genome_annotation_enum.mcf

# AssociationTypeEnum
Node: dcid:AssociationTypeEnum
name: "AssociationTypeEnum"
typeOf: schema:Class
subClassOf: dcs:Enumeration
description: "The way by which an association between two entities is made."

Node: dcid:AssociationTypeExperiment
typeOf: dcs:AssociationTypeEnum
name: "Experiment"
description: "An association between two things was made as a result of a scientific experiment or screening."

Node: dcid:AssociationTypeManuallyCurated
typeOf: dcs:AssociationTypeEnum
name: "Manually Curated"
description: "An association between two things was made through manual curation of scientific literature or database annotations."

Node: dcid:AssociationTypeTextMining
typeOf: dcs:AssociationTypeEnum
name: "Text Mining"
description: "An association between two things was made through automated text mining of the scientific literature."


# BiologicalTaxonomyGroupEnum
Node: dcid:BiologicalTaxonomyGroupEnum
name: "BiologicalTaxonomyGroupEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "Commonly used organism groups."

Node: dcid:BiologicalTaxonomyGroupArchaea
name: "Archaea"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes."
descriptionUrl: "https://en.wikipedia.org/wiki/Archaea"

Node: dcid:BiologicalTaxonomyGroupBacteria
name: "Bacteria"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. "
descriptionUrl: "https://en.wikipedia.org/wiki/Bacteria"

Node: dcid:BiologicalTaxonomyGroupFungi
name: "Fungi"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as one of the traditional eukaryotic kingdoms, along with Animalia, Plantae and either Protista or Protozoa and Chromista."
descriptionUrl: "https://en.wikipedia.org/wiki/Fungus"

Node: dcid:BiologicalTaxonomyGroupInvertebrate
name: "Invertebrate"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Invertebrates an umbrella term describing animals that neither develop nor retain a vertebral column (commonly known as a spine or backbone), which evolved from the notochord. It is a paraphyletic grouping including all animals excluding the chordate subphylum Vertebrata, i.e. vertebrates."
descriptionUrl: "https://en.wikipedia.org/wiki/Invertebrate"

Node: dcid:BiologicalTaxonomyGroupMetagenomes
name: "Metagenomes"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Metagenome is a sequence that comes from genetic material recovered directly from environmental or clinical samples."

Node: dcid:BiologicalTaxonomyGroupOther
name: "Other"
typeOf: dcs:BiologicalTaxonomyGroupEnum

Node: dcid:BiologicalTaxonomyGroupPlant
name: "Plant"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars from carbon dioxide and water, using the green pigment chlorophyll. Exceptions are parasitic plants that have lost the genes for chlorophyll and photosynthesis, and obtain their energy from other plants or fungi."
descriptionUrl: "https://en.wikipedia.org/wiki/Plant"

Node: dcid:BiologicalTaxonomyGroupProtozoa
name: "Protozoa"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Protozoa are a polyphyletic group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic debris."
descriptionUrl: "https://en.wikipedia.org/wiki/Protozoa"

Node: dcid:BiologicalTaxonomyGroupVertebrateMammalian
name: "Vertebrate, Mammalian"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "A mammal (from Latin mamma 'breast') is a vertebrate animal of the class Mammalia (/məˈmeɪli.ə/). Mammals are characterized by the presence of milk-producing mammary glands for feeding their young, a neocortex region of the brain, fur or hair, and three middle ear bones."
descriptionUrl: "https://en.wikipedia.org/wiki/Mammal"

Node: dcid:BiologicalTaxonomyGroupVertebrateOther
name: "Vertebrate, Other"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "Vertebrates (/ˈvɜːrtəbrɪts, -ˌbreɪts/) are deuterostomal animals with bony or cartilaginous axial endoskeleton — known as the vertebral column, spine or backbone — around and along the spinal cord. This group specifically refers to all vertebrates except for the subgroup mammals."
descriptionUrl: "https://en.wikipedia.org/wiki/Vertebrate"

Node: dcid:BiologicalTaxonomyGroupViral
name: "viral"
typeOf: dcs:BiologicalTaxonomyGroupEnum
description: "A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea."
descriptionUrl: "https://en.wikipedia.org/wiki/Virus"


# ClinSigEnum
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


# ClinVarReviewStatusEnum
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


# DNASequenceRoleEnum
Node: dcid:DNASequenceRoleEnum
name: "DNASequenceRoleEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "The role a defined sequence of DNA has in a genome assembly."

