genome_annotation.mcf

Node: dcid:BiologicalElement
name: "BiologicalElement"
typeOf: schema:Class
subClassOf: dcs:BiomedicalElement
description: "Biological entities."

Node: dcid:GenomeAnnotation
name: "GenomeAnnotation"
typeOf: schema:Class
subClassOf: dcs:BiologicalElement
description: "Entities or properties of the genome."

Node: dcid:GeneticAssociation
name: "GeneticAssociation"
typeOf: schema:Class
subClassOf: dcs:BiologicalElement
description: "Genetic associations with phenotypes."

Node: dcid:GenomeAssembly
name: "GenomeAssembly"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description:  "The reference genome to which the associated nucleotides have been aligned."

Node: dcid:GenomeAssemblyUnit
name: "GenomeAssemblyUnit"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description:  "The unit of assembling a reference genome to which the associated nucleotides have been aligned. Each unit is typically defined by the location of the cell from which the DNA is located such as the nucleus or an organelle."

Node: dcid:Nucleotide
name: "Nucleotide"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description: "A recorded nucleotide on the positive strand of a denoted genome assembly."

Node: dcid:Chromosome
name: "Chromosome"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description: "A threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes."

Node: dcid:RNATranscript
name: "RNATranscript"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description: "Recorded transcript. Unique identifier (GENCODE transcript ID for GENCODE Basic)."

Node: dcid:Gene
name: "Gene"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description: "Gene symbol of a gene, which is the basic hereditary unit of life."
sameAs: "https://bioportal.bioontology.org/ontologies/OGG"

Node: dcid:GeneticVariant
name: "GeneticVariant"
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
description:  "A single-nucleotide polymorphism, which is a substitution of a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population. These are defined by dbSNP and includes small indels as well."
sameAs: "http://rohsdb.usc.edu/GBshape/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=snp137&hgta_table=snp137&hgta_doSchema=describe+table+schema"

Node: dcid:GeneticVariantGeneAssociation
name: "GeneticVariantGeneAssociation"
typeOf: schema:Class
subClassOf: dcs:GeneticAssociation
description:  "An association between a genetic variant and a gene in a given tissue. This is determined by performing a regression analysis on paired genome sequencing and RNA-sequencing across a population."
sameAs: "https://storage.googleapis.com/gtex_analysis_v6p/single_tissue_eqtl_data/README_eQTL_v6p.txt"

Node: Position
typeOf: dcs:UnitOfMeasure
name: "Position"
dcid: "Position"
subClassOf: schema:Thing
description: "The location of an entity."

Node: dcid:BasePairs
typeOf: dcs:UnitOfMeasure
name: "BasePairs"
subClassOf: schema:Thing
description: "The number of pairs of complementary bases in a double-stranded nucleic acid molecule (DNA), consisting of a purine in one strand linked by hydrogen bonds to a pyrimidine in the other."

Node: dcid:Allele
typeOf: schema:Class
subClassOf: dcs:GenomeAnnotation
name: "Allele"

Node: dcid:frequency
typeOf: schema:Property
domainIncludes: dcid:Allele
rangeIncludes: schema:Number
name: "frequency"

Node: dcid:commonName
name: "commonName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: schema:Thing
description: "The vernacular name of a thing."

Node: dcid:ofSpecies
name: "ofSpecies"
typeOf: schema:Property
rangeIncludes: dcs:Species
domainIncludes: dcs:GenomeAnnotation,dcs:Disease
description: "Species"

Node: dcid:genomeAssemblyYear
name: "genomeAssemblyYear"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GenomeAssembly
description: "The year in which the genome assembly was released."

Node: dcid:genomeReferenceConsortiumAssemblyName
name: "genomeReferenceConsortiumAssemblyName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "The Genome Refrence Consortium name for the genome assembly."

Node: dcid:genBankAccession
name: "genBankAssemblyAccession"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly,dcs:GenomeAssemblyUnit,dcs:Chromosome
description: "The accession version of the GenBank assembly or sequence element."

