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gfvo.xml
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<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY dc "http://purl.org/dc/terms/" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY sio "http://semanticscience.org/resource/" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY faldo "http://biohackathon.org/resource/faldo#" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>
<rdf:RDF xmlns="https://github.com/BioInterchange/Ontologies/gfvo#"
xml:base="https://github.com/BioInterchange/Ontologies/gfvo"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:sio="http://semanticscience.org/resource/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:faldo="http://biohackathon.org/resource/faldo#">
<owl:Ontology rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#">
<owl:versionInfo>1.0.6</owl:versionInfo>
<dc:rights>CC0 [https://creativecommons.org/publicdomain/zero/1.0/].</dc:rights>
<dc:contributor xml:lang="en">Begum Durgahee</dc:contributor>
<rdfs:comment xml:lang="en">Best Practices
1.) The class hierarchy, object- and datatype-property hierarchies are modeled to match SIO's hierarchies.
2.) Every class and property has a label (rdfs:label) as well as a description (rdfs:comment). The description may contain an example of how a class/property is being applied.
3.) Classes that are directly related to either GFF3, GTF, GVF or VCF specification have a link-out to the specification's document as provenance indicator (via rdfs:isDefinedBy).
4.) Link-outs to Wikipedia are provided for classes wherever possible.
5.) Ontology terms are encoded in the URIs using camel case, i.e. letters following a white space in an ontology term are capitalized followed by the removal of the white space.
</rdfs:comment>
<dc:contributor xml:lang="en">Chris Mungall</dc:contributor>
<dc:contributor xml:lang="en">CODAMONO</dc:contributor>
<dc:contributor xml:lang="en">Erick Antezana</dc:contributor>
<dc:contributor xml:lang="en">Francesco Strozzi</dc:contributor>
<dc:title xml:lang="en">Genomic Feature and Variation Ontology (GFVO)</dc:title>
<dc:creator xml:lang="en">Joachim Baran</dc:creator>
<dc:contributor xml:lang="en">Joachim Baran</dc:contributor>
<dc:contributor xml:lang="en">Karen Eilbeck</dc:contributor>
<dc:contributor xml:lang="en">Michel Dumontier</dc:contributor>
<dc:contributor xml:lang="en">Raoul Bonnal</dc:contributor>
<dc:contributor xml:lang="en">Robert Hoehndorf</dc:contributor>
<dc:contributor xml:lang="en">Stephen Kan (GitHub: Helisquinde)</dc:contributor>
<dc:contributor xml:lang="en">Takatomo Fujisawa</dc:contributor>
<dc:description xml:lang="en">The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl).</dc:description>
<dc:contributor xml:lang="en">Toshiaki Katayama</dc:contributor>
<rdfs:seeAlso>https://github.com/BioInterchange/Ontologies</rdfs:seeAlso>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<owl:imports rdf:resource="http://semanticscience.org/ontology/sio.owl"/>
<owl:imports rdf:resource="http://biohackathon.org/resource/faldo.ttl"/>
<owl:imports rdf:resource="http://www.variationontology.org/vario_download/vario.owl"/>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#describes -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#describes">
<owl:equivalentProperty rdf:resource="&sio;SIO_000563"/>
<rdfs:label>describes</rdfs:label>
<rdfs:comment xml:lang="en">Links to an entity for which supportive information is being provided.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasAnnotation -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasAnnotation">
<owl:equivalentProperty rdf:resource="&sio;SIO_000255"/>
<rdfs:label>has annotation</rdfs:label>
<rdfs:comment xml:lang="en">Links to additional annotations about an entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute">
<owl:equivalentProperty rdf:resource="&sio;SIO_000008"/>
<rdfs:label>has attribute</rdfs:label>
<rdfs:comment xml:lang="en">Links out to aggregate information for an entity.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence">
<owl:equivalentProperty rdf:resource="&sio;SIO_000772"/>
<rdfs:label>has evidence</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides supporting/refuting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#references"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasFirstPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasFirstPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000971"/>
<rdfs:label>has first part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the first entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasIdentifier -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasIdentifier">
<owl:equivalentProperty rdf:resource="&sio;SIO_000671"/>
<rdfs:label>has identifier</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an identifier.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasInput -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasInput">
<owl:equivalentProperty rdf:resource="&sio;SIO_000230"/>
<rdfs:label>has input</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that is the input of a "Process" subclass.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasLastPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasLastPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000972"/>
<rdfs:label>has last part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the last entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasMember -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasMember">
<owl:equivalentProperty rdf:resource="&sio;SIO_000059"/>
<rdfs:label>has member</rdfs:label>
<rdfs:comment xml:lang="en">Denotes membership for "Collection", "Catalog" and "File" instances.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasOrderedPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000974"/>
<rdfs:label>has ordered part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasPart"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasOutput -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasOutput">