Node: dcid:DNASequenceRoleAssembledMolecule
name: "Assembled-Molecule"
typeOf: dcs:DNASequenceRoleEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help"
description: "The object represents a chromosome, linkage-group, or plasmid."

Node: dcid:DNASequenceRoleChromosome
name: "Chromosome"
typeOf: dcs:DNASequenceRoleEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help"
description: "The object represents a chromosome, linkage-group, or plasmid."

Node: dcid:DNASequenceRoleUnlocalizedScaffold
name: "Unlocalized Scaffold"
typeOf: dcs:DNASequenceRoleEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help"
description: "The object is a scaffold that is associated with a particular chromosome but has not been localized to a specific position on the chromosome."

Node: dcid:DNASequenceRoleUnplacedScaffold
name: "Unplaced Scaffold"
typeOf: dcs:DNASequenceRoleEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help"
description: "The object is a scaffold that does not have a chromosome assignment."

Node: dcid:DNASequenceRoleAltScaffold
name: "Alt-Scaffold"
typeOf: dcs:DNASequenceRoleEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help"
description: "The object is either an alternate loci scaffold or a patch scaffold."

Node: dcid:DNASequenceRoleFixPatch
name: "Fix-Patch"
typeOf: dcs:DNASequenceRoleEnum
description: "The object is a fix patch to the assembly-unit scaffold."

Node: dcid:DNASequenceRoleNovelPatch
name: "Novel-Patch"
typeOf: dcs:DNASequenceRoleEnum
description: "The object is a novel patch to the assembly-unit scaffold."


# ExonFramesEnum
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: "Frame 0"
typeOf: dcs:ExonFramesEnum

Node: dcid:ExonFrame1
name: "Frame 1"
typeOf: dcs:ExonFramesEnum

Node: dcid:ExonFrame2
name: "Frame 2"
typeOf: dcs:ExonFramesEnum

Node: dcid:ExonFrameNone
name: "None"
typeOf: dcs:ExonFramesEnum


# GeneticVariantAlignmentQualityEnum
Node: dcid:GeneticVariantAlignmentQualityEnum
name: "GeneticVariantAlignmentQualityEnum"
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


# GeneticVariantAttributeEnum
Node: dcid:GeneticVariantAttributeEnum
name: "GeneticVariantAttributeEnum"
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."


# GeneticVariantClassEnum
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 variation, variation, duplication, inversion, copy number loss, or copy number gain."

Node: dcid:GeneticVariantClassSingle
name: "Single Nucleotide Polymorphism"
typeOf: dcs:GeneticVariantClassEnum
abbreviation: "SNP","SNV"

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: "Multiple Nucleotide Polymorphism"
typeOf: dcs:GeneticVariantClassEnum
abbreviation: "MNP","MNV"

Node: dcid:GeneticVariantClassHet
name: "Heterozygous"
typeOf: dcs:GeneticVariantClassEnum
abbreviation: "het"

Node: dcid:GeneticVariantClassMicrosatellite
name: "Microsatellite"
typeOf: dcs:GeneticVariantClassEnum

Node: dcid:GeneticVariantClassInversion
name: "Inversion"
typeOf: dcs:GeneticVariantClassEnum

Node: dcid:GeneticVariantClassCopyNumberVariation
name: "Copy Number Variation"
typeOf: dcs:GeneticVariantClassEnum
abbreviation: "CNV"

Node: dcid:GeneticVariantClassVariation
name: "Variation"
typeOf: dcs:GeneticVariantClassEnum

Node: dcid:GeneticVariantClassDuplication
name: "Duplication"
typeOf: dcs:GeneticVariantClassEnum

Node: dcid:GeneticVariantClassCopyNumberGain
name: "Copy Number Gain"
typeOf: dcs:GeneticVariantClassEnum
specializationOf: dcs:GeneticVariantCopyNumberVariation

Node: dcid:GeneticVariantClassCopyNumberLoss
name: "Copy Number Loss"
typeOf: dcs:GeneticVariantClassEnum
specializationOf: dcs:GeneticVariantCopyNumberVariation


# GeneticVariantExceptionEnum
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."


# GeneticVariantFunctionalCategoryEnum
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:GeneticVariantFunctionalCategoryUTR5
name: "5' UTR"
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


