diff --git a/NF.jsonld b/NF.jsonld index afd7fdf3..a0cc72bd 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -764,6 +764,24 @@ }, "sms:displayName" : "sourceName", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:mosaicism", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:mosaic" + }, { + "@id" : "bts:notmosaic" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "mosaicism", + "rdfs:comment" : "Whether individual is mosaic.", + "@type" : "rdfs:Class", + "sms:displayName" : "mosaicism" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:readPairOrientation", @@ -795,6 +813,24 @@ }, "sms:displayName" : "fileSize", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:dermalSchwannoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "dermalSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Dermal schwannoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "dermalSchwannoma" }, { "@id" : "bts:benefactorId", "@type" : "rdfs:Class", @@ -806,6 +842,28 @@ }, "sms:displayName" : "benefactorId", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:spinalSchwannoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:single" + }, { + "@id" : "bts:multiple" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "spinalSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Spinal schwannoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "spinalSchwannoma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:accessType", @@ -824,6 +882,48 @@ "rdfs:comment" : "Indicates access type / possible procedures needed for access to the resource.", "@type" : "rdfs:Class", "sms:displayName" : "accessType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:spinalNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absent" + }, { + "@id" : "bts:levels1-3" + }, { + "@id" : "bts:alllevels" + } ], + "rdfs:label" : "spinalNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Spinal neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "spinalNeurofibromas" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:opticGlioma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present-asymptomatic" + }, { + "@id" : "bts:present-symptomatic-nottreated" + }, { + "@id" : "bts:present-symptomatic-treated" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "opticGlioma", + "rdfs:comment" : "Characterization of the manifestation of Optic glioma.", + "@type" : "rdfs:Class", + "sms:displayName" : "opticGlioma" }, { "@id" : "bts:createdOn", "@type" : "rdfs:Class", @@ -858,6 +958,24 @@ "rdfs:comment" : "Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity.", "@type" : "rdfs:Class", "sms:displayName" : "grantDOI" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:breastCancer", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "breastCancer", + "rdfs:comment" : "Characterization of the manifestation of Breast cancer.", + "@type" : "rdfs:Class", + "sms:displayName" : "breastCancer" }, { "@id" : "bts:reporterSubstance", "@type" : "rdfs:Class", @@ -931,15 +1049,25 @@ "sms:required" : "sms:false", "schema:rangeIncludes" : [ { "@id" : "bts:Neurofibromatosistype1" - }, { - "@id" : "bts:Neurofibromatosistype2" }, { "@id" : "bts:Schwannomatosis" + }, { + "@id" : "bts:NF2-relatedschwannomatosis" + }, { + "@id" : "bts:SMARCB1-relatedschwannomatosis" + }, { + "@id" : "bts:LZTR1-relatedschwannomatosis" + }, { + "@id" : "bts:22q-relatedschwannomatosis" + }, { + "@id" : "bts:Schwannomatosis-NOS" + }, { + "@id" : "bts:Schwannomatosis-NEC" }, { "@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.", + "rdfs:comment" : "Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.", "@type" : "rdfs:Class", "sms:displayName" : "diagnosis" }, { @@ -1109,6 +1237,24 @@ }, "sms:displayName" : "createdBy", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:otherTumors", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "otherTumors", + "rdfs:comment" : "Characterization of the manifestation of other tumors.", + "@type" : "rdfs:Class", + "sms:displayName" : "otherTumors" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:genePerturbationType", @@ -1121,6 +1267,24 @@ "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", "@type" : "rdfs:Class", "sms:displayName" : "genePerturbationType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:painStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notaproblem" + }, { + "@id" : "bts:occasional" + }, { + "@id" : "bts:disabling" + } ], + "rdfs:label" : "painStatus", + "rdfs:comment" : "Pain status rating.", + "@type" : "rdfs:Class", + "sms:displayName" : "painStatus" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:compoundDose", @@ -1216,6 +1380,30 @@ "rdfs:comment" : "Number of base pairs (bp) sequenced for a read", "@type" : "rdfs:Class", "sms:displayName" : "readLength" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:tumorTreatmentStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:nospecifictherapy" + }, { + "@id" : "bts:chemotherapy" + }, { + "@id" : "bts:surgery" + }, { + "@id" : "bts:radiation" + }, { + "@id" : "bts:targetedtherapy" + }, { + "@id" : "bts:clinicaltrial" + } ], + "rdfs:label" : "tumorTreatmentStatus", + "rdfs:comment" : "Tumor treatment status for the individual.", + "@type" : "rdfs:Class", + "sms:displayName" : "tumorTreatmentStatus" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:studyId", @@ -1239,6 +1427,26 @@ }, "sms:displayName" : "Filename", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:diffuseDermalNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "diffuseDermalNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Diffuse dermal neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "diffuseDermalNeurofibromas" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:readStrandOrigin", @@ -1267,18 +1475,6 @@ "rdfs:comment" : "Title of a custom series that this resource is part of, if any.", "@type" : "rdfs:Class", "sms:displayName" : "series" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:nf1Variant", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "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", @@ -1405,6 +1601,24 @@ "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:GIST", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "GIST", + "rdfs:comment" : "Characterization of the manifestation of Gastrointestinal stromal tumor (GIST).", + "@type" : "rdfs:Class", + "sms:displayName" : "GIST" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:immersion", @@ -1481,6 +1695,24 @@ "rdfs:comment" : "An ontology concept for experimental factor measured with this data.", "@type" : "rdfs:Class", "sms:displayName" : "experimentalFactor" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:stature", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:<5thcentile" + }, { + "@id" : "bts:5th-95thcentile" + }, { + "@id" : "bts:>95thcentile" + } ], + "rdfs:label" : "stature", + "rdfs:comment" : "Stature of the individual.", + "@type" : "rdfs:Class", + "sms:displayName" : "stature" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:readPair", @@ -1515,6 +1747,40 @@ "rdfs:comment" : "Unit for working distance.", "@type" : "rdfs:Class", "sms:displayName" : "workingDistanceUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nonopticGlioma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "nonopticGlioma", + "rdfs:comment" : "Characterization of the manifestation of Nonoptic glioma.", + "@type" : "rdfs:Class", + "sms:displayName" : "nonopticGlioma" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:germlineMutationIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:nottested" + }, { + "@id" : "bts:testedbutunknown" + } ], + "rdfs:label" : "germlineMutationIndicator", + "rdfs:comment" : "Indicates a summary testing result for individual's germline mutation only.", + "@type" : "rdfs:Class", + "sms:displayName" : "germlineMutationIndicator" }, { "@id" : "bts:antibodyID", "@type" : "rdfs:Class", @@ -1537,6 +1803,28 @@ }, "sms:displayName" : "specimenIDSource", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:vestibularSchwannoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:unilateral" + }, { + "@id" : "bts:bilateral" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "vestibularSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Vestibular schwannoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "vestibularSchwannoma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:isPairedEnd", @@ -1553,6 +1841,26 @@ "rdfs:comment" : "(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).", "@type" : "rdfs:Class", "sms:displayName" : "isPairedEnd" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:numberOfSchwannomas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:single" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "numberOfSchwannomas", + "rdfs:comment" : "Number of schwannomas.", + "@type" : "rdfs:Class", + "sms:displayName" : "numberOfSchwannomas" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:dataStatus", @@ -1931,6 +2239,24 @@ "rdfs:comment" : "Genotype of NF2 gene in the biospecimen from which the data were derived, if known", "@type" : "rdfs:Class", "sms:displayName" : "nf2Genotype" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:peripheralNeuropathy", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "peripheralNeuropathy", + "rdfs:comment" : "Characterization of the manifestation of Peripheral neuropathy.", + "@type" : "rdfs:Class", + "sms:displayName" : "peripheralNeuropathy" }, { "@id" : "bts:Component", "@type" : "rdfs:Class", @@ -1942,6 +2268,24 @@ }, "sms:displayName" : "Component", "sms:required" : "sms:true" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:scoliosis", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "scoliosis", + "rdfs:comment" : "Characterization of the manifestation of Scoliosis.", + "@type" : "rdfs:Class", + "sms:displayName" : "scoliosis" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:species", @@ -2032,6 +2376,44 @@ "rdfs:comment" : "Refers to the funding organization for the generated resource. This annotation is handled by the DCC.", "@type" : "rdfs:Class", "sms:displayName" : "fundingAgency" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:intellectualDisability", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "intellectualDisability", + "rdfs:comment" : "Characterization