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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 vario "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="http://www.biointerchange.org/gfvo#"
xml:base="http://www.biointerchange.org/gfvo"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:vario="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="http://www.biointerchange.org/gfvo#">
<dc:rights>CC0 [https://creativecommons.org/publicdomain/zero/1.0/].</dc:rights>
<dc:contributor xml:lang="en">Begum Durgahee</dc:contributor>
<dc:contributor xml:lang="en">Chris Mungall</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: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:versionInfo>0.9.32</owl:versionInfo>
<owl:imports rdf:resource="&vario;so.owl"/>
<owl:imports rdf:resource="http://semanticscience.org/ontology/sio.owl"/>
<owl:imports rdf:resource="http://www.biointerchange.org/faldo.owl"/>
<owl:imports rdf:resource="http://www.variationontology.org/vario_download/vario.owl"/>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.biointerchange.org/gfvo#describes -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/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>
<!-- http://www.biointerchange.org/gfvo#isAbout -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isAbout">
<owl:equivalentProperty rdf:resource="&sio;SIO_000332"/>
<rdfs:label>isAbout</rdfs:label>
<rdfs:comment xml:lang="en">References an entity about which information is provided for.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#describes"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasAnnotation -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasAnnotation">
<owl:equivalentProperty rdf:resource="&sio;SIO_000255"/>
<rdfs:label>hasAnnotation</rdfs:label>
<rdfs:comment xml:lang="en">Links to additional annotations about an entity.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasAttribute -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasAttribute">
<owl:equivalentProperty rdf:resource="&sio;SIO_000008"/>
<rdfs:label>hasAttribute</rdfs:label>
<rdfs:comment xml:lang="en">Links out to aggregate information for an entity.</rdfs:comment>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasEvidence -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasEvidence">
<owl:equivalentProperty rdf:resource="&sio;SIO_000772"/>
<rdfs:label>hasEvidence</rdfs:label>
<rdfs:comment xml:lang="en">References an entity or resource that provides supporting evidence.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#references"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasFirstPart -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasFirstPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000971"/>
<rdfs:label>hasFirstPart</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the first entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasIdentifier -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasIdentifier">
<owl:equivalentProperty rdf:resource="&sio;SIO_000671"/>
<rdfs:label>hasIdentifier</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an identifier.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasInput -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasInput">
<owl:equivalentProperty rdf:resource="&sio;SIO_000230"/>
<rdfs:label>hasInput</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="http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasLastPart -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasLastPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000972"/>
<rdfs:label>hasLastPart</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the last entity of an ordered part relationship.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasOrderedPart"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasMember -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasMember">
<owl:equivalentProperty rdf:resource="&sio;SIO_000059"/>
<rdfs:label>hasMember</rdfs:label>
<rdfs:comment xml:lang="en">Denotes membership for "Collection", "Catalog" and "File" instances.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasOrderedPart -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasOrderedPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000974"/>
<rdfs:label>hasOrderedPart</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="http://www.biointerchange.org/gfvo#hasPart"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasPart -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasPart">
<owl:equivalentProperty rdf:resource="&sio;SIO_000028"/>
<rdfs:label>hasPart</rdfs:label>
<rdfs:comment xml:lang="en">Denotes a compositional relationship to other entities.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasParticipant -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasParticipant">
<owl:equivalentProperty rdf:resource="&sio;SIO_000132"/>
<rdfs:label>hasParticipant</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the participation of other entities in processes.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasQuality -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasQuality">
<owl:equivalentProperty rdf:resource="&sio;SIO_000217"/>
<rdfs:label>hasQuality</rdfs:label>
<rdfs:comment xml:lang="en">Links out to an entity that provides qualitative information.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#hasSource -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#hasSource">
<owl:equivalentProperty rdf:resource="&sio;SIO_000253"/>
<rdfs:label>hasSource</rdfs:label>
<rdfs:comment xml:lang="en">Denotes information origin.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#hasAttribute"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isAfter -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isAfter">
<owl:equivalentProperty rdf:resource="&sio;SIO_000211"/>
<rdfs:label>isAfter</rdfs:label>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isBefore -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isBefore">
<owl:equivalentProperty rdf:resource="&sio;SIO_000240"/>
<rdfs:label>isBefore</rdfs:label>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isDescribedBy -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isDescribedBy">
<owl:equivalentProperty rdf:resource="&sio;SIO_000557"/>
<rdfs:label>isDescribedBy</rdfs:label>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isLocatedOn -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isLocatedOn">
<owl:equivalentProperty rdf:resource="&sio;SIO_000061"/>
<rdfs:label>isLocatedOn</rdfs:label>
<rdfs:comment xml:lang="en">Denotes the location of genomic feature on a landmark.</rdfs:comment>
<rdfs:subPropertyOf rdf:resource="http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo"/>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isParticipantIn -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isParticipantIn">
<owl:equivalentProperty rdf:resource="&sio;SIO_000062"/>
<rdfs:label>isParticipantIn</rdfs:label>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/gfvo#isSpatiotemporallyRelatedTo">
<owl:equivalentProperty rdf:resource="&sio;SIO_000322"/>
<rdfs:label>isSpatiotemporallyRelatedTo</rdfs:label>
<rdfs:comment xml:lang="en">Denotes spatio-temporal relations to other entities.</rdfs:comment>
</owl:ObjectProperty>
<!-- http://www.biointerchange.org/gfvo#references -->
