diff --git a/NF.jsonld b/NF.jsonld index be89d647..7a2c3623 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -934,12 +934,20 @@ "@id" : "bts:Filename" }, { "@id" : "bts:resourceType" + }, { + "@id" : "bts:title" }, { "@id" : "bts:author" }, { "@id" : "bts:citation" }, { "@id" : "bts:license" + }, { + "@id" : "bts:protocolAssay" + }, { + "@id" : "bts:protocolPurpose" + }, { + "@id" : "bts:sampleType" }, { "@id" : "bts:comments" } ], @@ -1224,6 +1232,61 @@ "@type" : "rdfs:Class", "sms:requiresDependency" : [ ], "sms:displayName" : "ImagingDataTemplate" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Template" + } ], + "@id" : "bts:DatasetTemplate", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : null, + "rdfs:label" : "DatasetTemplate", + "rdfs:comment" : "Template that specifies NF portal dataset properties should have for more consistent community-curated datasets.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:id" + }, { + "@id" : "bts:doi" + }, { + "@id" : "bts:title" + }, { + "@id" : "bts:creator" + }, { + "@id" : "bts:contributor" + }, { + "@id" : "bts:currentVersion" + }, { + "@id" : "bts:description" + }, { + "@id" : "bts:license" + }, { + "@id" : "bts:dataType" + }, { + "@id" : "bts:studyName" + }, { + "@id" : "bts:studyId" + }, { + "@id" : "bts:manifestation" + }, { + "@id" : "bts:diseaseFocus" + }, { + "@id" : "bts:fundingAgency" + }, { + "@id" : "bts:series" + }, { + "@id" : "bts:publisher" + }, { + "@id" : "bts:yearProcessed" + }, { + "@id" : "bts:yearPublished" + }, { + "@id" : "bts:datasetItemCount" + }, { + "@id" : "bts:datasetSizeInBytes" + } ], + "sms:displayName" : "DatasetTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:AssayDataTemplate" @@ -1607,6 +1670,17 @@ }, "sms:displayName" : "proportionCoverage30x", "sms:required" : "sms:false" + }, { + "@id" : "bts:description", + "@type" : "rdfs:Class", + "rdfs:comment" : "Text describing a resource.", + "rdfs:label" : "description", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "description", + "sms:required" : "sms:false" }, { "@id" : "bts:compoundDoseUnit", "@type" : "rdfs:Class", @@ -1695,6 +1769,17 @@ "rdfs:comment" : "The relative orientation of the reads in a paired-end protocol", "@type" : "rdfs:Class", "sms:displayName" : "readPairOrientation" + }, { + "@id" : "bts:fileSize", + "@type" : "rdfs:Class", + "rdfs:comment" : "Size of file in bytes.", + "rdfs:label" : "fileSize", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "fileSize", + "sms:required" : "sms:false" }, { "@id" : "bts:benefactorId", "@type" : "rdfs:Class", @@ -1717,6 +1802,17 @@ }, "sms:displayName" : "createdOn", "sms:required" : "sms:false" + }, { + "@id" : "bts:protocolPurpose", + "@type" : "rdfs:Class", + "rdfs:comment" : "Brief description of the protocol purpose.", + "rdfs:label" : "protocolPurpose", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "protocolPurpose", + "sms:required" : "sms:false" }, { "@id" : "bts:reporterSubstance", "@type" : "rdfs:Class", @@ -1792,6 +1888,17 @@ }, "sms:displayName" : "targetDepth", "sms:required" : "sms:false" + }, { + "@id" : "bts:creator", + "@type" : "rdfs:Class", + "rdfs:comment" : "An entity responsible for making the resource.", + "rdfs:label" : "creator", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "creator", + "sms:required" : "sms:true" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:age", @@ -1865,6 +1972,17 @@ "rdfs:comment" : "Method by which library was prepared", "@type" : "rdfs:Class", "sms:displayName" : "libraryPreparationMethod" + }, { + "@id" : "bts:publisher", + "@type" : "rdfs:Class", + "rdfs:comment" : "An entity responsible for making the resource