of the manifestation of Intellectual disability.", + "@type" : "rdfs:Class", + "sms:displayName" : "intellectualDisability" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:plexiformNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:present" + }, { + "@id" : "bts:absentbyMRI" + }, { + "@id" : "bts:absentclinically-noMRI" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "plexiformNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Plexiform neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "plexiformNeurofibromas" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:nucleicAcidSource", @@ -2109,10 +2491,28 @@ }, "sms:displayName" : "runtimePlatform", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MPNST", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "MPNST", + "rdfs:comment" : "Characterization of the manifestation of MPNST.", + "@type" : "rdfs:Class", + "sms:displayName" : "MPNST" }, { "@id" : "bts:nf1SomaticMutation", "@type" : "rdfs:Class", - "rdfs:comment" : "NF1 somatic mutation. Subproperty of nf1Variant.", + "rdfs:comment" : "NF1 somatic mutation, i.e. in tumor samples.", "rdfs:label" : "nf1SomaticMutation", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -2131,7 +2531,43 @@ "rdfs:label" : "manifestation", "rdfs:comment" : "An associated phenotype characteristic.", "@type" : "rdfs:Class", - "sms:displayName" : "manifestation" + "sms:displayName" : "manifestation" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:aqueductalStenosis", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "aqueductalStenosis", + "rdfs:comment" : "Characterization of the manifestation of aqueductal stenosis.", + "@type" : "rdfs:Class", + "sms:displayName" : "aqueductalStenosis" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:IrisLischNodules", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "IrisLischNodules", + "rdfs:comment" : "Characterization of the manifestation of Iris Lisch Nodules.", + "@type" : "rdfs:Class", + "sms:displayName" : "IrisLischNodules" }, { "@id" : "bts:concentrationNaCl", "@type" : "rdfs:Class", @@ -2230,6 +2666,24 @@ }, "sms:displayName" : "auxiliaryAsset", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:heartDefect", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "heartDefect", + "rdfs:comment" : "Characterization of the manifestation of Heart defect.", + "@type" : "rdfs:Class", + "sms:displayName" : "heartDefect" }, { "@id" : "bts:doi", "@type" : "rdfs:Class", @@ -2252,6 +2706,24 @@ }, "sms:displayName" : "readsDuplicatedPercent", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:pheochromocytoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "pheochromocytoma", + "rdfs:comment" : "Characterization of the manifestation of Pheochromocytoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "pheochromocytoma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:isMultiSpecimen", @@ -2299,6 +2771,28 @@ }, "sms:displayName" : "datasetSizeInBytes", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:diagnosisAgeGroup", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:infancy" + }, { + "@id" : "bts:childhood" + }, { + "@id" : "bts:adolescence" + }, { + "@id" : "bts:adulthood" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "diagnosisAgeGroup", + "rdfs:comment" : "Age group of the individual at the time of diagnosis.", + "@type" : "rdfs:Class", + "sms:displayName" : "diagnosisAgeGroup" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:yearProcessed", @@ -2357,6 +2851,24 @@ }, "sms:displayName" : "relatedDataset", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:inheritance", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:parentaffected" + }, { + "@id" : "bts:parentnotaffected" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "inheritance", + "rdfs:comment" : "Describes whether known inheritance from a parent.", + "@type" : "rdfs:Class", + "sms:displayName" : "inheritance" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:concentrationMaterialUnit", @@ -2901,6 +3413,28 @@ "rdfs:comment" : "For timed experiments this represents the unit of time measured", "@type" : "rdfs:Class", "sms:displayName" : "timepointUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:WHOPerformanceStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:0" + }, { + "@id" : "bts:1" + }, { + "@id" : "bts:2" + }, { + "@id" : "bts:3" + }, { + "@id" : "bts:4" + } ], + "rdfs:label" : "WHOPerformanceStatus", + "rdfs:comment" : "Score on the WHO scale describing patient's functional abilities.", + "@type" : "rdfs:Class", + "sms:displayName" : "WHOPerformanceStatus" }, { "@id" : "bts:currentVersion", "@type" : "rdfs:Class", @@ -2999,6 +3533,24 @@ "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" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:learningDisability", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "learningDisability", + "rdfs:comment" : "Characterization of the manifestation of Learning disability.", + "@type" : "rdfs:Class", + "sms:displayName" : "learningDisability" }, { "@id" : "bts:id", "@type" : "rdfs:Class", @@ -3037,6 +3589,24 @@ }, "sms:displayName" : "Resource_id", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:lenticularOpacity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "lenticularOpacity", + "rdfs:comment" : "Characterization of the manifestation of Lenticular opacity.", + "@type" : "rdfs:Class", + "sms:displayName" : "lenticularOpacity" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:drugScreenType", @@ -3068,6 +3638,24 @@ }, "sms:displayName" : "experimentalCondition", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:cafeaulaitMacules", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "cafeaulaitMacules", + "rdfs:comment" : "Characterization of cafe-au-lait macules.", + "@type" : "rdfs:Class", + "sms:displayName" : "cafeaulaitMacules" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:modelSystemName", @@ -3385,6 +3973,26 @@ "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)", "@type" : "rdfs:Class", "sms:displayName" : "modelSystemName" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:dermalNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "dermalNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Dermal neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "dermalNeurofibromas" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:proteinExtractSource", @@ -3473,6 +4081,24 @@ "rdfs:comment" : "Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.", "@type" : "rdfs:Class", "sms:displayName" : "bodySite" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:longBoneDysplasia", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "longBoneDysplasia", + "rdfs:comment" : "Characterization of the manifestation of Long bone dysplasia.", + "@type" : "rdfs:Class", + "sms:displayName" : "longBoneDysplasia" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:libraryPrep", @@ -3620,6 +4246,26 @@ "@id" : "bts:workingDistanceUnit" } ], "sms:displayName" : "workingDistance" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nonvestibularCranialSchwannoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "nonvestibularCranialSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Nonvestibular cranial schwannoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "nonvestibularCranialSchwannoma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:expressionUnit", @@ -3646,6 +4292,26 @@ "rdfs:comment" : "Measure used for transcript expression quantification", "@type" : "rdfs:Class", "sms:displayName" : "expressionUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:pubertyOnset", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:prebubertal" + }, { + "@id" : "bts:precocious" + }, { + "@id" : "bts:normal" + }, { + "@id" : "bts:late" + } ], + "rdfs:label" : "pubertyOnset", + "rdfs:comment" : "Puberty onset.", + "@type" : "rdfs:Class", + "sms:displayName" : "pubertyOnset" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:readsMappedPercent", @@ -3658,6 +4324,24 @@ "rdfs:comment" : "Percent of mapped reads collected from samtools", "@type" : "rdfs:Class", "sms:displayName" : "readsMappedPercent" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:glomusTumor", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "glomusTumor", + "rdfs:comment" : "Characterization of the manifestation of Glomus tumor.", + "@type" : "rdfs:Class", + "sms:displayName" : "glomusTumor" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:studyStatus", @@ -3676,6 +4360,73 @@ "rdfs:comment" : "Status of a study.", "@type" : "rdfs:Class", "sms:displayName" : "studyStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:sphenoidDysplasia", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "sphenoidDysplasia", + "rdfs:comment" : "Characterization of the manifestation of Sphenoid dysplasia.", + "@type" : "rdfs:Class", + "sms:displayName" : "sphenoidDysplasia" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nonvestibularSchwannomas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:onlybyimagingevidence" + }, { + "@id" : "bts:1pathogicallyconfirmed" + }, { + "@id" : "bts:2ormore,atleast1pathogicallyconfirmed" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "nonvestibularSchwannomas", + "rdfs:comment" : "Characterization of the manifestation of Nonvestibular schwannomas.", + "@type" : "rdfs:Class", + "sms:displayName" : "nonvestibularSchwannomas" + }, { + "@id" : "bts:germlineMutation", + "@type" : "rdfs:Class", + "rdfs:comment" : "The individual's actual germline mutation.", + "rdfs:label" : "germlineMutation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "germlineMutation", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:skinFoldFreckling", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "skinFoldFreckling", + "rdfs:comment" : "Characterization of skin fold freckling.", + "@type" : "rdfs:Class", + "sms:displayName" : "skinFoldFreckling" }, { "@id" : "bts:contentType", "@type" : "rdfs:Class", @@ -3698,6 +4449,44 @@ }, "sms:displayName" : "objective", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:leukemia", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "leukemia", + "rdfs:comment" : "Characterization of the manifestation of