<owl:ObjectProperty rdf:about="http://www.biointerchange.org/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>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.biointerchange.org/gfvo#hasValue -->
<owl:DatatypeProperty rdf:about="http://www.biointerchange.org/gfvo#hasValue">
<owl:equivalentProperty rdf:resource="&sio;SIO_000300"/>
<rdfs:label>hasValue</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 "hasValue" 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://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
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.biointerchange.org/gfvo#AlleleFrequency -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#AlleleFrequency">
<rdfs:label>Allele Frequency</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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="http://www.biointerchange.org/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.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#AminoAcid -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#AminoAcid">
<owl:equivalentClass rdf:resource="&sio;SIO_001224"/>
<rdfs:label>Amino Acid</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#ChemicalEntity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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:seeAlso>http://en.wikipedia.org/wiki/Amino_acid</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#AncestralSequence -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#AncestralSequence">
<rdfs:label>Ancestral Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#ReferenceSequence"/>
<rdfs:comment xml:lang="en">Denotes an ancestral allele of a feature. May be used to denote the 'ancestral allele' of VCF formatted files.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Ancestral_reconstruction</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#ArrayComparativeGenomicHybridization">
<rdfs:label>Array Comparative Genomic Hybridization</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature provenance is based on array-comparative genomic hybridization.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Attribute -->
<owl:Class rdf:about="http://www.biointerchange.org/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", "Mermaphrodite"), zygosity ("Hemizygous", "Heterozygous", "Homozygous"), etc.
The object property "hasQuality" (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 the involved entities..</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#AverageCoverage -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#AverageCoverage">
<rdfs:label>Average Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Coverage"/>
<rdfs:comment xml:lang="en">Average coverage depth for a genomic locus (a region or single base pair).</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#BiologicalEntity -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#BiologicalEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_010046"/>
<rdfs:label>Biological Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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 sub-classes of Chemical Entity.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#BiopolymerSequencing -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#BiopolymerSequencing">
<rdfs:label>Biopolymer Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Information about features and variants is based on biopolymer sequencing.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequencing</rdfs:seeAlso>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Breakpoint -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Breakpoint">
<rdfs:label>Breakpoint</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Catalog -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Catalog">
<owl:equivalentClass rdf:resource="&sio;SIO_001241"/>
<rdfs:label>Catalog</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Collection"/>
<rdfs:comment xml:lang="en">A catalog is a specialization of a "Collection", where all its contents are of the same type.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Cell -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Cell">
<owl:equivalentClass rdf:resource="&sio;SIO_010001"/>
<rdfs:label>Cell</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#BiologicalEntity"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Cell_(biology)</rdfs:seeAlso>
<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.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#ChemicalEntity -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#ChemicalEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_010004"/>
<rdfs:label>Chemical Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">A chemical entity is an entity related to chemistry. 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>
<!-- http://www.biointerchange.org/gfvo#Chromosome -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Chromosome">
<owl:equivalentClass rdf:resource="&sio;SIO_000899"/>
<rdfs:label>Chromosome</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#ChemicalEntity"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Chromosome</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A "Chromosome" instance is 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.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#CodingFrameOffset -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#CodingFrameOffset">
<rdfs:label>Coding Frame Offset</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quality"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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 the feature, if it is a coding sequence or feature that contributes to transcription and translation. It is referred to as "frame" in GTF, but called "phase" in GFF3 and GVF. A feature's coding frame offset can be either 0, 1, or 2.</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>
<!-- http://www.biointerchange.org/gfvo#CodonSequence -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#CodonSequence">
<rdfs:label>Codon Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#DNASequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
<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.ensembl.org/info/website/upload/gff.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Collection -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Collection">
<owl:equivalentClass rdf:resource="&sio;SIO_000616"/>
<rdfs:label>Collection</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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 a GFF3, GTF, GVF or VCF file, instances of "Collection" should be utilized too, or the more restrictive "Catalog" class should be used.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Comment -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Comment">
<owl:equivalentClass rdf:resource="&sio;SIO_001167"/>
<rdfs:label>Comment</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Contig -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Contig">
<rdfs:label>Contig</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Catalog"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Contig</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Coverage -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Coverage">