Node: dcid:refSeqAccession
name: "refSeqAssemblyAccession"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly,dcs:GenomeAssemblyUnit,dcs:Chromosome
description: "The accession version of the RefSeq assembly or sequence element."

Node: dcid:ncbiBioProject
name: "ncbiBioProject"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "A BioProject is a collection of biological data related to a single initiative originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data generated for that project and deposited into the archival databases maintained by members of the International Nucleotide Sequence Database Collaboration (INSDC). Typical examples of a BioProject include a multiisolate project for sequencing multiple strains of a bacterial species, or a monoisolate project for the genome and transcriptome of a particular organism."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/bioproject/docs/faq/"

Node: dcid:ncbiBioSample
name: "ncbiBioSample"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "A BioSample contains descriptive information about the physical biological specimen from which your experimental data are derived. Typical examples of a BioSample include a cell line, a tissue biopsy or an environmental isolate. The information you supply about the biological materials are critical for providing context to your experimental data."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/biosample/docs/submission/faq/"

Node: dcid:assemblyMethod
dcid: "assemblyMethod"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "The alogrithm used to assemble the genome from sequencing reads."

Node: dcid:genomeCoverage
name: "genomeCoverage"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GenomeAssembly
description: "Genome coverage is the coverage depth of a sequencing run. This is calculated as the number of bases of all short reads that match a genome divided by the length of this genome, which represents the average number of times a base of a genome is sequenced."

Node: dcid:wgsProject
name: "wgsProject"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "Whole Genome Shotgun (WGS) projects are genome assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are generally being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/genbank/wgs/"

Node: dcid:sequencingTechnology
name: "sequencingTechnology"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "The manufacturer and model of the sequencing machine used to generate the GenomeAssembly."

Node: dcid:infraspecificName
name: "infraspecificName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "The strain, breed, cultivar or ecotype of the organism from which the sequences in the assembly were derived. (Field is not shown if the source material for the assembly is only described at the species level.)"
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"

Node: dcid:genomeAssemblyType
name: "genomeAssemblyType"
typeOf: schema:Property
rangeIncludes: dcs:GenomeAssemblyTypeEnum
domainIncludes: dcs:GenomeAssembly
description: "The type of sequence model data defined in this genome assembly."

Node: dcid:genomeAssemblyReleaseType
name: "genomeAssemblyReleaseType"
typeOf: schema:Property
rangeIncludes: dcs:GenomeAssemblyReleaseTypeEnum
domainIncludes: dcs:GenomeAssembly
description: "Defines the update type of this genome assembly version release."

Node: dcid:genomeAssemblyLevel
name: "genomeAssemblyLevel"
typeOf: schema:Property
rangeIncludes: dcs:GenomeAssemblyLevelEnum
domainIncludes: dcs:GenomeAssembly
description: "The highest level of assembly for any object in the assembly."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"

Node: dcid:isGenomeRepresentationFull
name: "isGenomeRepresentationFull"
typeOf: schema:Property
rangeIncludes: schema:Boolean
domainIncludes: dcs:GenomeAssembly
description: "Whether the goal for the assembly was to represent the whole genome or only part of it."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#representation"

Node: dcid:isRefSeqGenBankAssembliesIdentical
name: "isRefSeqGenBankAssembliesIdentical"
typeOf: schema:Property
rangeIncludes: schema:Boolean
domainIncludes: dcs:GenomeAssembly
description: "Indicate whether the RefSeq and GenBank assemblies are identical."