<owl:equivalentProperty rdf:resource="&sio;SIO_000229"/>
<rdfs:label>has output</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that is the output of a "Process" subclass.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasPart -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000028"/>
<rdfs:label>has part</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a compositional relationship to other entities.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasParticipant -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasParticipant">
<owl:equivalentProperty rdf:resource="&sio;SIO_000132"/>
<rdfs:label>has participant</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the participation of other entities in processes.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasQuality -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasQuality">
<owl:equivalentProperty rdf:resource="&sio;SIO_000217"/>
<rdfs:label>has quality</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that provides qualitative information.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasSource -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasSource">
<owl:equivalentProperty rdf:resource="&sio;SIO_000253"/>
<rdfs:label>has source</rdfs:label>
<rdfs:comment xml:lang="en">Denotes information origin.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAbout -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAbout">
<owl:equivalentProperty rdf:resource="&sio;SIO_000332"/>
<rdfs:label>is about</rdfs:label>
<rdfs:comment xml:lang="en">References an entity about which information is provided for.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#describes"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAffectedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAffectedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_001159"/>
<rdfs:label>is affected by</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is affected by another entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAfter -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAfter">
<owl:equivalentProperty rdf:resource="&sio;SIO_000211"/>
<rdfs:label>is after</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the trailing occurrence or succession of the subject in regards to the object.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf">
<owl:equivalentProperty rdf:resource="&sio;SIO_000011"/>
<rdfs:label>is attribute of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is an attribute of the entity that this property links out to.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isBefore -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isBefore">
<owl:equivalentProperty rdf:resource="&sio;SIO_000240"/>
<rdfs:label>is before</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the leading occurrence or precedence of the subject in regards to the object.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isCreatedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isCreatedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_000365"/>
<rdfs:label>is created by</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the process or method that created an entity.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isDescribedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isDescribedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_000557"/>
<rdfs:label>is described by</rdfs:label>
<rdfs:comment xml:lang="en">Provides a description of the subject via reference to an object that provides further information on the subject.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn">
<owl:equivalentProperty rdf:resource="&sio;SIO_000061"/>
<rdfs:label>is located on</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the location of genomic feature on a landmark.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isPartOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isPartOf">
<owl:equivalentProperty rdf:resource="&sio;SIO_000068"/>
<rdfs:label>is part of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is an intrinsic component of an encapsulating entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isLocatedOn"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isParticipantIn">
<owl:equivalentProperty rdf:resource="&sio;SIO_000062"/>
<rdfs:label>is participant in</rdfs:label>
<rdfs:comment xml:lang="en">Denotes participation with another entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isRefutedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isRefutedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_000774"/>
<rdfs:label>is refuted by</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides refuting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSourceOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSourceOf">
<owl:equivalentProperty rdf:resource="&sio;SIO_000219"/>
<rdfs:label>is source of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes that an entity is the source of the entity that this property links out to.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isAttributeOf"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSpatiotemporallyRelatedTo">
<owl:equivalentProperty rdf:resource="&sio;SIO_000322"/>
<rdfs:label>is spatiotemporally related to</rdfs:label>
<rdfs:comment xml:lang="en">Denotes spatio-temporal relations to other entities.</rdfs:comment>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isSupportedBy -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isSupportedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_000206"/>
<rdfs:label>is supported by</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides supporting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasEvidence"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#isTemporarilyPartOf -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#isTemporarilyPartOf">
<rdfs:label>is temporarily part of</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a temporarily constraint "isPartOf" relationship. The temporal restriction expresses that the relationship is not universally true.
