Node: dcid:NucleicAcidEnum name: "NucleicAcidEnum" subClassOf: schema:Enumeration description: "A (Adenine), T (Thymine), G (Guanine), C (Cytosine), and N (unknown) nucleic acid status." typeOf: schema:Class Node: dcid:NucleicAcidStatusA name: "A" typeOf: dcs:NucleicAcidEnum Node: dcid:NucleicAcidStatusT name: "T" typeOf: dcs:NucleicAcidEnum Node: dcid:NucleicAcidStatusG name: "G" typeOf: dcs:NucleicAcidEnum Node: dcid:NucleicAcidStatusC name: "C" typeOf: dcs:NucleicAcidEnum Node: dcid:NucleicAcidStatusN name: "N" typeOf: dcs:NucleicAcidEnum Node: dcid:StrandOrientationEnum name: "StrandOrientationEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Denotes if the gene is on the forward (+) or reverse (-) DNA strands." Node: dcid:StrandOrientationPositive name: "Positive" typeOf: dcs:StrandOrientationEnum Node: dcid:StrandOrientationNegative name: "Negative" typeOf: dcs:StrandOrientationEnum Node: dcid:ExonFramesEnum name: "ExonFramesEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Denotes the exon frame {0,1,2}, or none if no frame for the exon." Node: dcid:ExonFrame0 name: "Frame0" typeOf: dcs:ExonFramesEnum Node: dcid:ExonFrame1 name: "Frame1" typeOf: dcs:ExonFramesEnum Node: dcid:ExonFrame2 name: "Frame2" typeOf: dcs:ExonFramesEnum Node: dcid:ExonFrameNone name: "None" typeOf: dcs:ExonFramesEnum Node: dcid:NomenclatureStatusEnum name: "NomenclatureStatuEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "The status of the name from the nomenclature committee: official, interim, or NCBI-supplied." Node: dcid:NomenclatureStatusOfficial name: "Official" typeOf: dcs:NomenclatureStatusEnum Node: dcid:NomenclatureStatusInterim name: "Interim" typeOf: dcs:NomenclatureStatusEnum Node: dcid:NomenclatureStatusNCBIsupplied name: "NCBI Supplied" typeOf: dcs:NomenclatureStatusEnum Node: dcid:TypeOfGeneEnum name: "TypeOfGeneEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "The type of gene as specified by NCBI: biological-region, ncRNA, other, protein-coding, pseudo, rRNA, scRNA, snRNA, snoRNA, tRNA, miscRNA, or unknown." Node: dcid:TypeOfGeneBiologicalRegion name: "BiologicalRegion" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenencRNA name: "ncRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGeneOther name: "Other" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGeneProteinCoding name: "ProteinCoding" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenePseudo name: "Pseudo" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenerRNA name: "rRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenescRNA name: "scRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenesnRNA name: "snRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenesnoRNA name: "snoRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenetRNA name: "tRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGenemiscRNA name: "miscRNA" typeOf: dcs:TypeOfGeneEnum Node: dcid:TypeOfGeneUnknown name: "Unknown" typeOf: dcs:TypeOfGeneEnum Node: dcid:GeneticVariantMolTypeEnum name: "GeneticVariantMolTypeEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Sample type from exemplar submitted GeneticVariants (cDNA, genomic, mitochondrial, or unknown)." Node: dcid:GeneticVariantMolTypecDNA name: "cDNA" typeOf: dcs:GeneticVariantMolTypeEnum Node: dcid:GeneticVariantMolTypeGenomic name: "Genomic" typeOf: dcs:GeneticVariantMolTypeEnum Node: dcid:GeneticVariantMolTypeMitochondrial name: "Mitochondrial" typeOf: dcs:GeneticVariantMolTypeEnum Node: dcid:GeneticVariantMolTypeUnknown name: "Unknown" typeOf: dcs:GeneticVariantMolTypeEnum Node: dcid:GeneticVariantClassEnum name: "GeneticVariantClassEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Class of variant: single_nucleotide_variant, deletion, insertion, in-del, named, mixed, mnp, het, microsatellite, inversion, copy_number_loss, variation, duplication, copy_number_gain, inversion, copy-number-loss, or copy-number-gain." Node: dcid:GeneticVariantClassSingle name: "Single Nucleotide Variant" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassDeletion name: "Deletion" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassInsertion name: "Insertion" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassIn-del name: "InDel" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassNamed name: "Named" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassMixed name: "Mixed" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassMNP name: "MNP" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassHet name: "Het" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassMicrosatellite name: "microsatellite" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassInversion name: "Inversion" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassCopyNumberLoss name: "CopyNumberLoss" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassVariation name: "Variation" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassDuplication name: "Duplication" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantClassCopyNumberGain name: "CopyNumberGain" typeOf: dcs:GeneticVariantClassEnum Node: dcid:GeneticVariantValidationStatusEnum name: "GeneticVariantValidationStatusEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Validation status of the genetic variant: cluster, frequency, 1000genomes, HapMap, 2hit-2allele, submitter, or unknown." Node: dcid:GeneticVariantValidationStatusFrequency name: "Frequency" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatusCluster name: "Cluster" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatus1000genomes name: "1000 Genomes" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatusHapMap name: "HapMap" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatusUnknown name: "uUknown" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatus2hit-2allele name: "2hit-2allele" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantValidationStatusSubmitter name: "Submitter" typeOf: dcs:GeneticVariantValidationStatusEnum Node: dcid:GeneticVariantFunctionalCategoryEnum name: "GeneticVariantFunctionalCategoryEnum" typeOf: schema:Class subClassOf: schema:Enumeration 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:GeneticVariantFunctionalCategoryncRNA name: "ncRNA" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryCodingSynon name: "Coding Synonomous" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategorySplice5 name: "Splice 5'" typeOf: dcs:GeneticVariantFunctionalCategoryEnum description: "In donor splice site" Node: dcid:GeneticVariantFunctionalCategoryMissense name: "Missense" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryFrameshift name: "Frameshift" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryNearGene5 name: "Near Gene 5'" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryUTR3 name: "3' UTR" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryUTR5 name: "5' UTR" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryNearGene3 name: "Near Gene 3'" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryNonsense name: "Nonsense" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategorySplice3 name: "Splice 3'" typeOf: dcs:GeneticVariantFunctionalCategoryEnum description: "In acceptor splice" Node: dcid:GeneticVariantFunctionalCategoryIntron name: "Intron" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryCDSReference name: "cds Reference" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryUnknown name: "Unknown" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCategoryStopLoss name: "Stop Loss" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantFunctionalCDSIndel name: "cds Indel" typeOf: dcs:GeneticVariantFunctionalCategoryEnum Node: dcid:GeneticVariantLocTypeEnum name: "GeneticVariantLocTypeEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Type of mapping inferred from size on reference; may not agree with class: between, exact, fuzzy, range, range deletion, range insertion, or range substitution." Node: dcid:GeneticVariantLocTypeBetween name: "Between" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeExact name: "Exact" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeRange name: "Range" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeRangeDeletion name: "RangeDeletion" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeRangeInsertion name: "RangeInsertion" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeRangeSubstitution name: "RangeSubstituation" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantLocTypeFuzzy name: "Fuzzy" typeOf: dcs:GeneticVariantLocTypeEnum Node: dcid:GeneticVariantAlignmentQualityEnum name: "GeneticVariantAlignmentQualityEnumm" typeOf: schema:Class subClassOf: schema:Enumeration description: "The quality of the alignment: unique mapping, non-unique, and many matches (1, 2, or 3+)." Node: dcid:GeneticVariantAlignmentQualityOne name: "Unique Mapping" typeOf: dcs:GeneticVariantAlignmentQualityEnum Node: dcid:GeneticVariantAlignmentQualityTwo name: "Non-unique Mapping" typeOf: dcs:GeneticVariantAlignmentQualityEnum Node: dcid:GeneticVariantAlignmentQualityThree name: "Many Matches" typeOf: dcs:GeneticVariantAlignmentQualityEnum Node: dcid:GeneticVariantAttributeEnum