# GeneticVariantLocTypeEnum
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: "Range Deletion"
typeOf: dcs:GeneticVariantLocTypeEnum

Node: dcid:GeneticVariantLocTypeRangeInsertion
name: "Range Insertion"
typeOf: dcs:GeneticVariantLocTypeEnum

Node: dcid:GeneticVariantLocTypeRangeSubstitution
name: "Range Substituation"
typeOf: dcs:GeneticVariantLocTypeEnum

Node: dcid:GeneticVariantLocTypeFuzzy
name: "Fuzzy"
typeOf: dcs:GeneticVariantLocTypeEnum


# GeneticVariantMolTypeEnum
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


# NomenclatureStatusEnum
Node: dcid:NomenclatureStatusEnum
name: "NomenclatureStatusEnum"
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


# GeneticVariantValidationStatusEnum
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: "Unknown"
typeOf: dcs:GeneticVariantValidationStatusEnum

Node: dcid:GeneticVariantValidationStatus2hit-2allele
name: "2hit-2allele"
typeOf: dcs:GeneticVariantValidationStatusEnum

Node: dcid:GeneticVariantValidationStatusSubmitter
name: "Submitter"
typeOf: dcs:GeneticVariantValidationStatusEnum


# GenomeAssemblyDerivedFromEnum
Node: dcid:GenomeAssemblyDerivedFromEnum
name: "GenomeAssemblyDerivedFromEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "Denotes the relation of the genome assembly with the type material from which it was derived."

Node: dcid:GenomeAssemblyDerivedFromTypeMaterial
name: “Assembly From Type Material”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from type material.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromSynonymTypeMaterial
name: “Assembly From Synonym Type Material”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from synonym type material.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromPathotypeMaterial
name: “Assembly From Pathotype Material”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from pathovar material.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromCladeExemplar
name: “Assembly Designated As Clade Exemplar”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from clade exemplar material.”

Node: dcid:GenomeAssemblyDerivedFromNeotype
name: “Assembly Designated As Neotype”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from neotype material.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromReftype
name: “Assembly Designated As Reftype”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “The sequences in the genome assembly were derived from reference material where type material never was available and is not likely to ever be available.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromIctvSpeciesExemplar
name: “ICTV Species Exemplar”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “ The International Committee on Taxonomy of Viruses (ICTV) designated the genome assembly as the exemplar for the virus species.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”

Node: dcid:GenomeAssemblyDerivedFromIctvAdditionalIsolate
name: “ICTV Additional Isolate”
typeOf: dcs:GenomeAssemblyDerivedFromEnum
description: “ The International Committee on Taxonomy of Viruses (ICTV) designated the genome assembly an additional isolate for the virus species.”
descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”


# GenomeAssemblyLevelEnum
Node: dcid:GenomeAssemblyLevelEnum
name: "GenomeAssemblyLevelEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "The highest level of assembly for any object in the assembly."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"

Node: dcid:GenomeAssemblyLevelCompleteGenome
name: "Complete Genome"
typeOf: dcs:GenomeAssemblyLevelEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
description: "All chromosomes are gapless and have no runs of 10 or more ambiguous bases (Ns), there are no unplaced or unlocalized scaffolds, and all the expected chromosomes are present (i.e. the assembly is not noted as having partial genome representation). Plasmids and organelles may or may not be included in the assembly but if present then the sequences are gapless."

Node: dcid:GenomeAssemblyLevelChromosome
name: "Chromosome"
typeOf: dcs:GenomeAssemblyLevelEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
description: "There is sequence for one or more chromosomes. This could be a completely sequenced chromosome without gaps or a chromosome containing scaffolds or contigs with gaps between them. There may also be unplaced or unlocalized scaffolds."

Node: dcid:GenomeAssemblyLevelScaffold
name: "Scaffold"
typeOf: dcs:GenomeAssemblyLevelEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
description: "Some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized."

Node: dcid:GenomeAssemblyLevelContig
name: "Contig"
typeOf: dcs:GenomeAssemblyLevelEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
description: "Nothing is assembled beyond the level of sequence contigs."


# GenomeAssemblyReleaseTypeEnum
Node: dcid:GenomeAssemblyReleaseTypeEnum
name: "GenomeAssemblyReleaseTypeEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "Defines the update type of this genome assembly version release."