Node: dcid:refSeqCategory
name: "refSeqCategory"
typeOf: schema:Property
rangeIncludes: dcs:RefSeqCategoryEnum
domainIncludes: dcs:GenomeAssembly
description: "Denotes that the assembly is a reference or representative genome in the NCBI Reference Sequence ( RefSeq ) project classification."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"

Node: dcid:ncbiAssemblyName
name: "ncbiAssemblyName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GenomeAssembly
description: "The submitter's name for the assembly when one was provided, otherwise a default name is provided by NCBI; this is linked to a view of the Assembly details page."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"

Node: dcid:nucleicAcid
name: "nucleicAcid"
typeOf: schema:Property
rangeIncludes: dcs:NucleicAcidEnum
domainIncludes: dcs:Nucleotide
description: "The nucleic acid molecule on the positive strand."

Node: dcid:chromosomeSize
name: "chromosomeSize"
typeOf: schema:Property
rangeIncludes: schema:Quantity
domainIncludes: dcs:Chromosome
description: "The number of nucleotides in a given chromosome."

Node: dcid:ncbiDNASequenceName
name: "ncbiDNASequenceName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Chromosome
description: "The name by which NIH NCBI refers to this defined segment of DNA sequence."

Node: dcid:dnaSequenceRole
name: "dnaSequenceRole"
typeOf: schema:Property
rangeIncludes: dcs:DNASequenceRoleEnum
domainIncludes: dcs:Chromosome
description: "The role a defined sequence of DNA has in a genome assembly."

Node: dcid:inChromosome
name: "inChromosome"
typeOf: schema:Property
rangeIncludes: dcs:Chromosome,schema:Text
domainIncludes: dcs:GenomeAnnotation,dcs:Chromosome
description: "A threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes."

Node: dcid:inGenomeAssembly
name: "inGenomeAssembly"
typeOf: schema:Property
rangeIncludes: dcs:GenomeAssembly
domainIncludes: dcs:GenomeAnnotation
description: "Genome assembly."

Node: dcid:genomicPosition
name: "genomicPosition"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:Nucleotide,dcs:GeneticVariant
description: "The genomic position of the nucleotide."

Node: dcid:refSeqID
name: "refSeqID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:RNATranscript,dcs:Gene,dcs:Protein
description: "A nucleotide sequence or protein annotated and curated by the National Center for Biotechnology Information."

Node: dcid:transcriptionCoordinates
name: "transcriptionCoordinates"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:RNATranscript
description: "Specifies the genomic coordinates associated with the transcription of a given RefSeq Accession number."

Node: codingCoordinates
dcid:codingCoordinates
name: "codingCoordinates"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:RNATranscript
description: "Specifies the genomic position of the genomic coordinates of the coding region associated with a given RefSeq Accession number."

Node: exonCoordinates
dcid:exonCoordinates
name: "exonCoordinates"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:RNATranscript
description: "Specifies the genomic position of the coordinates of exons associated with a given RefSeq Accession number."

Node: strandOrientation
dcid:strandOrientation
name: "strandOrientation"
typeOf: schema:Property
rangeIncludes: dcs:StrandOrientationEnum
domainIncludes: dcs:GenomeAnnotation
description: "The strand on which a given annotation is located."

Node: dcid:geneID
name: "geneID"
typeOf: schema:Property
rangeIncludes: dcs:Gene
domainIncludes: dcs:GeneticVariant,dcs:DiseaseGeneAssociation,dcs:GeneticVariantGeneAssociation,dcs:Protein,dcs:ChemicalCompoundGeneAssociation
description: "Link out to the Gene node associated with the current node."

Node: dcid:geneSymbol
name: "geneSymbol"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene,dcs:GeneticVariant,dcs:DiseaseGeneAssociation,dcs:GeneticVariantGeneAssociation,dcs:Protein
description: "Original gene symbol."

Node: dcid:makesProtein
name: "makesProtein"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:RNATranscript,dcs:Protein
description: "UniProt display ID, UniProt accession, or RefSeq protein ID representing the protein made by the corresponding gene or RNA transcript."

Node: dcid:exonFrame
name: "exonFrame"
typeOf: schema:Property
rangeIncludes: dcs:ExonFramesEnum
domainIncludes: dcs:RNATranscript
description: "Exon frame {0,1,2}, or -1 if no frame for exon."