<rdfs:label>Coverage</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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="http://www.biointerchange.org/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="http://www.biointerchange.org/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).</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#DNAMicroarray -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#DNAMicroarray">
<owl:equivalentClass rdf:resource="&sio;SIO_001076"/>
<rdfs:label>DNA Microarray</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#GenomicAscertainingMethod"/>
<rdfs:comment xml:lang="en">Feature information is based on DNA microarray probes.</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>
<!-- http://www.biointerchange.org/gfvo#DNASequence -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#DNASequence">
<owl:equivalentClass rdf:resource="&sio;SIO_010016"/>
<rdfs:label>DNA Sequence</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Sequence"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Dna_sequence</rdfs:seeAlso>
<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>
<!-- http://www.biointerchange.org/gfvo#DNASequencing -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#DNASequencing">
<rdfs:label>DNA Sequencing</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#BiopolymerSequencing"/>
<owl:disjointWith rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#ExperimentalMethod -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#ExperimentalMethod">
<owl:equivalentClass rdf:resource="&sio;SIO_000999"/>
<rdfs:label>Experimental Method</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#ExternalReference -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#ExternalReference">
<owl:equivalentClass rdf:resource="&sio;SIO_001171"/>
<rdfs:label>External Reference</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A cross-reference to associate an entity to a representation in another database.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Feature -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Feature">
<owl:equivalentClass rdf:resource="&sio;SIO_010065"/>
<rdfs:label>Feature</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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://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>
<!-- http://www.biointerchange.org/gfvo#Female -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Female">
<owl:equivalentClass rdf:resource="&sio;SIO_010052"/>
<rdfs:label>Female</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Sex"/>
<rdfs:comment xml:lang="en">Denoting sex of a female individual. A female is defined as an individual producing ova.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Female</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#File -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#File">
<owl:equivalentClass rdf:resource="&sio;SIO_000396"/>
<rdfs:label>File</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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, or the more restrictive "Catalog" class should be used.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#ForwardReferenceSequenceFrameshift">
<rdfs:label>Forward Reference Sequence Frameshift</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#SequenceAlignmentOperation"/>
<rdfs:comment xml:lang="en">Denotes a frameshift forward in the reference sequence.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#FragmentReadPlatform -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#FragmentReadPlatform">
<rdfs:label>Fragment Read Platform</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#SequencingTechnologyPlatform"/>
<owl:disjointWith rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#FunctionalSpecification -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#FunctionalSpecification">
<owl:equivalentClass rdf:resource="&sio;SIO_000315"/>
<rdfs:label>Functional Specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/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.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#GameticPhase -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#GameticPhase">
<rdfs:label>Gametic Phase</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quality"/>
<rdfs:comment xml:lang="en">Denotes the presence of information that required capturing the gametic phase. For diploid organisms, that means that information is available about which chromosome of a chromosome pair contributed data.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Gametic_phase</rdfs:seeAlso>
<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>
<!-- http://www.biointerchange.org/gfvo#Genome -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Genome">
<owl:equivalentClass rdf:resource="&sio;SIO_000984"/>
<rdfs:label>Genome</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#MaterialEntity"/>
<rdfs:comment xml:lang="en">Representation of a genome. Genomic features that constitute the genome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genome</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#GenomeAnalysis -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#GenomeAnalysis">
<rdfs:label>Genome Analysis</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#ExperimentalMethod"/>
<rdfs:comment xml:lang="en">A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genomics#Genome_analysis</rdfs:seeAlso>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#GenomicAscertainingMethod -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#GenomicAscertainingMethod">
<rdfs:label>Genomic Ascertaining Method</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#ExperimentalMethod"/>
<rdfs:comment xml:lang="en">Provides information about the source of the data.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Genotype -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Genotype">
<owl:equivalentClass rdf:resource="&sio;SIO_001079"/>
<rdfs:label>Genotype</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#FunctionalSpecification"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Genotype</rdfs:seeAlso>
<rdfs:comment xml:lang="en">The genotype is the genetic information captured in a particular genome. It can also refer to one or more populations, if statistical distributions are provided that assign genetic codes to groups of individuals.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Germline -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Germline">
<rdfs:label>Germline</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Cell"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Germline</rdfs:seeAlso>
<rdfs:comment xml:lang="en">The germline feature class captures information about genomic sequence features arising from germline cells.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Hemizygous -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Hemizygous">
<rdfs:label>Hemizygous</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Zygosity"/>
<rdfs:comment xml:lang="en">A sequence alteration with hemizygous alleles.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Zygosity#Hemizygous</rdfs:seeAlso>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Heritage -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Heritage">
<rdfs:label>Heritage</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quality"/>
