType,,"","",characteristic,Class,Data,Data_Class,"","","","" normalized,A data set that is produced as the output of a normalization data transformation.,"","",FALSE,http://purl.obolibrary.org/obo/OBI_0000451,dataSubtype,,"","",Normalized,Class,Data,Data_Level,"","","","" dataMatrix,A file of data containing multiple values for multiple samples.,"","",FALSE,"",dataSubtype,,"","",Data_Matrix,Class,Data,Data_Level,"","","","" raw,"A data file produced by an instrument, or one with very little subsequent processing.","","",FALSE,"",dataSubtype,,"","",Raw,Class,Data,Data_Level,"","","","" @@ -381,7 +382,7 @@ referenceSet,"A set of references (e.g., canonical assembled contigs) which defi reference sequence,Syntactic sequences that has a role as reference of an annotation.,,,FALSE,http://rdf.biosemantics.org/ontologies/rsa#ReferenceSequence,curatedDataType,,,,referenceSequence,Property,Data,annotationProperty,,,, dataSubtype,"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.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,,dataSubtype,Property,Data,annotationProperty,,Data_Level,one, metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,,metadataType,Property,Data,annotationProperty,,,, -dataType,"A type of experimental, clinical, or other data. This 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`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, +dataType,"A type of experimental, clinical, or other data. This 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`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants,characteristic",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, expressionUnit,"Measure used for transcript expression quantification","TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,,, failedQC,Whether the sample or data failed QC checks (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,,, Filename,The name of the file.,,"entityId,fileFormat",TRUE,Sage Bionetworks,NF,,,,fileName,Class,Data,annotationProperty,fileName,,one,Automatically filled when using the curator app. @@ -798,5 +799,5 @@ experimentComponent,Template component for describing core experimental paramete genePerturbComponent,Template component for adding genetic perturbation metadata. This applies only to some assays and does not make sense with e.g. behavioral assays.,"genePerturbed,genePerturbationType,genePerturbationTechnology","genePerturbed,genePerturbationType,genePerturbationTechnology",FALSE,Sage Bionetworks,template,,,,Gene_Perturb_Component,Class,Template,TemplateComponent,,,, fileComponent,Template component for describing some file on the NF-OSI Synapse platform.,"Filename,entityId,fileFormat,resourceType","Filename,entityId,fileFormat,resourceType",FALSE,Sage Bionetworks,template,,,,File_Component,Class,Template,TemplateComponent,,,, ngsComponent,Template component capturing Next Gen Sequencing/genomics attributes.,"runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource","runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource",FALSE,Sage Bionetworks,template,,,,NGS_Component,Class,Template,TemplateComponent,,,, -DynamicLightScatteringTemplate,"Template for dynamic light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)",,"Component,Filename,resourceType,dataType,assay,materialType,pH,concentrationMaterial,concentrationMaterialUnit,concentrationNaCl,concentrationNaClUnit",FALSE,Sage Bionetworks,template,,,,Dynamic_Light_Scattering_Template,Class,Template,Template,,,, +LightScatteringAssayTemplate,"Template for dynamic or static light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)",,"Component,Filename,resourceType,dataType,assay,materialType,specimenID,pH,concentrationMaterial,concentrationMaterialUnit,concentrationNaCl,concentrationNaClUnit,comments",FALSE,Sage Bionetworks,template,,,,Light_Scattering_Assay_Template,Class,Template,Template,,,, FlowCytometryTemplate,"Basic template for flow cytometry assay",,"Component,Filename,resourceType,dataType,assay,platform,individualID,specimenID,cellType,experimentalCondition,comments",FALSE,Sage Bionetworks,template,,,,FACS_Template,Class,Template,Template,,,, diff --git a/NF.jsonld b/NF.jsonld index cc5f0044..97639b3c 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -7184,6 +7184,28 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Characteristic", + "@type": "rdfs:Class", + "rdfs:comment": "Broad data type for measures that can encompass volume, weight, brightness, color, capacity, etc.", + "rdfs:label": "Characteristic", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "characteristic", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Assay" + } + ], + "sms:validationRules": [] + }, { "@id": "bts:Normalized", "@type": "rdfs:Class", @@ -9443,6 +9465,9 @@ }, { "@id": "bts:AnnotatedGermlineVariants" + }, + { + "@id": "bts:Characteristic" } ], "sms:displayName": "dataType", @@ -19391,10 +19416,10 @@ "sms:validationRules": [] }, { - "@id": "bts:DynamicLightScatteringTemplate", + "@id": "bts:LightScatteringAssayTemplate", "@type": "rdfs:Class", - "rdfs:comment": "Template for dynamic light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)", - "rdfs:label": "DynamicLightScatteringTemplate", + "rdfs:comment": "Template for dynamic or static light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)", + "rdfs:label": "LightScatteringAssayTemplate", "rdfs:subClassOf": [ { "@id": "bts:Template" @@ -19403,7 +19428,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DynamicLightScatteringTemplate", + "sms:displayName": "LightScatteringAssayTemplate", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -19424,6 +19449,9 @@ { "@id": "bts:materialType" }, + { + "@id": "bts:SpecimenID" + }, { "@id": "bts:PH" }, @@ -19438,6 +19466,9 @@ }, { "@id": "bts:ConcentrationNaClUnit" + }, + { + "@id": "bts:Comments" } ], "sms:validationRules": [] diff --git a/modules/Data/Data_Class.csv b/modules/Data/Data_Class.csv index 559304f0..00e9116c 100644 --- a/modules/Data/Data_Class.csv +++ b/modules/Data/Data_Class.csv @@ -28,3 +28,4 @@ immunoassay,Laboratory test involving interaction of antigens with specific anti electrophysiology,Data generated from an electrophysiology assay.,"","",FALSE,http://purl.obolibrary.org/obo/ERO_0000564,dataType,,"","",Electrophysiology,Class,Data,Data_Class,"","","","" mask image,"Image used as the mask for an image processing operation, such as subtraction.","","",FALSE,http://dicom.nema.org/resources/ontology/DCM/121321,dataType,,"","",Mask_Image,Class,Data,Data_Class,"","","","" curatedData,"Any file derived from or pertaining a manually or programatically curated data resource. Examples include: reference sequences, drug information databases, identifier maps""""","","",FALSE,"","",,"","",Curated_Data,Class,Data,Data_Class,"","","","" +characteristic,"Broad data type for measures that can encompass volume, weight, brightness, color, capacity, etc.","",assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25447,dataType,,"","",characteristic,Class,Data,Data_Class,"","","","" diff --git a/modules/Data/annotationProperty.csv b/modules/Data/annotationProperty.csv index 63e94709..182bec8a 100644 --- a/modules/Data/annotationProperty.csv +++ b/modules/Data/annotationProperty.csv @@ -4,7 +4,7 @@ referenceSet,"A set of references (e.g., canonical assembled contigs) which defi reference sequence,Syntactic sequences that has a role as reference of an annotation.,,,FALSE,http://rdf.biosemantics.org/ontologies/rsa#ReferenceSequence,curatedDataType,,,,referenceSequence,Property,Data,annotationProperty,,,, dataSubtype,"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.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,,dataSubtype,Property,Data,annotationProperty,,Data_Level,one, metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,,metadataType,Property,Data,annotationProperty,,,, -dataType,"A type of experimental, clinical, or other data. This 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`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, +dataType,"A type of experimental, clinical, or other data. This 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`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants,characteristic",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, expressionUnit,"Measure used for transcript expression quantification","TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,,, failedQC,Whether the sample or data failed QC checks (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,,, Filename,The name of the file.,,"entityId,fileFormat",TRUE,Sage Bionetworks,NF,,,,fileName,Class,Data,annotationProperty,fileName,,one,Automatically filled when using the curator app. diff --git a/modules/Template/Template.csv b/modules/Template/Template.csv index e278dc1e..6f8a719b 100644 --- a/modules/Template/Template.csv +++ b/modules/Template/Template.csv @@ -33,5 +33,5 @@ experimentComponent,Template component for describing core experimental paramete genePerturbComponent,Template component for adding genetic perturbation metadata. This applies only to some assays and does not make sense with e.g. behavioral assays.,"genePerturbed,genePerturbationType,genePerturbationTechnology","genePerturbed,genePerturbationType,genePerturbationTechnology",FALSE,Sage Bionetworks,template,,,,Gene_Perturb_Component,Class,Template,TemplateComponent,,,, fileComponent,Template component for describing some file on the NF-OSI Synapse platform.,"Filename,entityId,fileFormat,resourceType","Filename,entityId,fileFormat,resourceType",FALSE,Sage Bionetworks,template,,,,File_Component,Class,Template,TemplateComponent,,,, ngsComponent,Template component capturing Next Gen Sequencing/genomics attributes.,"runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource","runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource",FALSE,Sage Bionetworks,template,,,,NGS_Component,Class,Template,TemplateComponent,,,, -DynamicLightScatteringTemplate,"Template for dynamic light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)",,"Component,Filename,resourceType,dataType,assay,materialType,pH,concentrationMaterial,concentrationMaterialUnit,concentrationNaCl,concentrationNaClUnit",FALSE,Sage Bionetworks,template,,,,Dynamic_Light_Scattering_Template,Class,Template,Template,,,, +LightScatteringAssayTemplate,"Template for dynamic or static light scattering data adapted from ISA-TAB-Nano specs (https://wiki.nci.nih.gov/display/icr/isa-tab-nano)",,"Component,Filename,resourceType,dataType,assay,materialType,specimenID,pH,concentrationMaterial,concentrationMaterialUnit,concentrationNaCl,concentrationNaClUnit,comments",FALSE,Sage Bionetworks,template,,,,Light_Scattering_Assay_Template,Class,Template,Template,,,, FlowCytometryTemplate,"Basic template for flow cytometry assay",,"Component,Filename,resourceType,dataType,assay,platform,individualID,specimenID,cellType,experimentalCondition,comments",FALSE,Sage Bionetworks,template,,,,FACS_Template,Class,Template,Template,,,,