Node: dcid:genomicCoordinates
name: "genomicCoordinates"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:Gene
description: "Start position (0 based). End position (non-inclusive). Represents the genomic coordinates of an object of interest."

Node: dcid:mRNA
name: "mRNA"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "mRNA associated with a gene."

Node: dcid:ncbiProteinAccessionNumber
name: "ncbiProteinAccessionNumber"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene,dcs:Protein
description: "NCBI protein accession number."

Node: dcid:hasRNATranscript
name: "hasRNATranscript"
typeOf: schema:Property
rangeIncludes: dcs:RNATranscript
domainIncludes: dcs:Gene
description: "Recorded transcript. UCSC Gene ID."

Node: dcid:ncbiTaxonID
name: "ncbiTaxonID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene,dcs:Protein,dcs:GenomeAssembly
description: "NCBI Taxonomy database identifier."

Node: dcid:ncbiGeneID
name: "ncbiGeneID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene,dcs:GeneticVariant
description: "NCBI Entrez Gene database identifier."

Node: dcid:ncbiLocusTag
name: "ncbiLocusTag"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "Identifiers that are systematically applied to every gene in a genome."

Node: dcid:omimID
name: "omimID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Disease,dcs:Gene,dcs:GeneticVariant
description: "OMIM database identifier."

Node: dcid:onlineMendelianInheritanceInManID
name: "onlineMendelianInheritanceInManID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Disease,dcs:Gene,dcs:GeneticVariant
description: "Online Mendelian Inheritance in Man (OMIM) database identifier. Omim is /"an online catalog of human genes and genetic disorders/"."
descriptionUrl: "https://www.omim.org/"

Node: dcid:mondoID
name: "mondoID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "MONDO database identifier."

Node: dcid:hgncID
name: "hgncID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "HUGO Gene Nomenclature Committee identifier."

Node: dcid:ensemblID
name: "ensemblID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene,dcs:GeneticVariantGeneAssociation,dcs:Protein
description: "Ensembl ID, which describes a particular gene or protein."

Node: dcid:mapLocation
name: "mapLocation"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "The location of the gene on the chromosome."

Node: dcid:fullName
name: "fullName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "The full name of the gene."

Node: dcid:typeOfGene
name: "typeOfGene"
typeOf: schema:Property
rangeIncludes: dcs:TypeOfGeneEnum
domainIncludes: dcs:Gene
description: "The type of gene."

Node: dcid:nomenclatureStatus
name: "nomenclatureStatus"
typeOf: schema:Property
rangeIncludes:  dcs:NomenclatureStatusEnum
domainIncludes: dcs:Gene
description: "The status of the name from the nomenclature committee: official, interim, or NCBI-supplied."

Node: dcid:modificationDate
name: "modificationDate"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "The date of last modification on the NCBI database."

Node: dcid:referenceSNPClusterID
name: "referenceSNPClusterID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant,dcs:GeneticVariantGeneAssociation
description: "The accession number used to refer to a specific single nucleotide polymorphism (SNP)."

Node: dcid:geneticVariantID
name: "geneticVariantID"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariant
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "Link out to GeneticVariant node associated with the current node."

Node: dcid:referenceAlleleNCBI
name: "referenceAlleleNCBI"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Reference genomic sequence from dbSNP."

Node: dcid:referenceAlleleUCSC
name: "refUCSC"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Reference genomic sequence from UCSC."

Node: dcid:observedAllele
name: "observedAllele"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant,dcs:GeneticVariantGeneAssociation
description: "The sequences of the observed alleles from rs-fasta files. This is formated as major allele/minor allele."

Node: dcid:molecularType
name: "molecularType"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantMolTypeEnum
domainIncludes: dcs:GeneticVariant
description: "Sample type from exemplar submitted GeneticVariants (cDNA, genomic, mitochondrial, or unknown)."

