Patch/light scattering assays (#222)

* Add new data type * Patch template * Build jsonld Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Dec 2, 2022 · 7d92c50 · 7d92c50
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commit 7d92c50
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Showing 5 changed files with 41 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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,,,,