GBOL

Last uploaded: August 9, 2019
Preferred Name

Variation

Definitions

Defines a genomic variant #* The type of Variation varType type::VariationTypes; #* Allele of the alternate sequence alternate xsd:string*; #* Quality score of the marker quality xsd:string?; #* Allele of the reference sequence referenceAllele xsd:string?; #* Variant identification code ID xsd:string?; #* filter filter xsd:string?; #* Read depth readDepth xsd:string?; #* Number of Homozygous variant samples homozygousSamples xsd:Integer?; #* Number of Heterozygous variant samples heterozygousSamples xsd:Integer?; #* Number of wildtype samples wildtypeSamples xsd:Integer?; #* Number of samples not called numberNotCalled xsd:Integer?; #* Ancestral Allele ancestralAllele xsd:string?; #* Alelle Count alleleCount xsd:Integer?; #* Frequency in which the alternate allele is found alleleFreq xsd:string?; #* total number of alleles in called genotypes alleleNumber xsd:Integer?; #* RMS base quality baseQuality xsd:string?; #* Cigar string describing alignment of alternate allele to reference CIGAR xsd:string?; #* dbSNP membership dbSNP xsd:string?; #* The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. end @:Position?; #* Mapping Quality mapQuality xsd:string?; #* Number of samples with data numberOfSamples xsd:Integer?; #* Strand bias strandBias xsd:string?; #* Validated validated xsd:string?; #* Genotypes of the sample the variant was called on genotype @:VariantGenotype*;

ID

http://gbol.life/0.1/Variation

definition

Defines a genomic variant

label

Variation

prefixIRI

Variation

prefLabel

Variation

propertyDefinitions

#* The type of Variation varType type::VariationTypes; #* Allele of the alternate sequence alternate xsd:string*; #* Quality score of the marker quality xsd:string?; #* Allele of the reference sequence referenceAllele xsd:string?; #* Variant identification code ID xsd:string?; #* filter filter xsd:string?; #* Read depth readDepth xsd:string?; #* Number of Homozygous variant samples homozygousSamples xsd:Integer?; #* Number of Heterozygous variant samples heterozygousSamples xsd:Integer?; #* Number of wildtype samples wildtypeSamples xsd:Integer?; #* Number of samples not called numberNotCalled xsd:Integer?; #* Ancestral Allele ancestralAllele xsd:string?; #* Alelle Count alleleCount xsd:Integer?; #* Frequency in which the alternate allele is found alleleFreq xsd:string?; #* total number of alleles in called genotypes alleleNumber xsd:Integer?; #* RMS base quality baseQuality xsd:string?; #* Cigar string describing alignment of alternate allele to reference CIGAR xsd:string?; #* dbSNP membership dbSNP xsd:string?; #* The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. end @:Position?; #* Mapping Quality mapQuality xsd:string?; #* Number of samples with data numberOfSamples xsd:Integer?; #* Strand bias strandBias xsd:string?; #* Validated validated xsd:string?; #* Genotypes of the sample the variant was called on genotype @:VariantGenotype*;

subClassOf

http://gbol.life/0.1/VariationFeature

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http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25713 NLN LOOM
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25713 NCIT LOOM
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25713 NCIT LOOM
http://purl.obolibrary.org/obo/VariO_0001 VARIO LOOM
http://purl.obolibrary.org/obo/NCIT_C25713 PREMEDONTO LOOM
http://sweetontology.net/phenSystem/Variation SWEET LOOM
http://sweetontology.net/phenSystem/Variation SWEET LOOM
http://sweetontology.net/phenSystem/Variation SWEET LOOM
http://sweetontology.net/phenSystem/Variation SWEET LOOM