Node: dcid:geneticVariantClass
name: "class"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantClassEnum
domainIncludes: dcs:GeneticVariant
description: "Class of variant: single_nucleotide_variant, deletion, insertion, in-del, named, mixed, mnp, het, microsatellite, inversion, copy_number_loss, variation, duplication, or copy_number_gain."

Node: dcid:geneticVariantValidationStatus
name: "validationStatus"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantValidationStatusEnum
domainIncludes: dcs:GeneticVariant
description: "Validation status of the SNP."

Node: dcid:averageHeterozygosity
name: "averageHeterozygosity"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Average heterozygosity from all observations. Note: may be computed on small number of samples."

Node: dcid:averageHeterozygositySE
name: "averageHeterozygositySE"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Standard Error for the average heterozygosity."

Node: dcid:geneticVariantFunctionalCategory
name: "functionalCategory"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantFunctionalCategoryEnum
domainIncludes: dcs:GeneticVariant
description: "Functional category of the genetic variant (coding-synon, splice_5', missense, frameshift, near_gene_5', 3'_UTR, near_gene_3', nonsense, splice_3', intron, cds_reference, 5'_UTR, unknown, cds_indel, stop_loss, 5' UTR, or ncRNA.)"

Node: dcid:geneticVariantLocType
name: "locType"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantLocTypeEnum
domainIncludes: dcs:GeneticVariant
description: "Type of mapping inferred from size on reference; may not agree with class."

Node: dcid:geneticVariantAlignmentQuality
name: "alignmentQuality"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantAlignmentQualityEnum
domainIncludes: dcs:GeneticVariant
description: "The quality of the alignment: unique mapping, non-unique, and many matches (1, 2, or 3+)."

Node: dcid:geneticVariantExceptions
name: "exceptions"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantExceptionEnum
domainIncludes: dcs:GeneticVariant
description: "Unusual conditions noted by UCSC that may indicate a problem with the data."

Node: dcid:geneticVariantSubmitterCount
name: "submitterCount"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Number of distinct submitter handles for submitted SNPs for this ref SNP."

Node: dcid:submitter
name: "submitter"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "List of submitter handles."

Node: dcid:numberOfAllelesWithFreq
name: "numberOfAllelesWithFreq"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Number of observed alleles with frequency data."

Node: dcid:geneticVariantAttribute
name: "geneticVariantAttribute"
typeOf: schema:Property
rangeIncludes: dcs:GeneticVariantAttributeEnum
domainIncludes: dcs:GeneticVariant
description: "Genetic variant attributes extracted from dbSNP's SNP_bitfield table: clinically associated, MAF >5% in some populations, MAF >5% in all populations, has OMIM OMIA, microattribute tpa, submitted by locus-specific database, genotype conflict, rs cluster non-overlapping alleles, observed mismatch, pharmGKB, published, 3D structure, submitter link out, other variant with exact mapping, assembly specific,mutant, validated, included in high density kit, genotypes available, 1000 Genomes Phase 1, 1000 Genomes Phase 3, included in clinical diagnostic assay, withdrawn by some not all submitters, or common SNP."

Node: dcid:dbSNPBuildID
name: "dbSNPBuildID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "First dbSNP Build for RS."

Node: dcid:alleleOrigin
name: "alleleOrigin"
typeOf: schema:Property
rangeIncludes: dcs:VariantAlleleOriginEnum
domainIncludes: dcs:GeneticVariant
description: "Variant Allele Origin: unspecified, germline, somatic, both, inherited, paternal, maternal, uni-parental, bi-parental, not_tested, tested_inconclusive, de-novo, or other."

Node: dcid:suspectReasonCode
name: "suspectReasonCode"
typeOf: schema:Property
rangeIncludes: dcs:VariantSuspectReasonCodesEnum
domainIncludes: dcs:GeneticVariant
description: "Variant Suspect Reason Codes: unspecified, Paralog, byEST, oldAlign, Para_EST, 1kg_failed, or other."