name: "GeneticVariantAttributeEnumm" typeOf: schema:Class subClassOf: schema:Enumeration 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, reference present, 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:GeneticVariantAttributeClinicallyAssociated name: "Clinically Associated" typeOf: dcs:GeneticVariantAttributeEnum description: "Variant is Precious(Clinical,Pubmed Cited)." Node: dcid:GeneticVariantAttributeMAF5SomePop name: "MAF >5% In Some Populations" typeOf: dcs:GeneticVariantAttributeEnum description: ">5% minor allele frequency in 1+ populations." Node: dcid:GeneticVariantAttributeMAF5AllPop name: "MAF >5% In All Populations" typeOf: dcs:GeneticVariantAttributeEnum description: ">5% minor allele frequency in each and all populations." Node: dcid:GeneticVariantAttributOMIMOMIA name: "Has OMIM OMIA" typeOf: dcs:GeneticVariantAttributeEnum description: "Has OMIM/OMIA." Node: dcid:GeneticVariantAttributeMicroattributeTPA name: "Microattribute TPA" typeOf: dcs:GeneticVariantAttributeEnum description: "Microattribution/third-party annotation(TPA:GWAS,PAGE)." Node: dcid:GeneticVariantAttrbuteSubmittedByLSDB name: "Submitted By Locus Specific Database" typeOf: dcs:GeneticVariantAttributeEnum description: "Submitted from a locus-specific database." Node: dcid:GeneticVariantAttributeGenotypeConflict name: "Genotype Conflict" typeOf: dcs:GeneticVariantAttributeEnum description: "Has Assembly conflict. This is for non-unique and many matches that maps to different chromosomes on different assemblies." Node: dcid:GeneticVariantAttributersCluster name: "rs Cluster Non-overlapping Alleles" typeOf: dcs:GeneticVariantAttributeEnum description: "Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common." Node: dcid:GeneticVariantAttributeObservedMismatch name: "Observed Mismatch" typeOf: dcs:GeneticVariantAttributeEnum description: "Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation." Node: dcid:GeneticVariantAttributeReferencePresent name: "Reference Present" typeOf: dcs:GeneticVariantAttributeEnum description: "A coding region variation where one allele in the set is identical to the reference sequence." Node: dcid:GeneticVariantAttributePharmGKB name: "PharmGKB" typeOf: dcs:GeneticVariantAttributeEnum description: "Provisional Third Party Annotation(TPA) (currently rs from PHARMGKB who will give phenotype data)." Node: dcid:GeneticVariantAttributePublished name: "Published" typeOf: dcs:GeneticVariantAttributeEnum description: "Links exist to PubMed Central article." Node: dcid:GeneticVariantAttribute3DStructure name: "3D Structure" typeOf: dcs:GeneticVariantAttributeEnum description: "Has 3D structure - SNP3D table." Node: dcid:GeneticVariantAttributeSubmitterLinkOut name: "Submitter Link Out" typeOf: dcs:GeneticVariantAttributeEnum description: "Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out." Node: dcid:GeneticVariantAttributeOtherVariant name: "Other Variant With Exact Mapping" typeOf: dcs:GeneticVariantAttributeEnum description: "Has other variant with exactly the same set of mapped positions on NCBI reference assembly." Node: dcid:GeneticVariantAttributeAssembly name: "Assembly Specific" typeOf: dcs:GeneticVariantAttributeEnum description: "Is Assembly specific. This is set if the variant only maps to one assembly." Node: dcid:GeneticVariantAttributeMutant name: "Mutant" typeOf: dcs:GeneticVariantAttributeEnum description: "Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources." Node: dcid:GeneticVariantAttributeValidated name: "Validated" typeOf: dcs:GeneticVariantAttributeEnum description: "Is Validated. This bit is set if the variant has 2+ minor allele count based on frequency or genotype data." Node: dcid:GeneticVariantAttributeHighDensityKit name: "Included In High Density Kit(s)" typeOf: dcs:GeneticVariantAttributeEnum description: "Marker is on high density genotyping kit (50K density or greater). The variant may have phenotype associations present in dbGaP." Node: dcid:GeneticVariantAttributeGenotypesAvailable name: "Genotypes Available" typeOf: dcs:GeneticVariantAttributeEnum description: "Genotypes available. The variant has individual genotype (in SubInd table)." Node: dcid:GeneticVariantAttribute1000GenomesPhase1 name: "1000 Genomes Phase 1" typeOf: dcs:GeneticVariantAttributeEnum description: "1000 Genome phase 1 (incl. June Interim phase 1)." Node: dcid:GeneticVariantAttribute1000GenomesPhase3 name: "1000 Genomes Phase 3" typeOf: dcs:GeneticVariantAttributeEnum description: "1000 Genome phase 3." Node: dcid:GeneticVariantAttributeSomeWithdrawn name: "Withdrawn by some