Node: dcid:GenomeAssemblyReleaseTypeMajor
name: "Major"
typeOf: dcs:GenomeAssemblyReleaseTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
description: "Changes from the previous assembly version result in a significant change to the coordinate system. The first version of an assembly is always a major release. Most subsequent genome assembly updates are also major releases. [Field is not shown for major releases since this is the default type.]"

Node: dcid:GenomeAssemblyReleaseTypeMinor
name: "Minor"
typeOf: dcs:GenomeAssemblyReleaseTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
description: "Changes from the previous assembly version are limited to the following changes, none of which result in a significant change to the coordinate system of the primary assembly-unit: adding, removing or changing a non-nuclear assembly-unit; dropping unplaced or unlocalized scaffolds; adding up to 50 unplaced or unlocalized scaffolds which are shorter than the current scaffold-N50 value; or replacing a component with a gap of the same length."

Node: dcid:GenomeAssemblyReleaseTypePatch
name: "Patch"
typeOf: dcs:GenomeAssemblyReleaseTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
description: "The only change from the previous assembly version is the addition or modification of a patch assembly-unit (relevant for assemblies maintained by the Genome Reference Consortium)"


# GenomeAssemblyTypeEnum
Node: dcid:GenomeAssemblyTypeEnum
name: "GenomeAssemblyTypeEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "The type of sequence model data defined in this genome assembly."

Node: dcid:GenomeAssemblyTypeAssembly
name: "Assembly"
typeOf: dcs:GenomeAssemblyTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "The set of chromosomes, unlocalized and unplaced (sometimes called 'random') and alternate sequences used to represent an organism's genome. Assemblies are constructed from 1 or more assembly units."

Node: dcid:GenomeAssemblyTypeHaploidAssembly
name: "Haploid Assembly"
typeOf: dcs:GenomeAssemblyTypeEnum
specializationOf: dcs:GenomeAssemblyTypeAssembly
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "The collection of chromosome assemblies, unlocalized and unplaced sequences that represent an organism's genome. Any locus may be represented 0 or 1 time, and entire chromosomes are only represented 0 or 1 times."

Node: dcid:GenomeAssemblyTypeHaploidWithAltLoci
name: "Haploid with Alternate Loci"
typeOf: dcs:GenomeAssemblyTypeEnum
specializationOf: dcs:GenomeAssemblyTypeAssembly
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "The collection of chromosome assemblies, unlocalized and unplaced sequences and alternate loci that represent an organism's genome. Any locus may be represented 0, 1 or >1 time, but entire chromosomes are only represented 0 or 1 times."
synonym: "haploid with alt loci"

Node: dcid:GenomeAssemblyTypeDiploidAssembly
name: "Diploid Assembly"
typeOf: dcs:GenomeAssemblyTypeEnum
specializationOf: dcs:GenomeAssemblyTypeAssembly
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "A genome assembly for which a chromosome assembly is available for both sets of an individual's chromosomes. It is anticipated that a diploid genome assembly represents the genome of an individual, therefore, it is not expected that alternate loci will be defined for this assembly, although it is possible that unlocalized or unplaced sequences could be part of the assembly."

Node: dcid:GenomeAssemblyTypeUnresolvedDiploid
name: "Unresolved Diploid"
typeOf: dcs:GenomeAssemblyTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "A genome assembly from a diploid in which many of the haplotypic sequences have been resolved but the two haplotypes have not been separated. Consequently, the assembly will be much larger than the expected haploid genome size and many genes will be present in two copies."

Node: dcid:GenomeAssemblyTypeLinkedPseudohaplotypeAssemblies
name: "Pseudohaplotype Assemblies"
typeOf: dcs:GenomeAssemblyTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: "A genome assembly from a diploid in which many of the haplotypic sequences have been resolved, phased and the two haplotypes have been separated. The current state of the technology is that most assemblers produce blocks that are phased, separated by blocks where the haplotype cannot be distinguished. The typical result is that the "Principal Pseudohaplotype" assembly is a mosaic of haplotype blocks linked by unresolved segments and the "Alternate Pseudohaplotype" assembly is the other haplotype wherever the haplotypes can be distinguished. A pair of pseudohaplotype assemblies derived from the same diploid individual can be linked with a cross-reference."