available.", + "rdfs:label" : "publisher", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "publisher", + "sms:required" : "sms:false" }, { "@id" : "bts:averageBaseQuality", "@type" : "rdfs:Class", @@ -1967,6 +2085,17 @@ "rdfs:comment" : "Numeric value for concentration of the material", "@type" : "rdfs:Class", "sms:displayName" : "concentrationMaterial" + }, { + "@id" : "bts:fileCount", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of files in the resource collection.", + "rdfs:label" : "fileCount", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "fileCount", + "sms:required" : "sms:false" }, { "@id" : "bts:assayTarget", "@type" : "rdfs:Class", @@ -2001,6 +2130,17 @@ "rdfs:comment" : "Number of base pairs (bp) sequenced for a read", "@type" : "rdfs:Class", "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" : "studyId", + "sms:required" : "sms:true" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:Filename", @@ -2031,6 +2171,17 @@ "rdfs:comment" : "The strand from which the read originates in a strand-specific protocol", "@type" : "rdfs:Class", "sms:displayName" : "readStrandOrigin" + }, { + "@id" : "bts:series", + "@type" : "rdfs:Class", + "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" : "series", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:nf1Variant", @@ -2665,6 +2816,17 @@ "@id" : "bts:transplantationRecipientTissue" } ], "sms:displayName" : "transplantationType" + }, { + "@id" : "bts:yearPublished", + "@type" : "rdfs:Class", + "rdfs:comment" : "Year in which the resource was published.", + "rdfs:label" : "yearPublished", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "yearPublished", + "sms:required" : "sms:false" }, { "@id" : "bts:fundingAgency", "@type" : "rdfs:Class", @@ -2758,6 +2920,17 @@ }, "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", @@ -2845,6 +3018,17 @@ "rdfs:comment" : "Type of material in the characterization", "@type" : "rdfs:Class", "sms:displayName" : "materialType" + }, { + "@id" : "bts:doi", + "@type" : "rdfs:Class", + "rdfs:comment" : "Digital object identifier of the resource.", + "rdfs:label" : "doi", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "doi", + "sms:required" : "sms:false" }, { "@id" : "bts:readsDuplicatedPercent", "@type" : "rdfs:Class", @@ -2892,6 +3076,28 @@ "rdfs:comment" : "A mode used in MRI imaging", "@type" : "rdfs:Class", "sms:displayName" : "MRISequence" + }, { + "@id" : "bts:datasetSizeInBytes", + "@type" : "rdfs:Class", + "rdfs:comment" : "Size of dataset entity in bytes. Auto-calculated by Synapse.", + "rdfs:label" : "datasetSizeInBytes", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "datasetSizeInBytes", + "sms:required" : "sms:false" + }, { + "@id" : "bts:yearProcessed", + "@type" : "rdfs:Class", + "rdfs:comment" : "Year in which the resource was processed/derived.", + "rdfs:label" : "yearProcessed", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "yearProcessed", + "sms:required" : "sms:false" }, { "@id" : "bts:referenceSequence", "@type" : "rdfs:Class", @@ -2903,6 +3109,17 @@ }, "sms:displayName" : "referenceSequence", "sms:required" : "sms:false" + }, { + "@id" : "bts:title", + "@type" : "rdfs:Class", + "rdfs:comment" : "Title of a resource.", + "rdfs:label" : "title", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "title", + "sms:required" : "sms:true" }, { "@id" : "bts:documentation", "@type" : "rdfs:Class", @@ -2943,6 +3160,17 @@ }, "sms:displayName" : "proportionCoverage10x", "sms:required" : "sms:false" + }, { + "@id" : "bts:studyName", + "@type" : "rdfs:Class", + "rdfs:comment" : "Name of a study.", + "rdfs:label" : "studyName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "studyName", + "sms:required" : "sms:true" }, { "@id" : "bts:libraryID", "@type" : "rdfs:Class", @@ -2995,7 +3223,7 @@ }, { "@id" : "bts:sampleType", "@type" : "rdfs:Class", - "rdfs:comment" : "Type of sample", + "rdfs:comment" : "Type of sample used", "rdfs:label" : "sampleType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -3069,6 +3297,17 @@ "rdfs:comment" : "Tissue into which a xenograph sample is transplanted", "@type" : "rdfs:Class", "sms:displayName" : "transplantationRecipientTissue" + }, { + "@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", @@ -3113,6 +3352,17 @@ }, "sms:displayName" : "totalReads", "sms:required" : "sms:false" + }, { + "@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", @@ -4057,6 +4307,17 @@ }, "sms:displayName" : "parentId", "sms:required" : "sms:false" + }, { + "@id" : "bts:diseaseFocus", + "@type" : "rdfs:Class", + "rdfs:comment" : "Disease that acts as the main topic.", + "rdfs:label" : "diseaseFocus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "diseaseFocus", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:transplantationRecipientSpecies", @@ -4224,6 +4485,308 @@ "@id" : "bts:timePointUnit" } ], "sms:displayName" : "experimentalTimepoint" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:protocolAssay", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:immunoassay" + }, { + "@id" : "bts:Sangersequencing" + }, { + "@id" : "bts:ATAC-seq" + }, { + "@id" : "bts:RPPA" + }, { + "@id" : "bts:noveltyresponsebehaviorassay" + }, { + "@id" : "bts:autoradiography" + }, { + "@id" : "bts:genotyping" + }, { + "@id" : "bts:immunohistochemistry" + }, { + "@id" : "bts:highfrequencyultrasound" + }, { + "@id" : "bts:reactiveoxygenspeciesassay" + }, { + "@id" : "bts:contextualconditioningbehaviorassay" + }, { + "@id" : "bts:elevatedplusmazetest" + }, { + "@id" : "bts:lightscatteringassay" + }, { + "@id" : "bts:spatialfrequencydomainimaging" + }, { + "@id" : "bts:HI-C" + }, { + "@id" : "bts:ATPaseactivityassay" + }, { + "@id" : "bts:compoundscreen" + }, { + "@id" : "bts:quantitativePCR" + }, { + "@id" : "bts:combinationscreen" + }, { + "@id" : "bts:questionnaire" + }, { + "@id" : "bts:ChIP-seq" + }, { + "@id" : "bts:miRNAarray" + }, { + "@id" : "bts:whole-cellpatchclamp" + }, { + "@id" : "bts:2DIncucyte" + }, { + "@id" : "bts:electrochemiluminescence" + }, { + "@id" : "bts:laserspeckleimaging" + }, { + "@id" : "bts:westernblot" + }, { + "@id" : "bts:singlemoleculedrugscreenassay" + }, { + "@id" : "bts:sandwichELISA" + }, { + "@id" : "bts:massivelyparallelreporterassay" + }, { + "@id" : "bts:combinationlibraryscreen" + }, { + "@id" : "bts:invitrotumorigenesis" + }, { + "@id" : "bts:polymerasechainreaction" + }, { + "@id" : "bts:TMTquantitation" + }, { + "@id" : "bts:cellproliferation" + }, { + "@id" : "bts:reportergeneassay" + }, { + "@id" : "bts:ERRbisulfitesequencing" + }, { + "@id" : "bts:3Dimaging" + }, { + "@id" : "bts:positronemissiontomography" + }, { + "@id" : "bts:SNParray" + }, { + "@id" : "bts:differentialscanningcalorimetry" + }, { + "@id" : "bts:FTIRspectroscopy" + }, { + "@id" : "bts:functionalMRI" + }, { + "@id" : "bts:ISO-seq" + }, { + "@id" : "bts:localfieldpotentialrecording" + }, { + "@id" : "bts:cAMP-GloMaxAssay" + }, { + "@id" : "bts:magneticresonancespectroscopy" + }, { + "@id" : "bts:bluenativePAGE" + }, { + "@id" : "bts:immunocytochemistry" + }, { + "@id" : "bts:brightfieldmicroscopy" + }, { + "@id" : "bts:mRNAcounts" + }, { + "@id" : "bts:sorbitoldehydrogenaseactivitylevelassay" + }, { + "@id" : "bts:survival" + }, { + "@id" : "bts:wholeexomesequencing" + }, { + "@id" : "bts:staticlightscattering" + }, { + "@id" : "bts:immunofluorescence" + }, { + "@id" : "bts:oxygenconsumptionassay" + }, { + "@id" : "bts:rheometry" + }, { + "@id" : "bts:RNA-seq" + }, { + "@id" : "bts:lncRNA-seq" + }, { + "@id" : "bts:RiccardiandAblonscales" + }, { + "@id" : "