This property can be used to express "Derives_from" relations in GFF3.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#isPartOf"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#references -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#references">
<owl:equivalentProperty rdf:resource="&sio;SIO_000631"/>
<rdfs:label>references</rdfs:label>
<rdfs:comment xml:lang="en">References another entity or resource.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#refersTo"/>
</owl:ObjectProperty>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#refersTo -->
<owl:ObjectProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#refersTo">
<owl:equivalentProperty rdf:resource="&sio;SIO_000628"/>
<rdfs:label>refers to</rdfs:label>
<rdfs:comment xml:lang="en">References an entity, where additional information is provided to augment the reference.</rdfs:comment>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#hasValue -->
<owl:DatatypeProperty rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#hasValue">
<owl:equivalentProperty rdf:resource="&sio;SIO_000300"/>
<rdfs:label>has value</rdfs:label>
<rdfs:comment xml:lang="en">Representation of any literal that is associated with a GFVO class instance. Domain restrictions might apply. For example, "Codon Sequence" entities restrict "has value" to be a non-empty string consisting of A, C, G, or T letters, and whose length is a multiple of 3.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Alias -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Alias">
<rdfs:label>Alias</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Name"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Pseudonym</rdfs:seeAlso>
<rdfs:comment xml:lang="en">An alias is an alternative name for an entity. The use of an alias is mostly secondary, whereas instances of the "Name" class should be used to denote primary names.
Encodes for the "Alias" attribute in GFF3 and GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AlleleCount -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AlleleCount">
<rdfs:label>Allele Count</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:comment xml:lang="en">Count of a specific allele in genotypes.
Encodes for "AC" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AlleleFrequency -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AlleleFrequency">
<rdfs:label>Allele Frequency</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;double"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;double">1.0</xsd:maxInclusive>
</rdf:Description>
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;double">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;float"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;float">0.0</xsd:minInclusive>
</rdf:Description>
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;float">1.0</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Allele_frequency</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Proportion of a particular gene allele in a gene pool or genotype.
Encodes for "AF" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AminoAcid -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AminoAcid">
<owl:equivalentClass rdf:resource="&obo;SO_0001237"/>
<owl:equivalentClass rdf:resource="&sio;SIO_010074"/>
<rdfs:label>Amino Acid</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>[A-Z]</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">"Amino Acid" encodes for the "Variant_aa" and "Reference_aa" attributes in GVF files. Linking an "Amino Acid" instance to a "Reference Sequence" or "Sequence Variant" instance denotes the genomic context of the amino acid.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Amino_acid</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AncestralSequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AncestralSequence">
<rdfs:label>Ancestral Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ReferenceSequence"/>
<rdfs:comment xml:lang="en">Denotes an ancestral allele of a feature.
May be used to denote the "ancestral allele" ("AA" additional information) of VCF formatted files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Ancestral_reconstruction</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ArrayComparativeGenomicHybridization -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ArrayComparativeGenomicHybridization">
<rdfs:label>Array Comparative Genomic Hybridization</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature provenance is based on array-comparative genomic hybridization.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Attribute -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Attribute">
<owl:equivalentClass rdf:resource="&sio;SIO_000614"/>
<rdfs:label>Attribute</rdfs:label>
<rdfs:comment xml:lang="en">An attribute denotes characteristics of an entity. At this stage, "Quality" is the only direct subclass of "Attribute", whose subclasses denote qualitative properties such as sex ("Female", "Male", "Hermaphrodite"), zygosity ("Hemizygous", "Heterozygous", "Homozygous"), etc.