Node: dcid:GenomeAssemblyTypeAlternatePseudohaplotype
name: "Alternate Pseudohaplotype"
typeOf: dcs:GenomeAssemblyTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: “A genome assembly from a diploid in which many of the haplotypic sequences have been resolved, phased and the two haplotypes have been separated and the resulting haplotypes can be distinguished.”
specializationOf: dcs:GenomeAssemblyTypeLinkedPseudohaplotypeAssemblies

Node: dcid:GenomeAssemblyTypePrincipalPseudohaplotype
name: "Principal Pseudohaplotype"
typeOf: dcs:GenomeAssemblyTypeEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/model/#asmb_def"
description: “A genome assembly from a diploid in which many of the haplotypic sequences have been resolved, phased and the two haplotypes have been separated and the result is a mosaic of haplotype blocks linked by unresolved segments.“
specializationOf: dcs:GenomeAssemblyTypeLinkedPseudohaplotypeAssemblies


# GenVarSourceEnum
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
abbreviation: "HGP"

Node: dcid:GenVarSourceExomeAggregationConsortium
name: "Exome Aggregation Consortium"
url: "http://exac.broadinstitute.org/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "ExAC"

Node: dcid:GenVarSourceGOExomeSequencingProject
name: "GO Exome Sequencing Project"
url: "https://esp.gs.washington.edu/drupal/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "GO-ESP"

Node: dcid:GenVarSourceTOPMed
name: "Trans-Omics for Precision Medicine Program"
url: "https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program"
typeOf: dcs:GenVarSourceEnum
abbreviation: "TOPMed"

Node: dcid:GenVarSource1000Genomes
name: "1000 Genomes Project"
url: "https://www.internationalgenome.org/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "1KGP"

Node: dcid:GenVarSourceGnomAD
name: "Genome Aggregation Database"
url: "https://www.gnomad.broadinstitute.org/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "GnomAD"

Node: dcid:GenVarSourceGnomADexomes
name: "Genome Aggregation Database Exams"
url: "https://www.gnomad.broadinstitute.org/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "GnomAD Exomes"

Node: dcid:GenVarSourcePAGEStudy
name: "Population Architecture using Genomics and Epidemiology Study"
url: "https://www.pagestudy.org/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "PAGE Study"

Node: dcid:GenVarSourceNSDD
name: "Northern Sweden Diet Database"
url: "https://snd.gu.se/en/catalogue/study/ext0131"
typeOf: dcs:GenVarSourceEnum
abbreviation: "NSDD"

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: "https://www.bristol.ac.uk/alspac/"
typeOf: dcs:GenVarSourceEnum
abbreviation: "ALSPAC"

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


# NonCodingRNATypeEnum
Node: dcid:NonCodingRNATypeEnum
name: "NonCodingRNATypeEnum"
typeOf: schema:Class
subClassOf: dcs:Enumeration
description: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR."
descriptionUrl: "https://en.wikipedia.org/wiki/Non-coding_RNA"

Node: dcid:NonCodingRNATypeRibosomalRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "Ribosomal RNA"
shortDisplayName: "rRNA"
description: "Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells."
descriptionUrl: "https://en.wikipedia.org/wiki/Ribosomal_RNA"

Node: dcid:NonCodingRNATypeLongNonCodingRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "Long NonCoding RNA"
shortDisplayName: "lncRNA"
description: "Long noncoding RNA (LncRNA) is a large class of RNA molecules with size larger than 200 nucleotides. They exhibit cellular functions although having no protein-coding capability."
descriptionUrl: "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-noncoding-rna"

Node: dcid:NonCodingRNATypeLongIntergenicNonCodingRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "Long Intergenic NonCoding RNA"
shortDisplayName: "lincRNA"
description: "Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes."
descriptionUrl: "https://en.wikipedia.org/wiki/Long_non-coding_RNA"

Node: dcid:NonCodingRNATypeSmallNucleolarRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "Small Nucleolar RNA"
shortDisplayName: "snoRNA"
description: "Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_nucleolar_RNA"

Node: dcid:NonCodingRNATypeMicroRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "MicroRNA"
shortDisplayName: "miRNA"
description: "MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides."
descriptionUrl: "https://en.wikipedia.org/wiki/MicroRNA"

Node: dcid:NonCodingRNATypeCircularRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "CircularRNA"
shortDisplayName: "circRNA"
description: "Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop."
descriptionUrl: "https://en.wikipedia.org/wiki/Circular_RNA"

Node: dcid:NonCodingRNATypePromoterAssociatedRNA
typeOf: dcs:NonCodingRNATypeEnum
name: "Promoter-Associated RNA"
shortDisplayName: "pRNA"
description: "Promoter-associated RNAs (pRNAs) are a family of ~90–100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon."
descriptionUrl: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929421/"


# NucleicAcidEnum
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


# RefSeqCategoryEnum
Node: dcid:RefSeqCategoryEnum
name: "RefSeqCategoryEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
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:RefSeqCategoryReferenceGenome
name: "Reference Genome"
typeOf: dcs:RefSeqCategoryEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
description: "A manually selected high quality genome assembly that NCBI and the community have identified as being important as a standard against which other data are compared."