Node: dcid:clinVarAlleleID
name: "clinVarAlleleID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "ClinVar Allele ID."

Node: dcid:diseaseDescription
name: "diseaseDescription"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "ClinVar's preferred disease name for the concept specified by disease identifiers."

Node: dcid:diseaseName
name: "diseaseName"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "ClinVar's preferred disease name for the concept specified by disease identifiers."

Node: dcid:medGenID
name: "medGenID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "ID for organized information related to human medical genetics, such as attributes of conditions with a genetic contribution."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/medgen/"

Node: dcid:orphaNumber
name: "orphaNumber"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Disease,dcs:GeneticVariant
description: "Orphanet rare disease nomenclature"
descriptionUrl: "https://www.orpha.net/consor/cgi-bin/index.php"

Node: dcid:humanPhenotypeOntologyID
name: "humanPhenotypeOntologyID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "The Human Phenotype Ontology (HPO)"
descriptionUrl: "https://hpo.jax.org/app/"

Node: dcid:snomedCT
name: "snomedCT"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:Disease,dcs:GeneticVariant
description: "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms) is a standardized, multilingual vocabulary of clinical terminology that is used by physicians and other health care providers for the electronic exchange of clinical health information."
descriptionUrl: "http://www.snomed.org/"

Node: dcid:experimentalFactorOntologyID
name: "experimentalFactorOntologyID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalog."
descriptionUrl: "https://www.ebi.ac.uk/efo/"

Node: dcid:medicalSubjectHeadingID
name: "medicalSubjectHeadingID"
typeOf: schema:Property
rangeIncludes: schema:Number,dcs:MeSHDescriptor
domainIncludes: dcs:GeneticVariant,dcs:Disease
description: "Medical Subject Heading"
descriptionUrl: "https://meshb.nlm.nih.gov/search"

Node: dcid:humanGenomeVariationSocietyNomenclature
name: "humanGenomeVariationSocietyNomenclature"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Variant names from the Human Genome Variation Society"
descriptionUrl: "https://varnomen.hgvs.org/"

Node: dcid:pharmGKBID
name: "pharmGKBID"
typeOf: schema:Property
rangeIncludes: schema:Number,dcs:Text
domainIncludes: dcs:GeneticVariant,dcs:ChemicalCompound,dcs:Gene
description: "PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers."
descriptionUrl: "https://www.pharmgkb.org/"

Node: dcid:medicalGeneticSummariesID
name: "medicalGeneticSummariesID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Medical Genetics Summaries is a growing collection of summaries which describe the impact that specific sequence variations have on health. The summaries review genetic variants that underlie inherited conditions, affect the risk of developing a disease in the future, or influence how an individual may respond to a specific drug."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/books/NBK61999/"

Node: dcid:geneReviewsID
name: "geneReviewsID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "GeneReviews, an international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Each chapter in GeneReviews is written by one or more experts on the specific condition or disease and goes through a rigorous editing and peer review process before being published online."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/books/NBK1116/"

Node: dcid:geneticTestingRegistryID
name: "geneticTestingRegistryID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "The Genetic Testing Registry (GTR) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/gtr/"

Node: dcid:geneticsHomeReferenceID
name: "geneticsHomeReferenceID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Genetics Home Reference (GHR) provides consumer-friendly information about the effects of genetic variation on human health."
descriptionUrl: "https://ghr.nlm.nih.gov/"

Node: dcid:clinVarReviewStatus
name: "clinVarReviewStatus"
typeOf: schema:Property
rangeIncludes: dcs:ClinVarReviewStatusEnum
domainIncludes: dcs:GeneticVariant
description: "ClinVar review status: no assertion criteria provided, reviewed by expert panel, conflicting interpretations, criteria provided, non interpretation for the single variant, practice guideline, no conflicts, multiple submitters, or single_submitter."