but not all submitters" typeOf: dcs:GeneticVariantAttributeEnum description: "Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set. If all member ss' are withdrawn, then the rs is deleted to SNPHistory." Node: dcid:GeneticVariantAttributeClinicalDiagnosticAssay name: "Included In Clinical Diagnostic Kit(s)" typeOf: dcs:GeneticVariantAttributeEnum description: "Variation is interrogated in a clinical diagnostic assay." Node: dcid:GeneticVariantAttributeCommonSNP name: "Common SNP" typeOf: dcs:GeneticVariantAttributeEnum description: "RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency." Node: dcid:GeneticVariantExceptionEnum name: "GeneticVariantExceptionEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Unusual conditions noted by UCSC that may indicate a problem with the data: RefAlleleMismatch, RefAlleleRevComp, DuplicateObserved, MixedObserved, FlankMismatchGenomeLonger, FlankMismatchGenomeEqual, FlankMismatchGenomeShorter, NamedDeletionZeroSpan, NamedInsertionNonzeroSpan, SingleClassLongerSpan, SingleClassZeroSpan, SingleClassTriAllelic, SingleClassQuadAllelic, ObservedWrongFormat, ObservedTooLong, ObservedContainsIupac, 'ObservedMismatch, MultipleAlignments, NonIntegerChromCount, AlleleFreqSumNot1, SingleAlleleFreq, or InconsistentAlleles." Node: dcid:GeneticVariantExceptionRefAlleleMismatch name: "Reference Allele Mismatch" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionRefAlleleRevComp name: "Reference Allele Reverse Complement" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionDuplicateObserved name: "Duplicate Observed" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionMixedObserved name: "Mixed Observed" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionFlankMismatchGenomeLonger name: "Flank Mismatch Genome Longer" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionFlankMismatchGenomeEqual name: "Flank Mismatch Genome Equal" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionFlankMismatchGenomeShorter name: "Flank Mismatch Genome Shorter" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionNamedDeletionZeroSpan name: "Named Deletion Zero Span" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionNamedInsertionNonzeroSpan name: "Named Insertion Non-Zero Span" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionSingleClassLongerSpan name: "Single Class Longer Span" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionSingleClassZeroSpan name: "Single Class Zero Span" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionSingleClassTriAllelic name: "Single Class Tri-allelic" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionSingleClassQuadAllelic name: "Single Class Quad-allelic" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionObservedWrongFormat name: "Observed Wrong Format" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionObservedTooLong name: "Observed Too Long" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionObservedContainsIUPAC name: "Observed Contains IUPAC" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionObservedMismatch name: "Observed Mismatch" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionMultipleAlignments name: "Multiple Alignments" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionNonIntegerChromCount name: "Non-integer Chomosome Count" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionAlleleFreqSumNot1 name: "Allele Frequency Sum Not 1" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionSingleAlleleFreq name: "Single Allele Frequency" typeOf: dcs:GeneticVariantExceptionEnum Node: dcid:GeneticVariantExceptionInconsistentAlleles name: "Inconsistent Alleles" typeOf: dcs:GeneticVariantExceptionEnum description: "Inconsistent genotype submission for at least one sample." Node: dcid:VariantAlleleOriginEnum name: "VariantAlleleOriginEnum" typeOf: schema:Class subClassOf: schema:Enumeration 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:VariantAlleleOriginUnspecified name: "Unspecified" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginGermline name: "Germline" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginSomatic name: "Somatic" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginBoth name: "Both" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginInherited name: "Inherited" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginPaternal name: "Paternal" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginMaternal name: "Maternal" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginDeNovo name: "de novo" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginBiParental name: "Bi-parental" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginUniParental name: "Uni-parental" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginNotTested name: "Not Tested" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginTestedInconclusive name: "Tested Inconclusive" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantAlleleOriginOther name: "Other" typeOf: dcs:VariantAlleleOriginEnum Node: dcid:VariantSuspectReasonCodesEnum name: "VariantSuspectReasonCodesEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Variant Suspect Reason Codes: unspecified, Paralog, byEST, oldAlign, Para_EST, 1kg_failed, or other." Node: dcid:VariantSuspectReasonCodesUnspecified name: "Unspecified" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodesParalog name: "Paralog" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodesByEST name: "ByEST" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodesOldAlign name: "OldAlign" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodesParaEST name: "ParaEST" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodes1kgFailed name: "1kgFailed" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:VariantSuspectReasonCodesOther name: "Other" typeOf: dcs:VariantSuspectReasonCodesEnum Node: dcid:ClinVarReviewStatusEnum name: "ClinVarReviewStatusEnum" typeOf: schema:Class subClassOf: schema:Enumeration 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:ClinVarReviewStatusNoCriteria name: "No Assertion Criteria Provided" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusReviewed name: "Reviewed By Expert Panel" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusConflictingInterpretations name: "Conflicting Interpretations" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusCriteriaProvided name: "Criteria Provided" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusNoInterpretation name: "Non-interpretation For The Single Variant" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusPracticeGuideline name: "Practice Guideline" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusNoConflicts name: "No Conflicts" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusMultipleSubmitters name: "Multiple Submitters" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinVarReviewStatusSingleSubmitter name: "Single Submitter" typeOf: dcs:ClinVarReviewStatusEnum Node: dcid:ClinSigEnum name: "ClinSigEnum" typeOf: schema:Class subClassOf: schema:Enumeration 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:ClinSigOther name: "Other" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigAffects name: "Affects" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigUncertain name: "Uncertain Significance" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigPathogenic name: "Pathogenic" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigRiskFactor name: "Risk Factor" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigBenign name: "Benign" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigConflictingPathogenicity name: "Conflicting Interpretations Of Pathogenicity" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigAssociation name: "Association" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigLikelyPathogenic name: "Likely Pathogenic" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigProtective name: "Protective" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigLikelyBenign name: "Likely Benign" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigNotProvided name: "Not Provided" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigAssociationNotFound name: "Association Not Found" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigDrugResponse name: "Drug Response" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigPathogenicLikelyPathogenic name: "Pathogenic/Likely Pathogenic" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigBenignLikelyBenign name: "Benign/Likely Benign" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigUnknown name: "Unknown" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigUntested name: "Untested" typeOf: dcs:ClinSigEnum Node: dcid:ClinSigHistocompatability name: "Histocompatibility" typeOf: dcs:ClinSigEnum Node: dcid:VariationTypeEnum name: "VariationTypeEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Variation type of alternate allele." Node: dcid:VariationTypeCNV name: "Copy Number Variable Region" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeDEL name: "Deletion Relative To The Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeDUP name: "Region of Elevated