Node: dcid:RefSeqCategoryRepresentativeGenome
name: "Representative Genome"
typeOf: dcs:RefSeqCategoryEnum
descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
description: "A genome computationally or manually selected as a representative from among the best genomes available for a species or clade that does not have a designated reference genome."


# SequenceOntologySubsetEnum
Node: dcid:SequenceOntologySubsetEnum
name: "SequenceOntologySubsetEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "A subset of terms from The Sequence Ontology that can be useful for defined activities."

Node: dcid:SequenceOntologySubsetAllianceOfGenomeResources
name: "Alliance of Genome Resources"
typeOf: dcs:SequenceOntologySubsetEnum
description: "A subset of Sequence Ontology terms used to describe various types of genes."

Node: dcid:SequenceOntologySubsetBiosapiens
name: "Biosapienes"
typeOf: dcs:SequenceOntologySubsetEnum
description: "A set of terms with which to annotate polypeptide sequence, for structural data."
descriptionUrl: "http://www.sequenceontology.org/?page_id=267"

Node: dcid:SequenceOntologySubsetDbVar
name: "dbVar"
typeOf: dcs:SequenceOntologySubsetEnum
description: "A subset of Sequence Ontology terms used by dbVar to describe genetic variants."

Node: dcid:SequenceOntologySubsetSofa
name: "Sequence Ontology Feature Annotation"
typeOf: dcs:SequenceOntologySubsetEnum
abbreviation: "SOFA"
description: "A subset of terms from The Sequence Ontology (SO) consisting of some of those terms that can be located onto sequence has been selected; this condensed version of SO is especially well suited for labeling the outputs of automated or semi-automated sequence annotation pipelines."
descriptionUrl: "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r44"


# StrandOrientationEnum
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


# SynonymTypeEnum
Node: dcid:SynonymTypeEnum
name: "SynonymTypeEnum"
typeOf: schema:Class
subClassOf: schema:Enumeration
description: "The level of closeness of a match of a synonym to an original term of interest."

Node: dcid:SynonymTypeRelated
name: "Related Terms"
typeOf: dcs:SynonymTypeEnum
description: "The two terms are related."

Node: dcid:SynonymTypeNarrow
name: "Narrowly Related Terms"
typeOf: dcs:SynonymTypeEnum
description: "The two terms are narrowly related."

Node: dcid:SynonymTypeBroad
name: "Broadly Related Terms"
typeOf: dcs:SynonymTypeEnum
description: "The two terms are broadly related."

Node: dcid:SynonymTypeExact
name: “Exact Terms”
typeOf: dcs:SynonymTypeEnum
description: "The two terms are an exact match."


# TypeOfGeneEnum
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: "Biological Region"
typeOf: dcs:TypeOfGeneEnum

Node: dcid:TypeOfGeneexRNA
name: "extracellular RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesRNA
abbreviation: "exRNA"
description: "Extracellular RNA (exRNA) describes RNA species present outside of the cells in which they were transcribed. Carried within extracellular vesicles, lipoproteins, and protein complexes, exRNAs are protected from ubiquitous RNA-degrading enzymes. exRNAs may be found in the environment or, in multicellular organisms, within the tissues or biological fluids such as venous blood, saliva, breast milk, urine, semen, menstrual blood, and vaginal fluid. Although their biological function is not fully understood, exRNAs have been proposed to play a role in a variety of biological processes including syntrophy, intercellular communication, and cell regulation."
descriptionUrl: "https://en.wikipedia.org/wiki/Extracellular_RNA"

Node: dcid:TypeOfGenemiRNA
name: "microRNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenencRNA
abbreviation: "miRNA"
description: "MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRNAs base-pair to complementary sequences in mRNA molecules, then silence said mRNA molecules by one or more of the following processes: cleavage of the mRNA strand into two pieces, destabilization of the mRNA by shortening its poly(A) tail, or reducing translation of the mRNA into proteins. In cells of humans and other animals, miRNAs primarily act by destabilizing the mRNA."
descriptionUrl: "https://en.wikipedia.org/wiki/MicroRNA"

Node: dcid:TypeOfGenemiscRNA
name: "miscellaneous RNA"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "miscRNA"
description: "Miscellaneous RNA that are in no other classification."