Node: dcid:clinicalSignificanceConflicting
name: "clinicalSignificanceConflicting"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Conflicting clinical significance for this single variant."

Node: dcid:clinicalSignificance
name: "clinicalSignificance"
typeOf: schema:Property
rangeIncludes: dcs:ClinSigEnum
domainIncludes: dcs:GeneticVariant
description: "Clinical significance for this single variant: other, affects, uncertain_significance, pathogenic, risk_factor, benign, conflicting_interpretations_of_pathogenicity, association, likely_pathogenic, protective, likely_benign, not_provided, association_not_found, drug_response, pathogenic/likely_pathogenic,benign/likely_benign, unknown, untested, or histocompatibility."

Node: dcid:sequenceOntologyID
name: "sequenceOntologyID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Sequence Ontology ID: http://www.sequenceontology.org/"

Node: dcid:clinicalSource
name: "clinicalSource"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "The variant's clinical sources reported as tag-value pairs of database and variant identifier."

Node: dcid:clinVarID
name: "clinVarID"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "ClinVar Variation ID."

Node: dcid:variationType
name: "variationType"
typeOf: schema:Property
rangeIncludes: dcs:VariationTypeEnum
domainIncludes: dcs:GeneticVariant
description: "Variation type of alternate allele."

Node: dcid:variationEndCI
name: "variationEndCI"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Confidence interval around END for imprecise variants."

Node: dcid:variationPositionCI
name: "variationPositionCI"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Confidence interval around POS for imprecise variants."

Node: dcid:geneticVariantImpercise
name: "geneticVariantImpercise"
typeOf: schema:Property
rangeIncludes: schema:Boolean
domainIncludes: dcs:GeneticVariant
description: "Boolean of whether a variant is flagged as an imprecise structural variation."

Node: dcid:geneticVariantLength
name: "geneticVariantLength"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Difference in length between REF and ALT alleles (bp)."

Node: dcid:translocationToChromosome
name: "translocationToChromosome"
typeOf: schema:Property
rangeIncludes: dcs:Chromosome
domainIncludes: dcs:GeneticVariant
description: "Second (To) Chromosome in a translocation pair."

Node: dcid:alleleType
name: "alleleType"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "The allele of a genetic variant observed within a population."

Node: dcid:clinicalSignificanceType
name: "clinicalSignificanceType"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "A type of clinical significance report observed for a genetic variant."

Node: dcid:hg38GenomicLocation
name: "hg38GenomicLocation"
typeOf: schema:Property
rangeIncludes: dcs:QuantityRange
domainIncludes: dcs:GeneticVariant
description: "The genomic location of a genetic variant using the hg38 assembly. [chr start stop]."

Node: dcid:hg19GenomicLocation
name: "hg19GenomicLocation"
typeOf: schema:Property
rangeIncludes: dcs:QuantityRange
domainIncludes: dcs:GeneticVariant
description: "The genomic location of a genetic variant using the hg19 assembly. [chr start stop]."

Node: dcid:mm10GenomicLocation
name: "mm10GenomicLocation"
typeOf: schema:Property
rangeIncludes: dcs:QuantityRange
domainIncludes: dcs:GeneticVariant
description: "The genomic location of a genetic variant using the mm10 assembly. [chr start stop]."

Node: dcid:mm9GenomicLocation
name: "mm9GenomicLocation"
typeOf: schema:Property
rangeIncludes: dcs:QuantityRange
domainIncludes: dcs:GeneticVariant
description: "The genomic location of a genetic variant using the mm9 assembly. [chr start stop]."

Node: dcid:hg19GenomicPosition
name: "hg19GenomicPosition"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "The genomic position of a genetic variant using the hg19 assembly."

Node: dcid:hg38GenomicPosition
name: "hg38GenomicPosition"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant,dcs:GeneticVariantGeneAssociation
description: "The genomic position of a genetic variant using the hg38 assembly."