Leukemia.", + "@type" : "rdfs:Class", + "sms:displayName" : "leukemia" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:subcutaneousNodularNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "subcutaneousNodularNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Subcutaneous nodular neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "subcutaneousNodularNeurofibromas" }, { "@id" : "bts:averageInsertSize", "@type" : "rdfs:Class", @@ -3754,10 +4543,28 @@ }, { "@id" : "bts:No" } ], - "rdfs:label" : "failedQC", - "rdfs:comment" : "Whether the sample or data failed QC checks (Yes, No)", + "rdfs:label" : "failedQC", + "rdfs:comment" : "Whether the sample or data failed QC checks (Yes, No)", + "@type" : "rdfs:Class", + "sms:displayName" : "failedQC" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:vascularDisease", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "vascularDisease", + "rdfs:comment" : "Characterization of the manifestation of Vascular disease.", "@type" : "rdfs:Class", - "sms:displayName" : "failedQC" + "sms:displayName" : "vascularDisease" }, { "@id" : "bts:compoundName", "@type" : "rdfs:Class", @@ -3772,7 +4579,7 @@ }, { "@id" : "bts:nf1GermlineMutation", "@type" : "rdfs:Class", - "rdfs:comment" : "NF1 germline mutation. Subproperty of nf1Variant.", + "rdfs:comment" : "NF1 germline mutation.", "rdfs:label" : "nf1GermlineMutation", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -3831,6 +4638,24 @@ "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" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:attentionDeficitDisorder", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "attentionDeficitDisorder", + "rdfs:comment" : "Characterization of the manifestation of Attention Deficit Disorder.", + "@type" : "rdfs:Class", + "sms:displayName" : "attentionDeficitDisorder" }, { "@id" : "bts:parentId", "@type" : "rdfs:Class", @@ -4012,6 +4837,24 @@ "@id" : "bts:timepointUnit" } ], "sms:displayName" : "experimentalTimepoint" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:vitalStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:alive" + }, { + "@id" : "bts:deceased" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "vitalStatus", + "rdfs:comment" : "Vital status of the patient.", + "@type" : "rdfs:Class", + "sms:displayName" : "vitalStatus" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:protocolAssay", @@ -4703,6 +5546,28 @@ "rdfs:comment" : "The technology used to generate the data in this file.", "@type" : "rdfs:Class", "sms:displayName" : "assay" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:meningioma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:single" + }, { + "@id" : "bts:multiple" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "meningioma", + "rdfs:comment" : "Characterization of the manifestation of Meningioma.", + "@type" : "rdfs:Class", + "sms:displayName" : "meningioma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:studyFileviewId", @@ -4726,6 +5591,26 @@ }, "sms:displayName" : "averageReadLength", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:gliomaOrEpendymoma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "gliomaOrEpendymoma", + "rdfs:comment" : "Characterization of the manifestation of Glioma or ependymoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "gliomaOrEpendymoma" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:relatedStudies", @@ -4961,6 +5846,17 @@ }, "sms:displayName" : "FileFormatEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:MultipleImagingDiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with one or multiple sites being the most relevant result.", + "rdfs:label" : "MultipleImagingDiagnosisEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MultipleImagingDiagnosisEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:SexEnum", "@type" : "rdfs:Class", @@ -4983,6 +5879,28 @@ }, "sms:displayName" : "MRISequenceEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:AgeGroupEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AgeGroupEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeGroupEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TumorTreatmentEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TumorTreatmentEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TumorTreatmentEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:PlatformEnum", "@type" : "rdfs:Class", @@ -5016,6 +5934,28 @@ }, "sms:displayName" : "GenePerturbationEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:TestSummaryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TestSummaryEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TestSummaryEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SpinalNeuromaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of spinal neurofibromas, combining information on presence and the cervical locations.", + "rdfs:label" : "SpinalNeuromaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SpinalNeuromaManifestationEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:WorkflowEnum", "@type" : "rdfs:Class", @@ -5038,6 +5978,17 @@ }, "sms:displayName" : "BooleanEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:PubertyOnsetEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PubertyOnsetEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PubertyOnsetEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:GenePerturbationMethodEnum", "@type" : "rdfs:Class", @@ -5060,6 +6011,28 @@ }, "sms:displayName" : "Data", "sms:required" : "sms:false" + }, { + "@id" : "bts:PlexiformNeurofibromaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of plexiform neurofibromas, combining information on presence and the certainty via MRI imaging technique.", + "rdfs:label" : "PlexiformNeurofibromaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PlexiformNeurofibromaManifestationEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BinaryImagingDiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with mainly absent or present being the most relevant result.", + "rdfs:label" : "BinaryImagingDiagnosisEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BinaryImagingDiagnosisEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:SpeciesEnum", "@type" : "rdfs:Class", @@ -5093,6 +6066,28 @@ }, "sms:displayName" : "ProteinExtractSourceEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:VitalStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VitalStatusEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "VitalStatusEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MosaicismEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MosaicismEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MosaicismEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:WorkingDistanceUnitEnum", "@type" : "rdfs:Class", @@ -5170,6 +6165,17 @@ }, "sms:displayName" : "Tumor", "sms:required" : "sms:false" + }, { + "@id" : "bts:WHOPerformanceStatusScores", + "@type" : "rdfs:Class", + "rdfs:comment" : "https://www.ncbi.nlm.nih.gov/books/NBK97482/", + "rdfs:label" : "WHOPerformanceStatusScores", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "WHOPerformanceStatusScores", + "sms:required" : "sms:false" }, { "@id" : "bts:ConcentrationUnit", "@type" : "rdfs:Class", @@ -5203,6 +6209,17 @@ }, "sms:displayName" : "ReadPairOrientationEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:LateralManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging (MRI or other), where lateral information is most relevant.", + "rdfs:label" : "LateralManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LateralManifestationEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:LibraryPrepEnum", "@type" : "rdfs:Class", @@ -5214,6 +6231,17 @@ }, "sms:displayName" : "LibraryPrepEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:Percentiles-2SD", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations corresponding to 3 bins using 2 standard deviations as a cutoff.", + "rdfs:label" : "Percentiles-2SD", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Percentiles-2SD", + "sms:required" : "sms:false" }, { "@id" : "bts:Tissue", "@type" : "rdfs:Class", @@ -5401,6 +6429,28 @@ }, "sms:displayName" : "ManifestationEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:SchwannomaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of schwannomas.", + "rdfs:label" : "SchwannomaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SchwannomaManifestationEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:OpticGliomaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of optic gliomas, combining information on presence, symptoms, and treatment.", + "rdfs:label" : "OpticGliomaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OpticGliomaManifestationEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:TransplantationType", "@type" : "rdfs:Class", @@ -5489,6 +6539,17 @@ }, "sms:displayName" : "CuratedDataEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:NonvestibularSchwannomaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NonvestibularSchwannomaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "NonvestibularSchwannomaManifestationEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:DataStatusEnum", "@type" : "rdfs:Class", @@ -5522,6 +6583,17 @@ }, "sms:displayName" : "ReadStrandOriginEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:PainEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PainEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PainEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:License", "@type" : "rdfs:Class", @@ -5533,6 +6605,39 @@ }, "sms:displayName" : "License", "sms:required" : "sms:false" + }, { + "@id" : "bts:PresenceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumeration for binary + unknown for very basic classification of a manifestation in clinical context.", + "rdfs:label" : "PresenceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PresenceEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:NeurofibromaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing how neurofibromas can manifest more generally.", + "rdfs:label" : "NeurofibromaManifestationEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "NeurofibromaManifestationEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:InheritanceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "InheritanceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "InheritanceEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:AccessTypeEnum", "@type" : "rdfs:Class", @@ -5920,47 +7025,6 @@ "@id" : "bts:genePerturbationTechnology" } ], "sms:displayName" : "GeneralMeasureDataTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:PatientTemplate" - } ], - "@id" : "bts:PatientSpecimenTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "PatientSpecimenTemplate", - "rdfs:comment" : "Template for capturing specimen-level data from patients.