bts:array" + }, { + "@id" : "bts:FIA-MSMS" + }, { + "@id" : "bts:HPLC" + }, { + "@id" : "bts:NOMe-seq" + }, { + "@id" : "bts:oxBS-seq" + }, { + "@id" : "bts:nextgenerationtargetedsequencing" + }, { + "@id" : "bts:RNAarray" + }, { + "@id" : "bts:jumpinglibrary" + }, { + "@id" : "bts:smallmoleculelibraryscreen" + }, { + "@id" : "bts:ribo-seq" + }, { + "@id" : "bts:patternelectroretinogram" + }, { + "@id" : "bts:highcontentscreen" + }, { + "@id" : "bts:openfieldtest" + }, { + "@id" : "bts:3Dconfocalimaging" + }, { + "@id" : "bts:gelfiltrationchromatography" + }, { + "@id" : "bts:atomicforcemicroscopy" + }, { + "@id" : "bts:invivoPDXviability" + }, { + "@id" : "bts:longtermpotentiationassay" + }, { + "@id" : "bts:ultrahigh-performanceliquidchromatography/tandemmassspectrometry" + }, { + "@id" : "bts:DNAopticalmapping" + }, { + "@id" : "bts:activeavoidancelearningbehaviorassay" + }, { + "@id" : "bts:twinspotassay" + }, { + "@id" : "bts:focusformingassay" + }, { + "@id" : "bts:rotarodperformancetest" + }, { + "@id" : "bts:methylationarray" + }, { + "@id" : "bts:2DAlamarBlueabsorbance" + }, { + "@id" : "bts:2DAlamarBluefluorescence" + }, { + "@id" : "bts:Tcellreceptorrepertoiresequencing" + }, { + "@id" : "bts:dynamiclightscattering" + }, { + "@id" : "bts:invivotumorgrowth" + }, { + "@id" : "bts:bloodchemistrymeasurement" + }, { + "@id" : "bts:photograph" + }, { + "@id" : "bts:invivobioluminescence" + }, { + "@id" : "bts:bodysizetraitmeasurement" + }, { + "@id" : "bts:3Dmicrotissueviability" + }, { + "@id" : "bts:cellcompetition" + }, { + "@id" : "bts:ELISA" + }, { + "@id" : "bts:cellviabilityassay" + }, { + "@id" : "bts:wholegenomesequencing" + }, { + "@id" : "bts:tractionforcemicroscopy" + }, { + "@id" : "bts:CUT&RUN" + }, { + "@id" : "bts:Matrigel-basedtumorigenesisassay" + }, { + "@id" : "bts:perineurialcellthickness" + }, { + "@id" : "bts:SUSHI" + }, { + "@id" : "bts:spatialtranscriptomics" + }, { + "@id" : "bts:flowcytometry" + }, { + "@id" : "bts:phase-contrastmicroscopy" + }, { + "@id" : "bts:liquidchromatography/tandemmassspectrometry" + }, { + "@id" : "bts:opticalcoherencetomography" + }, { + "@id" : "bts:liquidchromatography/massspectrometry" + }, { + "@id" : "bts:miRNA-seq" + }, { + "@id" : "bts:optokineticreflexassay" + }, { + "@id" : "bts:MIB/MS" + }, { + "@id" : "bts:liquidchromatography-electrochemicaldetection" + }, { + "@id" : "bts:massspectrometry" + }, { + "@id" : "bts:calciumretentioncapacityassay" + }, { + "@id" : "bts:labelfreemassspectrometry" + }, { + "@id" : "bts:single-cellRNA-seq" + }, { + "@id" : "bts:clinicaldata" + }, { + "@id" : "bts:gaitmeasurement" + }, { + "@id" : "bts:high-performanceliquidchromatography/tandemmassspectrometry" + }, { + "@id" : "bts:MudPIT" + }, { + "@id" : "bts:VonFreytest" + }, { + "@id" : "bts:bisulfitesequencing" + }, { + "@id" : "bts:scCGI-seq" + }, { + "@id" : "bts:3Delectronmicroscopy" + }, { + "@id" : "bts:2DCellTiter-Glo" + }, { + "@id" : "bts:cellcount" + }, { + "@id" : "bts:targetedexomesequencing" + }, { + "@id" : "bts:conventionalMRI" + }, { + "@id" : "bts:scale" + }, { + "@id" : "bts:ChildBehaviorChecklistforAges1.5-5" + }, { + "@id" : "bts:ChildBehaviorChecklistforAges6-18" + }, { + "@id" : "bts:SocialResponsivenessScale" + }, { + "@id" : "bts:SocialResponsivenessScale,SecondEdition" + }, { + "@id" : "bts:NIHToolbox" + }, { + "@id" : "bts:multi-electrodearray" + }, { + "@id" : "bts:EdUproliferationassay" + }, { + "@id" : "bts:BrdUproliferationassay" + }, { + "@id" : "bts:TIDE" + }, { + "@id" : "bts:FLIPRhigh-throughputcellularscreening" + }, { + "@id" : "bts:microrheology" + }, { + "@id" : "bts:oscillatoryrheology" + }, { + "@id" : "bts:complexIIenzymeactivityassay" + } ], + "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", + "@type" : "rdfs:Class", + "sms:displayName" : "protocolAssay" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:assay", diff --git a/modules/Template/Template.yaml b/modules/Template/Template.yaml index 31512cd6..05ba6560 100644 --- a/modules/Template/Template.yaml +++ b/modules/Template/Template.yaml @@ -529,14 +529,18 @@ classes: ProtocolTemplate: is_a: ResearchToolsTemplate description: Template for describing a protocol document. - source: https://bioschema.org/profiles/LabProtocol/0.6-DRAFT-2020_12_08 + source: https://bioschemas.org/profiles/LabProtocol/0.7-DRAFT slots: - Component - Filename - resourceType + - title - author - citation - license + - protocolAssay + - protocolPurpose + - sampleType - comments annotations: requiresComponent: '' @@ -558,6 +562,38 @@ classes: requiresComponent: '' required: false +####################################### +# Other Artifacts +####################################### + + DatasetTemplate: + is_a: Template + description: Template that specifies NF portal dataset properties should have for more consistent community-curated datasets. + notes: + - This is intended to be compiled to JSON schema and bound to dataset entities, NOT used in DCA. + - While "publisher" (repository) may seem redundant, eventually may want to have symbolic datasets like Cancer Complexity Portal that describe datasets hosted somewhere else. + slots: + - id # Synapse id used as accession for citation when no doi + - doi + - title + - creator + - contributor + - currentVersion + - description + - license + - dataType + - studyName + - studyId + - manifestation + - diseaseFocus + - fundingAgency + - series + - publisher + - yearProcessed + - yearPublished + - datasetItemCount + - datasetSizeInBytes + ####################################### # PartialTemplate ####################################### diff --git a/modules/props.yaml b/modules/props.yaml index ebd4771a..6120e995 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -161,6 +161,16 @@ slots: notes: - Currently no dependencies or validation rules. required: false + contributor: + description: An entity responsible for making contributions to the resource. + meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#contributor + required: false + creator: + description: An entity responsible for making the resource. + notes: + - Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided. + meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#creator + required: true createdBy: description: Refers to the user who created the resource. in_subset: @@ -177,6 +187,7 @@ slots: required: false currentVersion: description: (Versionable entities only) The current version number of the resource. + meaning: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_version in_subset: - Synapse notes: @@ -204,12 +215,28 @@ slots: description: | 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`. required: false + datasetSizeInBytes: + description: Size of dataset entity in bytes. Auto-calculated by Synapse. + in_subset: + - Synapse + required: false + datasetItemCount: + description: Count of files in dataset. Auto-calculated by Synapse. + in_subset: + - Synapse + required: false + description: + description: Text describing a resource. + required: false diagnosis: description: A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. notes: - Currently no dependencies or validation rules. range: DiagnosisEnum required: false + diseaseFocus: + description: Disease that acts as the main topic. + required: false dissociationMethod: description: Procedure by which a biological specimen is dissociated into individual cells or a cell suspension notes: @@ -221,6 +248,9 @@ slots: notes: - Currently no