Node: dcid:clinVarQualityScore
name: "clinVarQualityScore"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariant
description: "Phred-scaled quality score for the assertion made in ALT. i.e. -10log10 prob(call in ALT is wrong)."

Node: dcid:clinVarFilterStatus
name: "clinVarFilterStatus"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Filter status: PASS if this position has passed all filters, i.e., a call is made at this position. Otherwise, if the filters that the site failed are recorded."

Node: dcid:dbVarID
name: "dbVarID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariant
description: "Accessions from dbVar for the genetic variant"
descriptionUrl: "https://www.ncbi.nlm.nih.gov/dbvar/"

Node: dcid:hg38DistanceFromTranscriptionStartSite
name: "hg38DistanceFromTranscriptionStartSite"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "In the hg38 genome assembly, the distance in base pairs between the associated genetic variant and gene."

Node: dcid:hg19DistanceFromTranscriptionStartSite
name: "hg19DistanceFromTranscriptionStartSite"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "In the hg19 genome assembly, the distance in base pairs between the associated genetic variant and gene."

Node: dcid:minorAlleleSampleNumber
name: "minorAlleleSampleNumber"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The number of samples carrying the minor allele."

Node: dcid:minorAlleleCount
name: "minorAlleleCount"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "Total number of minor alleles across individuals."

Node: dcid:pValueNominal
name: "pValueNominal"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The nominal p-value associated with the most significant variant for this gene."

Node: dcid:minimalPValueNominal
name: "minimalPValueNominal"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The smallest nominal p-value for the gene."

Node: dcid:pValueBeta
name: "pValueBeta"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The beta-approximated permutation p-value."

Node: dcid:pValueNominalThreshold
name: "pValueNominalThreshold"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The nominal p-value threshold for calling a variant-gene pair significant for the gene."

Node: dcid:variantNumber
name: "variantNumber"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The number of variants in cis-window (1 Mbp) with the associated gene."

Node: dcid:betaDistributionShapes
name: "betaShapeDistribution"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The shape parameters of the fitted Beta distribution: B(shape1, shape2)."

Node: dcid:trueDegreesOfFreedom
name: "trueDegreesOfFreedom"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The effective degrees of freedom the Beta distribution approximation."

Node: dcid:pValueTrueDegreesOfFreedom
name: "pValueTrueDegreesOfFreedom"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The p-value of the effective degrees of freedom the Beta distribution approximation."

Node: dcid:numberOfAlternativeAlleles
name: "numberOfAlternativeAlleles"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The number of alternative alleles observed at the genetic variant site."

Node: dcid:pValuePermutation
name: "pValuePermutation"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The permutation p-value."

Node: dcid:qValue
name: "qValue"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The Storey q-value derived from pval_beta."

Node: dcid:log2AllelicFoldChange
name: "log2AllelicFoldChange"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The allelic Fold Change in log2 of the change in gene expression of samples with or without the minor allele."

Node: dcid:log2AllelicFoldChangeConfidenceInterval
name: "log2AllelicFoldChangeConfidenceInterval"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The 95% confidence interval of the allelic Fold Change in log2 of the change in gene expression of samples with or without the minor allele: [lowerCI upperCI]."

Node: dcid:tissue
name: "tissue"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "The tissue in which the association between the genetic variant and the gene was made."

Node: dcid:gtexID
name: "gtexID"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:GeneticVariantGeneAssociation
description: "An ID denoting a unique gene and genetic variant association within the GTEx database."

Node: dcid:alternateGeneSymbol
name: "alternateGeneSymbol"
typeOf: schema:Property
rangeIncludes: schema:Text
domainIncludes: dcs:Gene
description: "Alternative or secondary symbol for a gene."

Node: dcid:regressionSlope
name: "regressionSlope"
typeOf: schema:Property
rangeIncludes: schema:Number
domainIncludes: dcs:StatisticalVariable