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:individualID" - }, { - "@id" : "bts:sex" - }, { - "@id" : "bts:age" - }, { - "@id" : "bts:ageUnit" - }, { - "@id" : "bts:species" - }, { - "@id" : "bts:diagnosis" - }, { - "@id" : "bts:nf1Genotype" - }, { - "@id" : "bts:nf2Genotype" - }, { - "@id" : "bts:parentSpecimenID" - }, { - "@id" : "bts:specimenID" - }, { - "@id" : "bts:aliquotID" - }, { - "@id" : "bts:tumorType" - }, { - "@id" : "bts:bodySite" - } ], - "sms:displayName" : "PatientSpecimenTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:NonBiologicalAssayDataTemplate" @@ -6098,6 +7162,33 @@ "@type" : "rdfs:Class", "sms:requiresDependency" : [ ], "sms:displayName" : "Template" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BiospecimenTemplate", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BiospecimenTemplate", + "rdfs:comment" : "Specimen-level data, whether from human or animal.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:individualID" + }, { + "@id" : "bts:parentSpecimenID" + }, { + "@id" : "bts:specimenID" + }, { + "@id" : "bts:aliquotID" + }, { + "@id" : "bts:tumorType" + }, { + "@id" : "bts:bodySite" + }, { + "@id" : "bts:experimentalCondition" + } ], + "sms:displayName" : "BiospecimenTemplate" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:PartialTemplate", @@ -6569,67 +7660,157 @@ } ], "sms:displayName" : "ProcessedAlignedReadsTemplate" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Template" - } ], - "@id" : "bts:ProtocolTemplate", + "rdfs:subClassOf" : [ ], + "@id" : "bts:HumanCohortTemplate", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "ProtocolTemplate", - "rdfs:comment" : "Template for describing a protocol document.", + "rdfs:label" : "HumanCohortTemplate", + "rdfs:comment" : "Data of biosamples from human patients. Adapted from Table 2 of http://nrs.harvard.edu/urn-3:HUL.InstRepos:32725809. This template should be used when biosamples are from NF patients to provides a more valuable characterization and make additional gene-phenotype insights possible.\n", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { - "@id" : "bts:title" + "@id" : "bts:individualID" }, { - "@id" : "bts:author" + "@id" : "bts:sex" }, { - "@id" : "bts:citation" + "@id" : "bts:age" }, { - "@id" : "bts:license" + "@id" : "bts:ageUnit" }, { - "@id" : "bts:protocolAssay" + "@id" : "bts:diagnosis" }, { - "@id" : "bts:protocolPurpose" + "@id" : "bts:diagnosisAgeGroup" }, { - "@id" : "bts:sampleType" + "@id" : "bts:inheritance" }, { - "@id" : "bts:comments" + "@id" : "bts:mosaicism" + }, { + "@id" : "bts:nf1Genotype" + }, { + "@id" : "bts:nf2Genotype" + }, { + "@id" : "bts:germlineMutationIndicator" + }, { + "@id" : "bts:species" + }, { + "@id" : "bts:vitalStatus" + }, { + "@id" : "bts:WHOPerformanceStatus" + }, { + "@id" : "bts:painStatus" + }, { + "@id" : "bts:tumorTreatmentStatus" + }, { + "@id" : "bts:cafeaulaitMacules" + }, { + "@id" : "bts:skinFoldFreckling" + }, { + "@id" : "bts:IrisLischNodules" + }, { + "@id" : "bts:dermalNeurofibromas" + }, { + "@id" : "bts:subcutaneousNodularNeurofibromas" + }, { + "@id" : "bts:diffuseDermalNeurofibromas" + }, { + "@id" : "bts:spinalNeurofibromas" + }, { + "@id" : "bts:plexiformNeurofibromas" + }, { + "@id" : "bts:opticGlioma" + }, { + "@id" : "bts:heartDefect" + }, { + "@id" : "bts:vascularDisease" + }, { + "@id" : "bts:pubertyOnset" + }, { + "@id" : "bts:stature" + }, { + "@id" : "bts:peripheralNeuropathy" + }, { + "@id" : "bts:aqueductalStenosis" + }, { + "@id" : "bts:longBoneDysplasia" + }, { + "@id" : "bts:sphenoidDysplasia" + }, { + "@id" : "bts:scoliosis" + }, { + "@id" : "bts:intellectualDisability" + }, { + "@id" : "bts:learningDisability" + }, { + "@id" : "bts:attentionDeficitDisorder" + }, { + "@id" : "bts:pheochromocytoma" + }, { + "@id" : "bts:glomusTumor" + }, { + "@id" : "bts:MPNST" + }, { + "@id" : "bts:nonopticGlioma" + }, { + "@id" : "bts:GIST" + }, { + "@id" : "bts:leukemia" + }, { + "@id" : "bts:breastCancer" + }, { + "@id" : "bts:otherTumors" + }, { + "@id" : "bts:vestibularSchwannoma" + }, { + "@id" : "bts:meningioma" + }, { + "@id" : "bts:gliomaOrEpendymoma" + }, { + "@id" : "bts:spinalSchwannoma" + }, { + "@id" : "bts:dermalSchwannoma" + }, { + "@id" : "bts:nonvestibularCranialSchwannoma" + }, { + "@id" : "bts:lenticularopacity" + }, { + "@id" : "bts:nonvestibularSchwannomas" + }, { + "@id" : "bts:numberOfSchwannomas" } ], - "sms:displayName" : "ProtocolTemplate" + "sms:displayName" : "HumanCohortTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:Template" } ], - "@id" : "bts:PatientTemplate", + "@id" : "bts:ProtocolTemplate", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "PatientTemplate", - "rdfs:comment" : "Template for collecting *minimal* individual-level data. \n", + "rdfs:label" : "ProtocolTemplate", + "rdfs:comment" : "Template for describing a protocol document.", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { - "@id" : "bts:individualID" + "@id" : "bts:title" }, { - "@id" : "bts:sex" + "@id" : "bts:author" }, { - "@id" : "bts:age" + "@id" : "bts:citation" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:license" }, { - "@id" : "bts:species" + "@id" : "bts:protocolAssay" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:protocolPurpose" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:sampleType" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:comments" } ], - "sms:displayName" : "PatientTemplate" + "sms:displayName" : "ProtocolTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:BulkSequencingAssayTemplate" @@ -7729,17 +8910,15 @@ } ], "sms:displayName" : "ImmunoMicroscopyTemplate" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:PatientTemplate" - } ], - "@id" : "bts:PatientXTemplate", + "rdfs:subClassOf" : [ ], + "@id" : "bts:AnimalIndividualTemplate", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "PatientXTemplate", - "rdfs:comment" : "(WIP / not yet used) Extended template for participant clinical data as recommended per Sundby et al.", + "rdfs:label" : "AnimalIndividualTemplate", + "rdfs:comment" : "Template for non-human individual-level data.", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:individualID" @@ -7749,16 +8928,26 @@ "@id" : "bts:age" }, { "@id" : "bts:ageUnit" - }, { - "@id" : "bts:species" }, { "@id" : "bts:diagnosis" + }, { + "@id" : "bts:diagnosisAgeGroup" + }, { + "@id" : "bts:inheritance" + }, { + "@id" : "bts:mosaicism" }, { "@id" : "bts:nf1Genotype" }, { "@id" : "bts:nf2Genotype" + }, { + "@id" : "bts:germlineMutation" + }, { + "@id" : "bts:species" + }, { + "@id" : "bts:modelSystemName" } ], - "sms:displayName" : "PatientXTemplate" + "sms:displayName" : "AnimalIndividualTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:BiologicalAssayDataTemplate" @@ -8339,6 +9528,17 @@ }, "sms:displayName" : "sNF94.3", "sms:required" : "sms:false" + }, { + "@id" : "bts:unilateral", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "unilateral", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "unilateral", + "sms:required" : "sms:false" }, { "@id" : "bts:ColumbiaU.intheCityofNewYork", "@type" : "rdfs:Class", @@ -8559,6 +9759,17 @@ }, "sms:displayName" : "University of Texas, Arlington", "sms:required" : "sms:false" + }, { + "@id" : "bts:absentclinically-noMRI", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "absentclinically-noMRI", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "absent clinically - no MRI", + "sms:required" : "sms:false" }, { "@id" : "bts:csi", "@type" : "rdfs:Class", @@ -8724,6 +9935,17 @@ }, "sms:displayName" : "audio transcript", "sms:required" : "sms:false" + }, { + "@id" : "bts:scattered", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "scattered", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "scattered", + "sms:required" : "sms:false" }, { "@id" : "bts:MIB/MS", "@type" : "rdfs:Class", @@ -9538,6 +10760,17 @@ }, "sms:displayName" : "SUNY, Downstate Health Sciences University", "sms:required" : "sms:false" + }, { + "@id" : "bts:parentaffected", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "parentaffected", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "parent affected", + "sms:required" : "sms:false" }, { "@id" : "bts:SC4[Mouseschwannoma]", "@type" : "rdfs:Class", @@ -9780,6 +11013,17 @@ }, "sms:displayName" : "University of Illinois, Chicago", "sms:required" : "sms:false" + }, { + "@id" : "bts:2ormore,atleast1pathogicallyconfirmed", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "2ormore,atleast1pathogicallyconfirmed", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "2 or more, at least 1 pathogically confirmed", + "sms:required" : "sms:false" }, { "@id" : "bts:Drosophilamelanogaster", "@type" : "rdfs:Class", @@ -9912,6 +11156,17 @@ }, "sms:displayName" : "FACE-Q Appearance-related Distress", "sms:required" : "sms:false" + }, { + "@id" : "bts:precocious", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "precocious", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "precocious", + "sms:required" : "sms:false" }, { "@id" : "bts:xml", "@type" : "rdfs:Class", @@ -10946,6 +12201,17 @@ }, "sms:displayName" : "mM", "sms:required" : "sms:false" + }, { + "@id" : "bts:surgery", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "surgery", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "surgery", + "sms:required" : "sms:false" }, { "@id" : "bts:UniversityofMiami", "@type" : "rdfs:Class", @@ -11078,6 +12344,17 @@ }, "sms:displayName" : "Illinois Institute of Technology", "sms:required" : "sms:false" + }, { + "@id" : "bts:nottested", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "nottested", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "not tested", + "sms:required" : "sms:false" }, { "@id" : "bts:stool", "@type" : "rdfs:Class", @@ -11210,6 +12487,17 @@ }, "sms:displayName" : "small