Copy Number Relative to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeINS name: "Insertion of Sequence Relative to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeINV name: "Inversion of Reference Sequence" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeDupTandem name: "Tandem Duplication" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeInsertME name: "Insertion of a Mobile Element Relative to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeDelME name: "Deletion of a Mobile Element Relative to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeInsertMEALU name: "Insertion of an Alu Mobile Element Relative to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeInsertDelALU name: "DeletionOfAnAluMobileElementRelativeToTheReference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeInsertNovel name: "Insertion of Sequence that Does Not Map to the Reference" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeSNV name: "Single Nucleotide Variation" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeMNV name: "Multiple Nucleotide Variations" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeDIV name: "Deletion Insertion Variation" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeHeterozygous name: "Heterozygous" typeOf: dcs:VariationTypeEnum description: "Variable, but undefined at nucleotide level." Node: dcid:VariationTypeSTR name: "Short Tandem (microsatellite) Repeat" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeNamed name: "Insertion/deletion variation of named repetitive element" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeNoVariation name: "No Variation" typeOf: dcs:VariationTypeEnum description: "Sequence scanned for variation, but none observed." Node: dcid:VariationTypeMixed name: "Mixed" typeOf: dcs:VariationTypeEnum description: "Cluster contains submissions from 2 or more allelic classes." Node: dcid:VariationTypeException name: "Exception" typeOf: dcs:VariationTypeEnum Node: dcid:VariationTypeINDEL name: "insertion-deletion" typeOf: dcs:VariationTypeEnum Node: dcid:GenVarSourceEnum name: "GenVarSourceEnum" typeOf: schema:Class subClassOf: schema:Enumeration description: "Sources for observations of genetic variant allele and population frequencies: GenVarSourceUCSCGenomeBrowser, GenVarSourceTheHumanGeneomeProject, GenVarSourceExomeAggregationConsortium, GenVarSourceGOExomeSequencingProject, GenVarSourceTOPMed, GenVarSource1000Genomes, GenVarSourceGnomAD, GenVarSourceGnomADexomes, or GenVarSourcePAGEstudy." Node: dcid:GenVarSourceUCSCGenomeBrowser name: " UCSC Genome Browser" url: "https://genome.ucsc.edu/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceTheHumanGenomeProject name: "The Human Genome Project" url: "https://www.genome.gov/human-genome-project" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceExomeAggregationConsortium name: "Exome Aggregation Consortium" url: "http://exac.broadinstitute.org/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceGOExomeSequencingProject name: "GO Exome Sequencing Project" url: "https://esp.gs.washington.edu/drupal/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceTOPMed name: "Trans-Omics for Precision Medicine (TOPMed) Program" url: "https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSource1000Genomes name: "1000 Genomes Project" url: "https://www.internationalgenome.org/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceGnomAD name: "Genome Aggregation Database" url: "https://www.gnomad.broadinstitute.org/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceGnomADexomes name: "Genome Aggregation Database Exams" url: "https://www.gnomad.broadinstitute.org/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourcePAGEStudy name: "Population Architecture using Genomics and Epidemiology Study" url: "https://www.pagestudy.org/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceNSDD name: "Northern Sweden Diet Database" url: "https://snd.gu.se/en/catalogue/study/ext0131" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceTwinsUK name: "Twins UK" url: "https://twinsuk.ac.uk/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceALSPAC name: "Avon Longitudinal Study of Parents and Children" url: "http://www.bristol.ac.uk/alspac/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceVietnameseGenomeProject name: "Vietnamese Genetic Variation Database" url: "https://genomes.vn/" typeOf: dcs:GenVarSourceEnum Node: dcid:GenVarSourceEstonianGenomeProject name: "Estonian Genome Project" url: "https://genomics.ut.ee/en/about-us/estonian-genome-centre/" typeOf: dcs:GenVarSourceEnum