dependencies or validation rules. required: false + doi: + description: Digital object identifier of the resource. + required: false drugScreenType: description: String describing general class of drug screen notes: @@ -266,6 +296,18 @@ slots: - Currently no dependencies or validation rules. range: BooleanEnum required: false + fileCount: + description: Number of files in the resource collection. + notes: + - This is auto-generated by Synapse for datasets. + in_subset: + - Synapse + required: false + fileSize: + description: Size of file in bytes. + in_subset: + - Synapse + required: false fileFormat: description: 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 notes: @@ -387,6 +429,9 @@ slots: notes: - Currently no dependencies or validation rules. required: false + manifestation: + description: An associated phenotype characteristic. + required: false materialType: description: Type of material in the characterization enum_range: @@ -529,6 +574,18 @@ slots: - Currently no dependencies or validation rules. range: ProteinExtractSourceEnum required: false + protocolAssay: + description: > + 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. + range: AssayEnum + required: false + protocolPurpose: + description: Brief description of the protocol purpose. + required: false + publisher: + description: An entity responsible for making the resource available. + meaning: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher + required: false readDepth: description: If available, the coverage statistic as output from bedtools coverage or samtools stats. notes: @@ -604,7 +661,7 @@ slots: - Currently no dependencies or validation rules. required: false sampleType: - description: Type of sample + description: Type of sample used notes: - Currently no dependencies or validation rules. required: false @@ -623,6 +680,10 @@ slots: notes: - Currently no dependencies or validation rules. required: false + series: + description: Which series this resource belongs to, can be a name or link. + meaning: http://www.w3.org/ns/dcat#inSeries + required: false species: description: The name of a species (typically a taxonomic group) of organism. notes: @@ -645,6 +706,12 @@ slots: - Currently no dependencies or validation rules. range: SpecimenPreparationMethodEnum required: false + studyId: + description: Id of study. + required: true + studyName: + description: Name of a study. + required: true targetCaptureKitID: description: 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. notes: @@ -667,6 +734,10 @@ slots: - Currently no dependencies or validation rules. range: TissueEnum required: false + title: + description: Title of a resource. + meaning: https://www.w3.org/TR/vocab-dcat-3/#Property:resource_title + required: true totalReads: description: If available, the total number of reads collected from samtools. notes: @@ -705,6 +776,12 @@ slots: notes: - Currently no dependencies or validation rules. required: false + yearProcessed: + description: Year in which the resource was processed/derived. + required: false + yearPublished: + description: Year in which the resource was published. + required: false workflow: annotations: requiresDependency: workflowLink diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh index 0e5ce2b8..50a97768 100755 --- a/tests/generate/basic_templates.sh +++ b/tests/generate/basic_templates.sh @@ -7,7 +7,7 @@ CREDS=creds.json DATA_MODEL_PATH=../../NF.jsonld DATA_MODEL=NF.jsonld LOG_DIR=logs -SLEEP_THROTTLE=13 # API rate-limiting, need to better figure out dynamically based on # of templates +SLEEP_THROTTLE=17 # API rate-limiting, need to better figure out dynamically based on # of templates # Setup for creds # If testing locally, it might already be in folder;