The object property "has quality" (or subproperties thereof) should be utilized to express qualities of entities. The "hasAttribute" object property should be used to denote relationships to "Object" or "Process" instances, unless there is a better object property suitable to represent the relationship between entities.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#AverageCoverage -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#AverageCoverage">
<rdfs:label>Average Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Coverage"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Average coverage depth for a genomic locus (a region or single base pair), i.e. the average number of reads representing a given nucleotide in the reconstructed sequence.
Captures the "technology-platform" structured pragma in GVF files ("Average_coverage" tag).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BaseQuality -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BaseQuality">
<rdfs:label>Base Quality</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Score"/>
<rdfs:comment xml:lang="en">Root mean square base quality.
Accounts for "BQ" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_010046"/>
<rdfs:label>Biological Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">A biological entity an entity that contains genomic material or utilizes genomic material during its existance. Genomic material itself is represented as subclasses of "Chemical Entity".</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing">
<rdfs:label>Biopolymer Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Information about features and variants is based on biopolymer sequencing.
This class is not directly instantiated, but its subclasses "DNA Sequencing" and "RNA Sequencing" are used to describe the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequencing</rdfs:seeAlso>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Breakpoint -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Breakpoint">
<owl:equivalentClass rdf:resource="&obo;SO_0000699"/>
<rdfs:label>Breakpoint</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Locus"/>
<rdfs:comment xml:lang="en">A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see "Breakpoint_detail" in http://sequenceontology.org/resources/gvf.html). Breakpoint coordinates should be provided using classes of the Feature Annotation Location Description Ontology.
The class encodes for the "Breakpoint_detail" and "Breakpoint_range" attributes in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Catalog -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Catalog">
<owl:equivalentClass rdf:resource="&sio;SIO_001241"/>
<rdfs:label>Catalog</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A catalog is a specialization of a "Collection", where all of its contents are of the same type. The requirement of same type cannot be enforced formally via this ontology; data providers need to verify this condition manually or programmatically, or alternatively, use the more generic "Collection" class instead.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Cell -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Cell">
<owl:equivalentClass rdf:resource="&sio;SIO_010001"/>
<rdfs:label>Cell</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity"/>
<rdfs:comment xml:lang="en">A cell is a biological unit that in itself forms a living organism or is part of a larger organism that is composed of many other cells. The subclasses "Germline Cell" and "Somatic Cell" can be used to denote the biological material that was used in an experiment.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Cell_(biology)</rdfs:seeAlso>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_010004"/>
<rdfs:label>Chemical Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">A chemical entity is an entity related to biochemistry. This class is typically not instantiated, but instead, its subclasses "Amino Acid", "Chromosome", "Peptide Sequence", etc., are used to represent specific chemical entities.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Chromosome -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Chromosome">
<owl:equivalentClass rdf:resource="&obo;SO_0000340"/>
<owl:equivalentClass rdf:resource="&sio;SIO_000899"/>
<rdfs:label>Chromosome</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#ChemicalEntity"/>
<rdfs:comment xml:lang="en">A chromosome can be used as an abstract representation of a (not necessarily named) chromosome to represent ploidy within a data set. The "Chromosome" instance is then used for for denoting the locus of phased genotypes.
For placing genomic features ("Feature" class instances) on a chromosome, contig, scaffold, etc., please see the "Landmark" class. It is encouraged that Sequence Ontology terms are used to annotate a Landmark with a biological type (s.a. "chromosome", "contig", etc.).
Encodes for "sequencing-scope" pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Chromosome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CircularHelix -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CircularHelix">
<rdfs:label>Circular Helix</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#HelixStructure"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#WatsonCrickHelix"/>
<rdfs:comment xml:lang="en">A circular helix structure.
Can be used to indicate a true "Is_circular" attribute in GFF3 and GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Circular_DNA</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CodingFrameOffset -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CodingFrameOffset">
<rdfs:label>Coding Frame Offset</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quality"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;integer"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;integer">0</xsd:minInclusive>
</rdf:Description>
<rdf:Description>
<xsd:maxInclusive rdf:datatype="&xsd;integer">2</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Reading_frame</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Coding frame offset of a genomic feature that is a coding sequence or other genomic feature that contributes to transcription and translation. A feature's coding frame offset can be either 0, 1, or 2.