molecule library screen", "sms:required" : "sms:false" + }, { + "@id" : "bts:absentbyimaging", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "absentbyimaging", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "absent by imaging", + "sms:required" : "sms:false" }, { "@id" : "bts:PhilipsAchieva3T", "@type" : "rdfs:Class", @@ -11331,6 +12619,17 @@ }, "sms:displayName" : "traction force microscopy", "sms:required" : "sms:false" + }, { + "@id" : "bts:<5thcentile", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "<5thcentile", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "< 5th centile", + "sms:required" : "sms:false" }, { "@id" : "bts:hTERTNF1ipNF95.6", "@type" : "rdfs:Class", @@ -11914,6 +13213,17 @@ }, "sms:displayName" : "Pleomorphic Xanthoastrocytoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:targetedtherapy", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "targetedtherapy", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "targeted therapy", + "sms:required" : "sms:false" }, { "@id" : "bts:MercerUniversity", "@type" : "rdfs:Class", @@ -12431,6 +13741,17 @@ }, "sms:displayName" : "metastatic/recurrent tumor", "sms:required" : "sms:false" + }, { + "@id" : "bts:occasional", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "occasional", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "occasional", + "sms:required" : "sms:false" }, { "@id" : "bts:dataIndex", "@type" : "rdfs:Class", @@ -12739,6 +14060,17 @@ }, "sms:displayName" : "Schwann cell i28cNF NF1 -/- (#14)", "sms:required" : "sms:false" + }, { + "@id" : "bts:>95thcentile", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : ">95thcentile", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "> 95th centile", + "sms:required" : "sms:false" }, { "@id" : "bts:StanfordUniversity", "@type" : "rdfs:Class", @@ -12849,6 +14181,17 @@ }, "sms:displayName" : "University of Dayton", "sms:required" : "sms:false" + }, { + "@id" : "bts:notaproblem", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "notaproblem", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "not a problem", + "sms:required" : "sms:false" }, { "@id" : "bts:flowcytometry", "@type" : "rdfs:Class", @@ -12871,6 +14214,17 @@ }, "sms:displayName" : "ST88-14", "sms:required" : "sms:false" + }, { + "@id" : "bts:adolescence", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "adolescence", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "adolescence", + "sms:required" : "sms:false" }, { "@id" : "bts:massivelyparallelreporterassay", "@type" : "rdfs:Class", @@ -12992,6 +14346,17 @@ }, "sms:displayName" : "Brigham Young University, Provo", "sms:required" : "sms:false" + }, { + "@id" : "bts:dense", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "dense", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "dense", + "sms:required" : "sms:false" }, { "@id" : "bts:clinicaldata", "@type" : "rdfs:Class", @@ -13267,6 +14632,17 @@ }, "sms:displayName" : "University of North Carolina, Charlotte", "sms:required" : "sms:false" + }, { + "@id" : "bts:clinicaltrial", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "clinicaltrial", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "clinical trial", + "sms:required" : "sms:false" }, { "@id" : "bts:DescriptiveMetadata", "@type" : "rdfs:Class", @@ -13278,6 +14654,17 @@ }, "sms:displayName" : "Descriptive Metadata", "sms:required" : "sms:false" + }, { + "@id" : "bts:5th-95thcentile", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "5th-95thcentile", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "5th-95th centile", + "sms:required" : "sms:false" }, { "@id" : "bts:PacBioSequelIIeSystem", "@type" : "rdfs:Class", @@ -13509,6 +14896,17 @@ }, "sms:displayName" : "Virginia Polytechnic Institute and State University", "sms:required" : "sms:false" + }, { + "@id" : "bts:adulthood", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "adulthood", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "adulthood", + "sms:required" : "sms:false" }, { "@id" : "bts:scalp", "@type" : "rdfs:Class", @@ -13663,6 +15061,17 @@ }, "sms:displayName" : "University of California, Santa Cruz", "sms:required" : "sms:false" + }, { + "@id" : "bts:alllevels", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "alllevels", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "all levels", + "sms:required" : "sms:false" }, { "@id" : "bts:tetrode", "@type" : "rdfs:Class", @@ -13740,6 +15149,17 @@ }, "sms:displayName" : "Zeno Electronic Walkway", "sms:required" : "sms:false" + }, { + "@id" : "bts:present-asymptomatic", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "present-asymptomatic", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "present - asymptomatic", + "sms:required" : "sms:false" }, { "@id" : "bts:CincinnatiChildren'sHospitalMedicalCenter", "@type" : "rdfs:Class", @@ -13795,6 +15215,17 @@ }, "sms:displayName" : "calcium retention capacity assay", "sms:required" : "sms:false" + }, { + "@id" : "bts:normal", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "normal", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "normal", + "sms:required" : "sms:false" }, { "@id" : "bts:MemorialSloaneKetteringCancerCenter", "@type" : "rdfs:Class", @@ -13949,6 +15380,17 @@ }, "sms:displayName" : "allograft", "sms:required" : "sms:false" + }, { + "@id" : "bts:levels1-3", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "levels1-3", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "levels 1-3", + "sms:required" : "sms:false" }, { "@id" : "bts:SchwanncellNF1-/-withWTtaggedmNf1cDNA", "@type" : "rdfs:Class", @@ -14004,6 +15446,17 @@ }, "sms:displayName" : "Nanostring GeoMx", "sms:required" : "sms:false" + }, { + "@id" : "bts:testedbutunknown", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "testedbutunknown", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "tested but unknown", + "sms:required" : "sms:false" }, { "@id" : "bts:RockefellerUniversity", "@type" : "rdfs:Class", @@ -14290,17 +15743,6 @@ }, "sms:displayName" : "Illumina Infinium MethylationEPIC BeadChip v1.0 (850k)", "sms:required" : "sms:false" - }, { - "@id" : "bts:Neurofibromatosistype2", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Neurofibromatosistype2", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Neurofibromatosis type 2", - "sms:required" : "sms:false" }, { "@id" : "bts:i18cNF", "@type" : "rdfs:Class", @@ -15819,6 +17261,17 @@ }, "sms:displayName" : "Fibrosarcoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:present-symptomatic-treated", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "present-symptomatic-treated", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "present - symptomatic - treated", + "sms:required" : "sms:false" }, { "@id" : "bts:BGISEQ-500", "@type" : "rdfs:Class", @@ -15896,6 +17349,17 @@ }, "sms:displayName" : "B", "sms:required" : "sms:false" + }, { + "@id" : "bts:late", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "late", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "late", + "sms:required" : "sms:false" }, { "@id" : "bts:MalignantPeripheralNerveSheathTumor", "@type" : "rdfs:Class", @@ -16061,6 +17525,17 @@ }, "sms:displayName" : "Illumina TruSeq DNA Nano", "sms:required" : "sms:false" + }, { + "@id" : "bts:mosaic", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "mosaic", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "mosaic", + "sms:required" : "sms:false" }, { "@id" : "bts:Drop-Seq", "@type" : "rdfs:Class", @@ -16226,6 +17701,17 @@ }, "sms:displayName" : "cNF97.5", "sms:required" : "sms:false" + }, { + "@id" : "bts:absentbyMRI", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "absentbyMRI", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "absent by MRI", + "sms:required" : "sms:false" }, { "@id" : "bts:NTAP", "@type" : "rdfs:Class", @@ -16336,6 +17822,17 @@ }, "sms:displayName" : "Affymetrix Human Gene 1.0 ST Array", "sms:required" : "sms:false" + }, { + "@id" : "bts:notimaged", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "notimaged", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "not imaged", + "sms:required" : "sms:false" }, { "@id" : "bts:Children'sDermatologyLifeQualityIndexQuestionnaire", "@type" : "rdfs:Class", @@ -16479,6 +17976,17 @@ }, "sms:displayName" : "Pilocytic Astrocytoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:childhood", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "childhood", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "childhood", + "sms:required" : "sms:false" }, { "@id" : "bts:UniversityofSouthFlorida,SaintPetersburg", "@type" : "rdfs:Class", @@ -18393,6 +19901,17 @@ }, "sms:displayName" : "Nf1-C383X/Flox", "sms:required" : "sms:false" + }, { + "@id" : "bts:0", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "0", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "0", + "sms:required" : "sms:false" }, { "@id" : "bts:Memory", "@type" : "rdfs:Class", @@ -19009,6 +20528,17 @@ }, "sms:displayName" : "CDX tissue", "sms:required" : "sms:false" + }, { + "@id" : "bts:present", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "present", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "present", + "sms:required" : "sms:false" }, { "@id" : "bts:FIA-MSMS", "@type" : "rdfs:Class", @@ -19383,6 +20913,17 @@ }, "sms:displayName" : "conventional MRI", "sms:required" : "sms:false" + }, { + "@id" : "bts:onlybyimagingevidence", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "onlybyimagingevidence", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "only by imaging evidence", + "sms:required" : "sms:false" }, { "@id" : "bts:patternelectroretinogram", "@type" : "rdfs:Class", @@ -19427,6 +20968,17 @@ }, "sms:displayName" : "JH-2-002-CL", "sms:required" : "sms:false" + }, { + "@id" : "bts:single", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "single", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "single", + "sms:required" : "sms:false" }, { "@id" : "bts:millimeter", "@type" : "rdfs:Class", @@ -19471,6 +21023,28 @@ }, "sms:displayName" : "Rhesus macaque", "sms:required" : "sms:false" + }, { + "@id" : "bts:notmosaic", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "notmosaic", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "not mosaic", + "sms:required" : "sms:false" + }, { + "@id" : "bts:1pathogicallyconfirmed", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "1pathogicallyconfirmed", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "1 pathogically confirmed", + "sms:required" : "sms:false" }, { "@id" : "bts:overexpression", "@type" : "rdfs:Class", @@ -19526,6 +21100,17 @@ }, "sms:displayName" : "Langston University", "sms:required" : "sms:false" + }, { + "@id" : "bts:disabling", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "disabling", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "disabling", + "sms:required" : "sms:false" }, { "@id" : "bts:bam", "@type" : "rdfs:Class", @@ -20054,6 +21639,17 @@ }, "sms:displayName" : "Marshall University", "sms:required" : "sms:false" + }, { + "@id" : "bts:alive", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "alive", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "alive", + "sms:required" : "sms:false" }, { "@id" : "bts:JHU2-079-PDX", "@type" : "rdfs:Class", @@ -20175,6 +21771,17 @@ }, "sms:displayName" : "Southern Methodist University", "sms:required" : "sms:false" + }, { + "@id" : "bts:bilateral", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "bilateral", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "bilateral", + "sms:required" : "sms:false" }, { "@id" : "bts:UniformedServicesUniversityoftheHealthSciences", "@type" : "rdfs:Class", @@ -20230,6 +21837,17 @@ }, "sms:displayName" : "HEK293 NF1 -/- with R681X mNf1 cDNA", "sms:required" : "sms:false" + }, { + "@id" : "bts:parentnotaffected", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "parentnotaffected", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "parent not affected", + "sms:required" : "sms:false" }, { "@id" : "bts:demographics", "@type" : "rdfs:Class", @@ -20296,6 +21914,17 @@ }, "sms:displayName" : "Spectramax M Series", "sms:required" : "sms:false" + }, { + "@id" : "bts:infancy", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "infancy", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "infancy", + "sms:required" : "sms:false" }, { "@id" : "bts:RutgersStateUniversityofNewJersey,NewBrunswick", "@type" : "rdfs:Class", @@ -20450,6 +22079,17 @@ }, "sms:displayName" : "University of Tennessee, Health Science Center", "sms:required" : "sms:false" + }, { + "@id" : "bts:present-symptomatic-nottreated", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "present-symptomatic-nottreated", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "present - symptomatic - not treated", + "sms:required" : "sms:false" }, { "@id" : "bts:RensselaerPolytechnicInstitute", "@type" : "rdfs:Class", @@ -20494,6 +22134,17 @@ }, "sms:displayName" : "University of New Orleans", "sms:required" : "sms:false" + }, { + "@id" : "bts:absent", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "absent", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "absent", + "sms:required" : "sms:false" }, { "@id" : "bts:AuburnUniversity,Auburn", "@type" : "rdfs:Class", @@ -21154,6 +22805,17 @@ }, "sms:displayName" : "Hemorrhagic Neoplasm", "sms:required" : "sms:false" + }, { + "@id" : "bts:nospecifictherapy", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "nospecifictherapy", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "no specific therapy", + "sms:required" : "sms:false" }, { "@id" : "bts:rawcounts", "@type" : "rdfs:Class", @@ -21231,6 +22893,17 @@ }, "sms:displayName" : "Illumina MouseWG-6 v2.0 expression beadchip", "sms:required" : "sms:false" + }, { + "@id" : "bts:prebubertal", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "prebubertal", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "prebubertal", + "sms:required" : "sms:false" }, { "@id" : "bts:neuropsychologicalassessment", "@type" : "rdfs:Class", @@ -21264,6 +22937,17 @@ }, "sms:displayName" : "cNF98.4d", "sms:required" : "sms:false" + }, { + "@id" : "bts:deceased", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "deceased", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "deceased", + "sms:required" : "sms:false" }, { "@id" : "bts:Susscrofa", "@type" : "rdfs:Class", @@ -21902,6 +23586,17 @@ }, "sms:displayName" : "FLIPR high-throughput cellular screening", "sms:required" : "sms:false" + }, { + "@id" : "bts:radiation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "radiation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "radiation", + "sms:required" : "sms:false" }, { "@id" : "bts:EutropicsPharmaceuticals", "@type" : "rdfs:Class", @@ -22023,6 +23718,17 @@ }, "sms:displayName" : "Nf1-R681X/Flox", "sms:required" : "sms:false" + }, { + "@id" : "bts:chemotherapy", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "chemotherapy", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "chemotherapy", + "sms:required" : "sms:false" }, { "@id" : "bts:iPSC-derivedneuron", "@type" : "rdfs:Class", @@ -22045,6 +23751,17 @@ }, "sms:displayName" : "hTERT NF1 ipNF04.4", "sms:required" : "sms:false" + }, { + "@id" : "bts:multiple", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "multiple", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "multiple", + "sms:required" : "sms:false" }, { "@id" : "bts:dorsolateralprefrontalcortex", "@type" : "rdfs:Class", diff --git a/dca-template-config.json b/dca-template-config.json index 2bb71611..2ee46760 100644 --- a/dca-template-config.json +++ b/dca-template-config.json @@ -19,7 +19,10 @@ {"display_name": "Processed Expression Data", "schema_name": "ProcessedExpressionTemplate", "type": "file"}, {"display_name": "FACS Template", "schema_name": "FlowCytometryTemplate", "type": "file"}, {"display_name": "Light Scattering Assay", "schema_name": "LightScatteringAssayTemplate", "type": "file"}, - {"display_name": "Protocol Resource", "schema_name": "ProtocolTemplate", "type": "file"} + {"display_name": "Protocol Resource", "schema_name": "ProtocolTemplate", "type": "file"}, + {"display_name": "Human Individuals", "schema_name": "HumanCohortTemplate", "type": "record"}, + {"display_name": "Animal Individuals", "schema_name": "AnimalIndividualTemplate", "type": "record"}, + {"display_name": "Biopecimens", "schema_name": "BiospecimenTemplate", "type": "record"} ], "main_fileview" : "syn16858331", "community" : "NF", diff --git a/modules/Sample/Diagnosis.yaml b/modules/Sample/Diagnosis.yaml index 3fa97df9..908c3cea 100644 --- a/modules/Sample/Diagnosis.yaml +++ b/modules/Sample/Diagnosis.yaml @@ -5,17 +5,184 @@ enums: description: > (NF1) - A disease characterized by patches of skin pigmentation (cafe-au-lait spots), Lisch nodules of the iris, tumors in the peripheral nervous system and fibromatous skin tumors. Individuals with the disorder have increased susceptibility to the development of benign and malignant tumors. - Neurofibromatosis type 2: - description: > - (NF2) - Genetic disorder characterized by bilateral vestibular schwannomas (formerly called acoustic neuromas), schwannomas of other cranial and peripheral nerves, meningiomas, and ependymomas. - It is inherited in an autosomal dominant fashion with full penetrance. - meaning: https://www.ebi.ac.uk/ols/ontologies/cco/terms?iri=http%3A%2F%2Fidentifiers.org%2Fomim%2F101000 + #Neurofibromatosis type 2: + # description: > + # (NF2) - Genetic disorder characterized by bilateral vestibular schwannomas (formerly called acoustic neuromas), schwannomas of other cranial and peripheral nerves, meningiomas, and ependymomas. + # It is inherited in an autosomal dominant fashion with full penetrance. + # meaning: https://www.ebi.ac.uk/ols/ontologies/cco/terms?iri=http%3A%2F%2Fidentifiers.org%2Fomim%2F101000 Schwannomatosis: description: A rare genetic disorder characterized by the presence of multiple schwannomas. meaning: https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C6557 + NF2-related schwannomatosis: + description: Previously known as Neurofibromatosis type 2. + SMARCB1-related schwannomatosis: + LZTR1-related schwannomatosis: + 22q-related schwannomatosis: + Schwannomatosis-NOS: + Schwannomatosis-NEC: Sporadic Schwannoma: description: > Sporadic schwannomas and neurofibromas are tumors that arise from the nerve sheaths of cranial nerves, nerve roots, spinal nerves, and peripheral nerves. Most schwannomas originate from the eighth cranial nerve, whereas neurofibromas more commonly arise along the spinal nerve roots. notes: - Not in NCIT as of 2023-06-07 + + AgeGroupEnum: + permissible_values: + infancy: + childhood: + adolescence: + adulthood: + unknown: + + InheritanceEnum: + permissible_values: + parent affected: + parent not affected: + unknown: + + MosaicismEnum: + permissible_values: + mosaic: + not mosaic: + unknown: + + TestSummaryEnum: + permissible_values: + not tested: + tested but unknown: + + VitalStatusEnum: + permissible_values: + alive: + deceased: + unknown: + + WHOPerformanceStatusScores: + description: https://www.ncbi.nlm.nih.gov/books/NBK97482/ + permissible_values: + '0': + '1': + '2': + '3': + '4': + + PainEnum: + permissible_values: + not a problem: + occasional: + disabling: + + TumorTreatmentEnum: + permissible_values: + no specific therapy: + chemotherapy: + surgery: + radiation: + targeted therapy: + clinical trial: + + PresenceEnum: + description: Enumeration for binary + unknown for very basic classification of a manifestation in clinical context. + permissible_values: + absent: + present: + unknown: + + NeurofibromaManifestationEnum: + description: Enumerations describing how neurofibromas can manifest more generally. + permissible_values: + absent: + scattered: + dense: + unknown: + + SpinalNeuromaManifestationEnum: + description: Enumerations describing the manifestation of spinal neurofibromas, combining information on presence and the cervical locations. + permissible_values: + not imaged: + absent: + levels 1-3: + all levels: + + PlexiformNeurofibromaManifestationEnum: + description: Enumerations describing the manifestation of plexiform neurofibromas, combining information on presence and the certainty via MRI imaging technique. + permissible_values: + present: + absent by MRI: + absent clinically - no MRI: + unknown: + + OpticGliomaManifestationEnum: + description: Enumerations describing the manifestation of optic gliomas, combining information on presence, symptoms, and treatment. + permissible_values: + absent: + present - asymptomatic: + present - symptomatic - not treated: + present - symptomatic - treated: + unknown: + + PubertyOnsetEnum: + permissible_values: + prebubertal: + precocious: + normal: + late: + + Percentiles-2SD: + description: Enumerations corresponding to 3 bins using 2 standard deviations as a cutoff. + permissible_values: + '< 5th centile': + '5th-95th centile': + '> 95th centile': + + BinaryImagingDiagnosisEnum: + description: Enumerations describing the manifestation of tumors confirmed via imaging with mainly absent or present being the most relevant result. + permissible_values: + not imaged: + absent by imaging: + present: + unknown: + + MultipleImagingDiagnosisEnum: + description: Enumerations describing the manifestation of tumors confirmed via imaging with one or multiple sites being the most relevant result. + permissible_values: + not imaged: + absent by imaging: + single: + multiple: + unknown: + + LateralManifestationEnum: + description: Enumerations describing the manifestation of tumors confirmed via imaging (MRI or other), where lateral information is most relevant. + permissible_values: + not imaged: + absent by imaging: + unilateral: + bilateral: + unknown: + + + SchwannomaManifestationEnum: + description: Enumerations describing the manifestation of schwannomas. + permissible_values: + single: + scattered: + dense: + unknown: + + NonvestibularSchwannomaManifestationEnum: + permissible_values: + only by imaging evidence: + '1 pathogically confirmed': + '2 or more, at least 1 pathogically confirmed': + unknown: + + + + + + + + + diff --git a/modules/Template/Biosample.yaml b/modules/Template/Biosample.yaml new file mode 100644 index 00000000..f7035426 --- /dev/null +++ b/modules/Template/Biosample.yaml @@ -0,0 +1,123 @@ +# Important editor notes +# - Here [mappings](https://linkml.io/linkml/schemas/uris-and-mappings.html#mappings) indicate closely related templates in other data models +# - Here `extensions.suggests` are used to track the relationship between templates and their intended application to assay data types +# - `abstract` means the template is not meant to be used for annotation, it's just there for others to inherit props from + +classes: + +####################################### +# Patient Clinical Data +####################################### + + + AnimalIndividualTemplate: + description: Template for non-human individual-level data. + slots: + - individualID + - sex + - age + - ageUnit + - diagnosis + - diagnosisAgeGroup + - inheritance + - mosaicism + - nf1Genotype + - nf2Genotype + - germlineMutation + - species + - modelSystemName + annotations: + requiresComponent: '' + required: false + + BiospecimenTemplate: + description: Specimen-level data, whether from human or animal. + annotations: + requiresComponent: '' + required: false + slots: + - individualID + - parentSpecimenID + - specimenID + - aliquotID + - tumorType + - bodySite + - experimentalCondition + + HumanCohortTemplate: + description: > + Data of biosamples from human patients. Adapted from Table 2 of http://nrs.harvard.edu/urn-3:HUL.InstRepos:32725809. + This template should be used when biosamples are from NF patients to provides a more valuable characterization and make additional gene-phenotype insights possible. + notes: + - Instead of collecting birth month/year, age is collected. + - What has been required is still required, while all new recommendations are optional. + - Include attributes used for the portal but not in recommendations (nf1Genotype, nf1Genotype, species). + annotations: + requiresComponent: '' + required: false + slots: + + # Base / demographics + - individualID + # - individualIDSource # do we need this? Id formats are obvious, e.g. JHU-123 vs WU-123, but might be good to know the id authority + - sex + - age + - ageUnit + - diagnosis + - diagnosisAgeGroup + - inheritance + - mosaicism + - nf1Genotype + - nf2Genotype + - germlineMutationIndicator + - species # this is a little awkward/redundant + + # General clinical statuses + - vitalStatus + - WHOPerformanceStatus + - painStatus + - tumorTreatmentStatus + + # NF1-relevant clinical phenotypes + - cafeaulaitMacules + - skinFoldFreckling + - IrisLischNodules + - dermalNeurofibromas + - subcutaneousNodularNeurofibromas + - diffuseDermalNeurofibromas + - spinalNeurofibromas + - plexiformNeurofibromas + - opticGlioma + - heartDefect + - vascularDisease + - pubertyOnset + - stature + - peripheralNeuropathy + - aqueductalStenosis + - longBoneDysplasia + - sphenoidDysplasia + - scoliosis + - intellectualDisability + - learningDisability + - attentionDeficitDisorder + - pheochromocytoma + - glomusTumor + - MPNST + - nonopticGlioma + - GIST + - leukemia + - breastCancer + - otherTumors + + # NF2-relevant clinical phenotypes + - vestibularSchwannoma + - meningioma + - gliomaOrEpendymoma + - spinalSchwannoma + - dermalSchwannoma + - nonvestibularCranialSchwannoma + - lenticular opacity + + # Scwhwannomatosis-relevant clinical phenotypes, some overlapping with NF2 are already captured above + - nonvestibularSchwannomas + - numberOfSchwannomas diff --git a/modules/Template/Patient.yaml b/modules/Template/Patient.yaml deleted file mode 100644 index 32258aac..00000000 --- a/modules/Template/Patient.yaml +++ /dev/null @@ -1,49 +0,0 @@ -# Important editor notes -# - Here [mappings](https://linkml.io/linkml/schemas/uris-and-mappings.html#mappings) indicate closely related templates in other data models -# - Here `extensions.suggests` are used to track the relationship between templates and their intended application to assay data types -# - `abstract` means the template is not meant to be used for annotation, it's just there for others to inherit props from - -classes: - -####################################### -# Patient Clinical Data -####################################### - - PatientTemplate: - is_a: Template - description: > - Template for collecting *minimal* individual-level data. - slots: - - individualID - - sex - - age - - ageUnit - - species # should be constrained to human - - diagnosis - - nf1Genotype - - nf2Genotype - annotations: - requiresComponent: '' - required: false - - PatientXTemplate: - is_a: PatientTemplate - description: (WIP / not yet used) Extended template for participant clinical data as recommended per Sundby et al. - slots: - annotations: - requiresComponent: '' - required: false - - PatientSpecimenTemplate: - is_a: PatientTemplate - description: Template for capturing specimen-level data from patients. - slots: - - parentSpecimenID - - specimenID - - aliquotID - - tumorType - - bodySite - annotations: - requiresComponent: '' - required: false - diff --git a/modules/props.yaml b/modules/props.yaml index 1be15302..56c86dd4 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -5,6 +5,11 @@ slots: Filename: description: The name of the file. required: false + GIST: + description: Characterization of the manifestation of Gastrointestinal stromal + tumor (GIST). + range: PresenceEnum + required: false InChIKey: description: > A unique hash key for a compound, e.g. for “Selumetinib”, the key @@ -13,6 +18,16 @@ slots: is a more reliable identifier than the compound name and should be used if available. required: false + IrisLischNodules: + description: Characterization of the manifestation of Iris Lisch Nodules. + range: PresenceEnum + required: false + title: Iris Lisch nodules + MPNST: + description: Characterization of the manifestation of MPNST. + range: PresenceEnum + required: false + title: MPNST MRISequence: description: A mode used in MRI imaging range: MRISequenceEnum @@ -20,6 +35,10 @@ slots: Resource_id: description: A UUID for a Resource from the NF Research Tools Database required: false + WHOPerformanceStatus: + description: Score on the WHO scale describing patient's functional abilities. + range: WHOPerformanceStatusScores + title: WHO performance status accessRequirements: description: Statement describing access requirements for an entity. in_subset: @@ -54,6 +73,11 @@ slots: antibodyID: description: Antibody ID such as RRID if available, otherwise use vendor ID. required: false + aqueductalStenosis: + description: Characterization of the manifestation of aqueductal stenosis. + range: PresenceEnum + required: false + title: Aqueductal stenosis assay: description: The technology used to generate the data in this file. range: AssayEnum @@ -62,6 +86,11 @@ slots: description: Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay. required: false + attentionDeficitDisorder: + description: Characterization of the manifestation of Attention Deficit Disorder. + range: PresenceEnum + required: false + title: Attention deficit disorder author: description: The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not. @@ -106,6 +135,15 @@ slots: range: BodyPartEnum required: false slot_uri: https://cancerdhc.github.io/ccdhmodel/v1.1/BodySite/ + breastCancer: + description: Characterization of the manifestation of Breast cancer. + range: PresenceEnum + required: false + title: Breast cancer + cafeaulaitMacules: + description: Characterization of cafe-au-lait macules. + range: PresenceEnum + title: Six or more cafe-au-lait macules captureArea: description: > One of the either four or two active regions where tissue can be @@ -271,6 +309,16 @@ slots: in_subset: - Synapse required: false + dermalNeurofibromas: + description: Characterization of the manifestation of Dermal neurofibromas. + range: NeurofibromaManifestationEnum + required: false + title: Dermal neurofibromas + dermalSchwannoma: + description: Characterization of the manifestation of Dermal schwannoma. + range: PresenceEnum + required: false + title: Dermal schwannoma description: description: Text describing a resource. in_subset: @@ -278,10 +326,18 @@ slots: range: string required: false diagnosis: - description: A diagnosis is the result of a medical investigation to identify a - disorder from its signs and symptoms. + description: Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies. range: DiagnosisEnum required: false + diagnosisAgeGroup: + description: Age group of the individual at the time of diagnosis. + range: AgeGroupEnum + title: Diagnosis age group + diffuseDermalNeurofibromas: + description: Characterization of the manifestation of Diffuse dermal neurofibromas. + range: NeurofibromaManifestationEnum + required: false + title: Diffuse dermal