Node: dcid:TypeOfGenencRNA
name: "non-coding RNA"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "ncRNA"
description: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR."
descriptionUrl: "https://en.wikipedia.org/wiki/Non-coding_RNA"

Node: dcid:TypeOfGeneOther
name: "Other"
typeOf: dcs:TypeOfGeneEnum

Node: dcid:TypeOfGenepiRNA
name: "Piwi-interacting RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesRNA
abbreviation: "piRNA"
description: "Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi-subfamily Argonaute proteins. These piRNA complexes are mostly involved in the epigenetic and post-transcriptional silencing of transposable elements and other spurious or repeat-derived transcripts, but can also be involved in the regulation of other genetic elements in germ line cells."
descriptionUrl: "https://en.wikipedia.org/wiki/Piwi-interacting_RNA"

Node: dcid:TypeOfGeneProteinCoding
name: "Protein Coding"
typeOf: dcs:TypeOfGeneEnum
description: "Protein-coding sequences represent the most widely studied and best understood component of the human genome. These sequences ultimately lead to the production of all human proteins, although several biological processes (e.g. DNA rearrangements and alternative pre-mRNA splicing) can lead to the production of many more unique proteins than the number of protein-coding genes."
descriptionUrl: "https://en.wikipedia.org/wiki/Human_genome#Coding_sequences_(protein-coding_genes)"

Node: dcid:TypeOfGenePseudo
name: "Pseudogene"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "pseudo"
description: "Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by gene duplication or indirectly by reverse transcription of an mRNA transcript. Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons."
descriptionUrl: "https://en.wikipedia.org/wiki/Pseudogene"

Node: dcid:TypeOfGenerRNA
name: "ribosomal RNA"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "rRNA"
specializationOf: dcs:TypeOfGenencRNA
description: "Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins.[1] Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes."
descriptionUrl: "https://en.wikipedia.org/wiki/Ribosomal_RNA"

Node: dcid:TypeOfGenescaRNA
name: "Small Cajal body-specific RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesnoRNA
abbreviation: "scaRNA"
description: "Small Cajal body-specific RNAs (scaRNAs) are a class of small nucleolar RNAs (snoRNAs) that specifically localise to the Cajal body, a nuclear organelle (cellular sub-organelle) involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs or snurps). ScaRNAs guide the modification (methylation and pseudouridylation) of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_Cajal_body-specific_RNA"

Node: dcid:TypeOfGenescRNA
name: "small conditional RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesRNA
abbreviation: "scRNA"
description: "A small conditional RNA (scRNA) is a small RNA molecule or complex (typically less than approximately 100 nt) engineered to interact and change conformation conditionally in response to cognate molecular inputs so as to perform signal transduction in vitro, in situ, or in vivo."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_conditional_RNA"

Node: dcid:TypeOfGenesiRNA
name: "small interfering RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesRNA
abbreviation: "siRNA"
synonym: "short interfering RNA", "silencing RNA"
description: "Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20–24 (normally 21) base pairs in length, similar to miRNA, and operating within the RNA interference (RNAi) pathway. It interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation. It was discovered in 1998, by Andrew Fire at Carnegie Institution for Science in Washington DC and Craig Mello at University of Massachusetts in Worcester."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_interfering_RNA"

Node: dcid:TypeOfGenesRNA
name: "small RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenencRNA
abbreviation: "sRNA"
description: "Small RNA (sRNA) are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding. RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies repeat associated small interfering RNA (rasiRNA). Small RNA is unable to induce RNAi alone, and to accomplish the task it must form the core of the RNA–protein complex termed the RNA-induced silencing complex (RISC), specifically with Argonaute protein."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_RNA"

Node: dcid:TypeOfGenesnRNA
name: "small nuclear RNA"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "snRNA"
specializationOf: dcs:TypeOfGenesRNA
description: "Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III.[1] Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. They have also been shown to aid in the regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), and maintaining the telomeres."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_nuclear_RNA"