It is referred to as "frame" in GTF, but called "phase" in GFF3 and GVF. "phase" is defined in GVF, but unused.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#CodonSequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#CodonSequence">
<owl:equivalentClass rdf:resource="&obo;SO_0000360"/>
<rdfs:label>Codon Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#DNASequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>([ACGT]{3})+</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Codon</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A codon sequence is a nucleotide sequence underlying a potential amino acid sequence. Codon sequences are three bases of length or multiples thereof.
Encodes for "Variant_codon" and "Reference_codon" attributes in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Collection -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Collection">
<owl:equivalentClass rdf:resource="&sio;SIO_000616"/>
<rdfs:label>Collection</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A collection is a container for genomic data. A collection may contain information about genomic data including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by "File" class instances, whereas the result of unions or intersections between different "File" class instances should be captured within this format-independent "Collection" class. When importing data whose provenance is not file based, instances of "Collection" should be utilized (e.g., database exports).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Comment -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Comment">
<owl:equivalentClass rdf:resource="&sio;SIO_001167"/>
<rdfs:label>Comment</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A comment is a remark about a piece of information, an observation or statement. In the context of GFF3, GVF, etc., genomic feature and variation descriptions, "isAfter" and "isBefore" relationships should be used to indicate where a comment is situated between pragma or feature statements of GFF3, GTF, GVF or VCF files.
For specific descriptions or textual annotations of genomic features, the use of the "Note" class is encouraged.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ConditionalGenotypeQuality -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ConditionalGenotypeQuality">
<rdfs:label>Conditional Genotype Quality</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PhredScore"/>
<rdfs:comment xml:lang="en">Conditional genotype quality expressed in form of a "Phred Score". It denotes the score of the genotype being wrong under the assumption/condition that the genomic site is a sequence variant.
Encodes for "GQ" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Contig -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Contig">
<owl:equivalentClass rdf:resource="&obo;SO_0000149"/>
<rdfs:label>Contig</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments. "Contig" is a specialization of a "Collection" and should be used to aggregate features, but not for indicating that a "Landmark" is representing a contig. It is encouraged that the latter is annotated by a term of the Sequence Ontology.
Encodes for "sequencing-scope" in GVF and the "contig" information field in VCF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Contig</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Coverage -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Coverage">
<rdfs:label>Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;double"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;double">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;float"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;float">0.0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;integer"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="&xsd;integer">0</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Number of nucleic acid sequence reads for a particular genomic locus (a region or single base pair).
Accounts for "DP" additional information in VCF files.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNAMicroarray -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNAMicroarray">
<owl:equivalentClass rdf:resource="&sio;SIO_001076"/>
<rdfs:label>DNA Microarray</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature information is based on DNA microarray probes.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/DNA_microarray_experiment</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNASequence -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNASequence">
<owl:equivalentClass rdf:resource="&sio;SIO_010016"/>
<rdfs:label>DNA Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Sequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#hasValue"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="&xsd;string"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:pattern>([ACGT])+</xsd:pattern>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PeptideSequence"/>
<rdfs:comment xml:lang="en">A DNA sequence is a sequence of nucleic acids.
It can be used to describe "FASTA" annotations in both GFF3 and GVF files as well as short sequences in VCF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Dna_sequence</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#DNASequencing -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#DNASequencing">
<rdfs:label>DNA Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiopolymerSequencing"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#RNASequencing"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/DNA_sequencing</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Information about features and variants is based on DNA sequencing.
Used by the "data-source" structured pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Exome -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Exome">
<rdfs:label>Exome</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#BiologicalEntity"/>
<rdfs:comment xml:lang="en">Representation of an exome. Features that constitute the exome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances.