neurofibromas diseaseFocus: description: Disease that acts as the main topic. in_subset: @@ -389,6 +445,16 @@ slots: description: Link to genome reference data file used for alignment in processing workflow required: false + gliomaOrEpendymoma: + description: Characterization of the manifestation of Glioma or ependymoma. + range: BinaryImagingDiagnosisEnum + required: false + title: Glioma or ependymoma + glomusTumor: + description: Characterization of the manifestation of Glomus tumor. + range: PresenceEnum + required: false + title: Glomus tumor grantDOI: description: Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity. @@ -396,6 +462,11 @@ slots: - portal range: string required: false + heartDefect: + description: Characterization of the manifestation of Heart defect. + range: PresenceEnum + required: false + title: Heart defect id: description: The entity id for the resource automatically assigned by the platform. required: false @@ -416,6 +487,10 @@ slots: notes: - Legacy key used in a couple of old studies required: false + inheritance: + description: Describes whether known inheritance from a parent. + range: InheritanceEnum + title: Inheritance initiative: description: Refers to a funding initiative. Typically handled by the DCC. in_subset: @@ -426,6 +501,11 @@ slots: description: Link to affiliated institution. range: Institution required: false + intellectualDisability: + description: Characterization of the manifestation of Intellectual disability. + range: PresenceEnum + required: false + title: Intellectual disability isCellLine: description: Whether or not sample source is a cell line (Yes; No) range: BooleanEnum @@ -462,11 +542,26 @@ slots: description: Whether or not sample source is a xenograft (Yes; No) range: BooleanEnum required: false + learningDisability: + description: Characterization of the manifestation of Learning disability. + range: PresenceEnum + required: false + title: Learning disability lensAperture: annotations: validationRules: num description: Numerical aperture of the lens. Floating point value > 0. required: false + lenticularOpacity: + description: Characterization of the manifestation of Lenticular opacity. + range: PresenceEnum + required: false + title: Lenticular opacity + leukemia: + description: Characterization of the manifestation of Leukemia. + range: PresenceEnum + required: false + title: Leukemia libraryID: description: '' required: false @@ -495,6 +590,11 @@ slots: - portal range: string required: false + longBoneDysplasia: + description: Characterization of the manifestation of Long bone dysplasia. + range: PresenceEnum + required: false + title: Long bone dysplasia manifestation: description: An associated phenotype characteristic. in_subset: @@ -513,6 +613,11 @@ slots: description: Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools required: false + meningioma: + description: Characterization of the manifestation of Meningioma. + range: MultipleImagingDiagnosisEnum + required: false + title: Meningioma modelSystemName: annotations: validationRules: list like @@ -529,6 +634,10 @@ slots: in_subset: - Synapse required: false + mosaicism: + description: Whether individual is mosaic. + range: MosaicismEnum + title: Mosaicism nf1Genotype: any_of: - range: Genotype @@ -539,18 +648,21 @@ slots: see_also: - nf1Variant - nf2Genotype + germlineMutationIndicator: + description: Indicates a summary testing result for individual's germline mutation only. + range: TestSummaryEnum + germlineMutation: + description: The individual's actual germline mutation. + notes: + - More sensitive information than germlineMutationIndicator. + - Free-text field that possibly suggests *any* mutations could be put here, while nf1GermlineMutation, etc. are more specific in terms of disease. nf1GermlineMutation: - description: NF1 germline mutation. Subproperty of nf1Variant. - notes: Usually a supplemental clinical data property. + description: NF1 germline mutation. + notes: + - Unlike nf1Variant, this is free-text and not constrained to enumerated values of known variants, making it more flexible for new mutations and different nomenclatures. required: false nf1SomaticMutation: - description: NF1 somatic mutation. Subproperty of nf1Variant. - notes: Usually a supplemental clinical data property. - required: false - nf1Variant: - description: Named variant (mutation) in the NF1 gene/protein in the biospecimen - from which the data were derived, if known/applicable. - range: NF1VariantEnum + description: NF1 somatic mutation, i.e. in tumor samples. required: false nf2Genotype: any_of: @@ -565,24 +677,58 @@ slots: description: magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. required: false + nonopticGlioma: + description: Characterization of the manifestation of Nonoptic glioma. + range: PresenceEnum + required: false + title: Nonoptic glioma + nonvestibularCranialSchwannoma: + description: Characterization of the manifestation of Nonvestibular cranial schwannoma. + range: BinaryImagingDiagnosisEnum + required: false + title: Nonvestibular cranial schwannoma + nonvestibularSchwannomas: + description: Characterization of the manifestation of Nonvestibular schwannomas. + range: NonvestibularSchwannomaManifestationEnum + required: false + title: Nonvestibular schwannomas nucleicAcidSource: description: Source of the extracted nucleic acid used in the experiment range: NucleicAcidSourceEnum required: false + numberOfSchwannomas: + description: Number of schwannomas. + range: SchwannomaManifestationEnum + required: false + title: Number of schwannomas objective: description: Microscope objective. required: false + opticGlioma: + description: Characterization of the manifestation of Optic glioma. + range: OpticGliomaManifestationEnum + required: false + title: Optic glioma organ: description: 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. range: OrganEnum required: false + otherTumors: + description: Characterization of the manifestation of other tumors. + range: PresenceEnum + required: false + title: Other tumors pH: annotations: validationRules: num description: Numeric value for pH (range 0-14) required: false + painStatus: + description: Pain status rating. + range: PainEnum + title: Pain status pairsOnDifferentChr: annotations: validationRules: int @@ -595,11 +741,26 @@ slots: description: | 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. required: false + peripheralNeuropathy: + description: Characterization of the manifestation of Peripheral neuropathy. + range: PresenceEnum + required: false + title: Peripheral neuropathy + pheochromocytoma: + description: Characterization of the manifestation of Pheochromocytoma. + range: PresenceEnum + required: false + title: Pheochromocytoma platform: description: A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. range: PlatformEnum required: true + plexiformNeurofibromas: + description: Characterization of the manifestation of Plexiform neurofibromas. + range: PlexiformNeurofibromaManifestationEnum + required: false + title: Plexiform neurofibromas programmingLanguage: description: A computer programming language enum_range: @@ -660,6 +821,11 @@ slots: protocolPurpose: description: Brief description of the protocol purpose. required: false + pubertyOnset: + description: Puberty onset. + range: PubertyOnsetEnum + required: false + title: Puberty onset publisher: description: An entity responsible for making the resource available. in_subset: @@ -759,6 +925,11 @@ slots: sampleType: description: Type of sample used required: false + scoliosis: + description: Characterization of the manifestation of Scoliosis. + range: PresenceEnum + required: false + title: Scoliosis series: description: Title of a custom series that this resource is part of, if any. in_subset: @@ -774,6 +945,10 @@ slots: description: Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other. required: false + skinFoldFreckling: + description: Characterization of skin fold freckling. + range: PresenceEnum + title: Skin fold freckling slideID: description: > Unique identifier printed on the label of each Visium slide. The @@ -827,6 +1002,26 @@ slots: includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. required: false + sphenoidDysplasia: + description: Characterization of the manifestation of Sphenoid dysplasia. + range: PresenceEnum + required: false + title: Sphenoid dysplasia + spinalNeurofibromas: + description: Characterization of the manifestation of Spinal neurofibromas. + range: SpinalNeuromaManifestationEnum + required: false + title: Spinal neurofibromas + spinalSchwannoma: + description: Characterization of the manifestation of Spinal schwannoma. + range: MultipleImagingDiagnosisEnum + required: false + title: Spinal schwannoma + stature: + description: Stature of the individual. + range: Percentiles-2SD + required: false + title: Stature studyFileviewId: description: Links a Synapse project to its fileview. in_subset: @@ -857,6 +1052,12 @@ slots: - portal range: StudyStatusEnum required: true + subcutaneousNodularNeurofibromas: + description: Characterization of the manifestation of Subcutaneous nodular + neurofibromas. + range: NeurofibromaManifestationEnum + required: false + title: Subcutaneous nodular neurofibromas summary: description: A short description (an abstract). in_subset: @@ -902,6 +1103,10 @@ slots: description: Type of transplantation involved in the experiment, derived from MESH range: TransplantationType required: false + tumorTreatmentStatus: + description: Tumor treatment status for the individual. + range: TumorTreatmentEnum + title: Tumor treatment status tumorType: description: The type of tumor that the biospecimen used to generate the data were collected from. @@ -912,6 +1117,20 @@ slots: in_subset: - Synapse required: false + vascularDisease: + description: Characterization of the manifestation of Vascular disease. + range: PresenceEnum + required: false + title: Vascular disease + vestibularSchwannoma: + description: Characterization of the manifestation of Vestibular schwannoma. + range: LateralManifestationEnum + required: false + title: Vestibular schwannoma + vitalStatus: + description: Vital status of the patient. + range: VitalStatusEnum + title: Vital status workflow: annotations: requiresDependency: workflowLink