Node: dcid:TypeOfGenesnoRNA
name: "small nucleolar RNA"
typeOf: dcs:TypeOfGeneEnum
specializationOf: dcs:TypeOfGenesRNA
abbreviation: "snoRNA"
description: "In molecular biology, small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes or the guide RNAs (gRNAs) used by Cas9 for CRISPR gene editing."
descriptionUrl: "https://en.wikipedia.org/wiki/Small_nucleolar_RNA"

Node: dcid:TypeOfGenetRNA
name: "transfer RNA"
typeOf: dcs:TypeOfGeneEnum
abbreviation: "tRNA"
specializationOf: dcs:TypeOfGenencRNA
description: "Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein-synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code."
descriptionUrl: "https://en.wikipedia.org/wiki/Transfer_RNA"

Node: dcid:TypeOfGeneUnknown
name: "Unknown"
typeOf: dcs:TypeOfGeneEnum


# VariantAlleleOriginEnum
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


# VariantSuspectReasonCode
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


# VariationTypeEnum
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
abbreviation: "CNV"

Node: dcid:VariationTypeDEL
name: "Deletion"
typeOf: dcs:VariationTypeEnum
abbreviation: "del"
description: "Deletion relative to the reference."

Node: dcid:VariationTypeDUP
name: "Duplication"
typeOf: dcs:VariationTypeEnum
abbreviation: "dup"
definition: "Region of elevated copy number relative to the reference."

Node: dcid:VariationTypeINS
name: "Insertion"
typeOf: dcs:VariationTypeEnum
abbreviation: "INS"
description: "Insertion of sequence relative to the reference."

Node: dcid:VariationTypeINV
name: "Inversion"
typeOf: dcs:VariationTypeEnum
abbreviation: "INV"
description: "Inversion of Reference Sequence."

Node: dcid:VariationTypeDupTandem
name: "Tandem Duplication"
typeOf: dcs:VariationTypeEnum
abbreviation: "Dup Tandem"

Node: dcid:VariationTypeInsertME
name: "Insertion of a Mobile Element"
typeOf: dcs:VariationTypeEnum
abbreviation: "Insert ME"
description: "Insertion of a mobile element relative to the reference."

Node: dcid:VariationTypeDelME
name: "Deletion of a Mobile Element"
typeOf: dcs:VariationTypeEnum
abbreviation: "del ME"
description: "Deletion of a mobile element relative to the reference."

Node: dcid:VariationTypeInsertMEALU
name: "Insertion of an Alu Mobile Element"
typeOf: dcs:VariationTypeEnum
abberviation: "Insert ME ALU"
description: "Insertion of an Alu mobile element relative to the reference."

Node: dcid:VariationTypeInsertDelALU
name: "Deletion of an Alu Mobile Element"
typeOf: dcs:VariationTypeEnum
abbreviation: "del ALU"
description: "Deletion of an Alu mobile element relative to the reference."

Node: dcid:VariationTypeInsertNovel
name: "Novel Insertion"
typeOf: dcs:VariationTypeEnum
description: "Insertion of sequence that does not map to the reference."

Node: dcid:VariationTypeSNV
name: "Single Nucleotide Variation"
typeOf: dcs:VariationTypeEnum
abbreviation: "SNP","SNV"

Node: dcid:VariationTypeMNV
name: "Multiple Nucleotide Variations"
typeOf: dcs:VariationTypeEnum
abbreviation: "MNP","MNV"

Node: dcid:VariationTypeDIV
name: "Deletion Insertion Variation"
typeOf: dcs:VariationTypeEnum
abbreviation: "DIV"

Node: dcid:VariationTypeHeterozygous
name: "Heterozygous"
typeOf: dcs:VariationTypeEnum
description: "Variable, but undefined at nucleotide level."
abbreviation: "het"

Node: dcid:VariationTypeSTR
name: "Short Tandem (microsatellite) Repeat"
typeOf: dcs:VariationTypeEnum
abbreviation: "STR"

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
abbreviation: "INDEL"

Node: dcid:GeneticAssoication
typeOf: schema:Class
subClassOf: schema:Enumeration
name: "GeneticAssoication"

Node: dcid:GeneticVariantCopyNumberVariation
typeOf: schema:Class
subClassOf: schema:Enumeration
name: "GeneticVariantCopyNumberVariation"