"Exome" can be used for describing data contents of the "sequencing-scope" pragma in GVF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Exome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ExperimentalMethod">
<owl:equivalentClass rdf:resource="&sio;SIO_000999"/>
<rdfs:label>Experimental Method</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Process"/>
<rdfs:comment xml:lang="en">An experimental method is a procedure that yields an experimental outcome (result). Experimental methods can be in vivo, in vitro or in silico procedures that are well described and can be referenced.
Encodes for "source" column contents of GFF3, GTF, and GVF file formats as well as the "CHROM" column in VCF. Can be used to describe the "capture-method" pragma in GVF; it can describe "VALIDATED" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ExternalReference -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ExternalReference">
<owl:equivalentClass rdf:resource="&sio;SIO_001171"/>
<rdfs:label>External Reference</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A cross-reference to associate an entity to a representation in another database.
Encodes for the "Dbxref" attribute in GFF3 and GVF. Can be used to describe the contents of the "source" column in GTF files. Captures the "genome-build" pragma, "source-method", "attribute-method", "phenotype-description", and "phased-genotypes" structured pragmas in GVF. Accounts for the "assembly" and "pedigreeDB" information fields, and "DB", "H2", "H3", "1000G" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Feature -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Feature">
<owl:equivalentClass rdf:resource="&obo;SO_0000110"/>
<owl:equivalentClass rdf:resource="&sio;SIO_010065"/>
<rdfs:label>Feature</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">The feature class captures information about genomic sequence features and variations. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#Female -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#Female">
<owl:equivalentClass rdf:resource="&sio;SIO_010052"/>
<rdfs:label>Female</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Sex"/>
<rdfs:comment xml:lang="en">Denoting sex of a female individual, who is defined as an individual producing ova.
This quality can be used to encode for the "sex" pragma in GVF files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Female</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#File -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#File">
<owl:equivalentClass rdf:resource="&sio;SIO_000396"/>
<rdfs:label>File</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between "File" class instances should be capture with the generic "Collection" class, which is format independent.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
<rdfs:isDefinedBy rdf:resource="http://www.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#ForwardReferenceSequenceFrameshift -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#ForwardReferenceSequenceFrameshift">
<rdfs:label>Forward Reference Sequence Frameshift</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#SequenceAlignmentOperation"/>
<rdfs:comment xml:lang="en">Denotes a frameshift forward in the reference sequence.
Encodes for the "Target" attribute in GFF3, encodes for "Target" attribute and "sequence-alignment" pragma in GVF, and, encodes "CIGAR" additional information in VCF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.1.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://samtools.github.io/hts-specs/VCFv4.2.pdf"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#FragmentReadPlatform -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#FragmentReadPlatform">
<rdfs:label>Fragment Read Platform</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#SequencingTechnologyPlatform"/>
<owl:disjointWith rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#PairedEndReadPlatform"/>
<rdfs:comment xml:lang="en">Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set.
Encodes for the "technology-platform-read-type" pragma in GVF.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#FunctionalSpecification -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#FunctionalSpecification">
<owl:equivalentClass rdf:resource="&sio;SIO_000315"/>
<rdfs:label>Functional Specification</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function. This class should not be directly instantiated, but instead, its subclass "Genotype" should be used.</rdfs:comment>
</owl:Class>
<!-- https://github.com/BioInterchange/Ontologies/gfvo#GameticPhase -->
<owl:Class rdf:about="https://github.com/BioInterchange/Ontologies/gfvo#GameticPhase">
<rdfs:label>Gametic Phase</rdfs:label>
<rdfs:subClassOf rdf:resource="https://github.com/BioInterchange/Ontologies/gfvo#Quality"/>
<rdfs:comment xml:lang="en">Denotes the presence of information that required capturing the gametic phase. For diploid organisms, this quality indicates that information is available about which chromosome of a chromosome pair contributed data.
"Gametic Phase" encodes for the "Phase" attribute in GVF. It encodes for "GT" and "PS" additional information in VCF.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Gametic_phase</rdfs:seeAlso>