<rdfs:comment xml:lang="en">Heritage denotes the passing of traints from parents to ancestors. Passed traits may not be visible as a phenotype, but instead, might only manifest as genetic inheritance.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Heredity</rdfs:seeAlso>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Hermaphrodite -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Hermaphrodite">
<owl:equivalentClass rdf:resource="&sio;SIO_000784"/>
<rdfs:label>Hermaphrodite</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Sex"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Hermaphrodite</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Denoting sex of an individual that contains both male and female gemetes.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Heterozygous -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Heterozygous">
<rdfs:label>Heterozygous</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Zygosity"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Zygosity#Heterozygous</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A sequence alteration with heterozygous alleles.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Homozygous -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Homozygous">
<rdfs:label>Homozygous</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Zygosity"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Zygosity#Homozygous</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A sequence alteration with homozygous alleles.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Identifier -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Identifier">
<owl:equivalentClass rdf:resource="&sio;SIO_000115"/>
<rdfs:label>Identifier</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Label"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Identifier</rdfs:seeAlso>
<rdfs:comment xml:lang="en">An identifier labels an entity with a single term that is interpreted as an accession. An accession labels entities that are part of a collection of similar type.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#InformationContentEntity -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#InformationContentEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_000015"/>
<rdfs:label>Information Content Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Object"/>
<rdfs:comment xml:lang="en">An information content entity requires background information or specific domain knowledge to be interpreted correctly.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Interaction -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Interaction">
<owl:equivalentClass rdf:resource="&sio;SIO_000593"/>
<rdfs:label>Interaction</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Process"/>
<rdfs:comment xml:lang="en">Describing interaction between features, such as the effect of a feature variant on another feature.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Label -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Label">
<owl:equivalentClass rdf:resource="&sio;SIO_000179"/>
<rdfs:label>Label</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#InformationContentEntity"/>
<rdfs:comment xml:lang="en">A label is a term or short list of terms that name an entity for the purpose of lexicographically distinguishing the entity from entities of similar type.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Landmark -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Landmark">
<rdfs:label>Landmark</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Identifier"/>
<rdfs:comment xml:lang="en">A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor "Feature" class instances. For expressing ploidy within a data set, please refer to the "Chromosome" class.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Locus -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Locus">
<owl:equivalentClass rdf:resource="&sio;SIO_000056"/>
<rdfs:label>Locus</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#InformationContentEntity"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Locus_(genetics)</rdfs:seeAlso>
<rdfs:comment xml:lang="en">A locus refers to a position (possibly multi-dimensional) within a genome or proteome.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Male -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Male">
<owl:equivalentClass rdf:resource="&sio;SIO_010048"/>
<rdfs:label>Male</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Sex"/>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Male</rdfs:seeAlso>
<rdfs:comment xml:lang="en">Denoting sex of a male individual. A male is defined as an individual producing spermatozoa.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Match -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Match">
<rdfs:label>Match</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#SequenceAlignmentOperation"/>
<rdfs:comment xml:lang="en">Denotes a match between the reference sequence and target sequence.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
<rdfs:isDefinedBy rdf:resource="http://sequenceontology.org/resources/gvf.html"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#MaterialEntity -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#MaterialEntity">
<owl:equivalentClass rdf:resource="&sio;SIO_000004"/>
<rdfs:label>Material Entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Object"/>
<rdfs:comment xml:lang="en">A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc.</rdfs:comment>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Maternal -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Maternal">
<rdfs:label>Maternal</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Heritage"/>
<owl:disjointWith rdf:resource="http://www.biointerchange.org/gfvo#Paternal"/>
<rdfs:comment xml:lang="en">Maternal heritage is the passing of traits from a female to her ancestors.</rdfs:comment>
<rdfs:seeAlso>http://en.wikipedia.org/wiki/Maternal_effect</rdfs:seeAlso>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#MobileElementSequenceVariant -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#MobileElementSequenceVariant">
<rdfs:label>Mobile Element Sequence Variant</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#SequenceVariant"/>
<rdfs:comment xml:lang="en">Insertion or deletion of a mobile element. The exact modification is determined by a type of the Variation Ontology.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41"/>
</owl:Class>
<!-- http://www.biointerchange.org/gfvo#Name -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#Name">
<owl:equivalentClass rdf:resource="&sio;SIO_000116"/>
<rdfs:label>Name</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Label"/>
<rdfs:comment xml:lang="en">A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity..</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#NumberOfReads -->
<owl:Class rdf:about="http://www.biointerchange.org/gfvo#NumberOfReads">
<rdfs:label>Number of Reads</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.biointerchange.org/gfvo#Quantity"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biointerchange.org/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>
</rdfs:subClassOf>
<rdfs:comment xml:lang="en">Number of reads supporting a particular feature or variant.</rdfs:comment>
<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>
<!-- http://www.biointerchange.org/gfvo#Object -->