Overview

BioInterchange makes use of several external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and we welcome contributions of ontologies that permit including more file formats for RDF conversion.

External ontologies used in BioInterchange:

One particular ontology — the Genomic Feature and Variation Ontology — is being used for converting GFF3, GTF, GVF, and VCF file formats into RDF as described below.

Genomic Feature and Variation Ontology (GFVO)

The Genomic Feature and Variation Ontology (GFVO) enables the RDFization of genomic feature and variation data. It particularly addresses the representation of data in GFF3, GVF, GTF, and VCF formats.

The ontology is available under the CC0 1.0 Universal license, and therefore, de-facto within the public domain.

GFVO can be loaded into Protégé or TopBraid Composer via: http://www.biointerchange.org/gfvo

GFVO's development version can be found on GitHub: https://github.com/BioInterchange/Ontologies

Table of Contents

  1. Overview
  2. External Ontologies and Linked Data
  3. Data Structure Mappings between GFVO and Genomic Files
  4. Examples
    1. Example 1: Loci and Basic Genomic Feature Annotation of a Gene and its Transcription Factor Binding Site
    2. Example 2: Encoding of a Sequence Alignment
    3. Example 3: Phased and Unphased Genotype and its Sequence Variants
    4. Example 4: Encoding of a Phred Score
  5. Ontology Reference

Note: GFF3GTFGVFand VCF badges indicate a particular class or property definition's origin. The application of the ontology is not restricted to those file formats though.

GFVO is being developed as the joint work of Joachim Baran (corresponding author, joachim.baran@gmail.com), Erick Antezana, Begum Durgahee, Karen Eilbeck, Robert Hoehndorf, and Michel Dumontier.

Feedback on the ontology has been provided by Raoul Bonnal, Takatomo Fujisawa, Toshiaki Katayama, Chris Mungall, and Francesco Strozzi.

Overview

An overview of GFVO is available through its BioPortal web-page.

 Due to technical limitations of BioPortal, GFVO in BioPortal does not import other ontologies nor does it contain SIO class- or property-equivalences.

It is necessary to use Protege or TopBraid Composer for viewing the ontology properly (e.g., to see GFF3/GTF/GVF/VCF specification annotations, Wikipedia linkouts, class-/property-equivalences, etc.).

The BioPortal GFVO version is available at: http://www.biointerchange.org/gfvo_bioportal

External Ontologies and Linked Data

GFVO makes use of the Sequence Ontology for annotating genomic features and variants as well as the Feature Annotation Location Description Ontology (FALDO) for describing genomic locations such as genomic features, breakpoints, and coordinate ranges for fuzzy/probabilistic coordinate ranges. We also integrate the Variation Ontology (VariO) for describing variants, their effects and consequences.

Species are represented as linked data by URIs to NCBI's species taxonomy. We encourage the use of identifiers.org URIs for other entities, which eventually be automatically generated in a future release of BioInterchange.

The design patterns of GFVO follow the SIO and equivalence mappings are provided for GFVO's classes, object- and datatype-properties where applicable.

Statistics

Summary statistics about the number of classes and properties of GFVO are provided in the following table. The breakdown of the classes based on their modeling origin does not sum up to the total number of classes, because some modeled classes appear in multiple specifications (e.g., "DNA Sequence" appears in all four specifications).

Total Number Number of Equivalences to SIO Number of Equivalences to SO
Classes1024013
…modeled from GFF323113
…modeled from GTF13112
…modeled from GVF622312
…modeled from VCF42157
Class Metadata
…Wikipedia references53n/an/a
…pairwise disjoint axioms6n/an/a
…disjoint collection axioms13n/an/a
…with property restrictions32n/an/a
Datatype properties110
Object properties32310

Data Structure Mappings between GFVO and Genomic Files

GFVO ClassGFF3 Data StructureGTF Data StructureGVF Data StructureVCF Data Structure
Alias"Alias" attributen/a"Alias" attributen/a
AlleleCountn/an/an/a"AC" additional information; "EC" additional information (requires link to alternate allele)
AlleleFrequencyn/an/a"Variant_freq" attribute"AF" additional information
AminoAcidn/an/a"Variant_aa" attribute; "Reference_aa" attribute; (see GFVO classes "Sequence Variant" and "Reference Sequence" for annotating the amino acid sequence)n/a
AncestralSequencen/an/an/a"AA" additional information
ArrayComparativeGenomicHybridizationn/an/a"data-source" structured pragman/a
Attributecontents of the "attributes" column that are not mapped otherwise"attribute" columncontents of the "attributes" column that are not mapped otherwisecontents of the "INFO" column that are not mapped otherwise
AverageCoveragen/an/a"technology-platform-average-coverage" pragman/a
Base Qualityn/an/an/a"BQ" additional information
BiologicalEntitysee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
BiopolymerSequencingn/an/asee GFVO subclasses "DNASequencing" and "RNASequencing" for applicationsn/a
Breakpointn/an/a"Breakpoint_detail" attribute and "Breakpoint_range" attribute (see also FALDO in Table 4)n/a
Catalogn/an/an/asee GFVO subclass "Haplotype"
Celln/an/asee GFVO subclasses "GermlineCell" and "SomaticCell" and "PrenatalCell"n/a
ChemicalEntitysee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
Chromosomen/an/a"sequencing-scope" pragma (for use with targeted sequencing)n/a
CircularHelix"Is_circular" attribute (see also GFVO class "WatsonCrickHelix")n/a"Is_circular" attribute (see also GFVO class "WatsonCrickHelix")n/a
CodingFrameOffset"phase" column"frame" columnn/a ("phase" column unused)n/a
CodonSequencen/an/a"Variant_codon" attribute; "Reference_codon" attribute; (see GFVO classes "Sequence Variant" and "Reference Sequence" for annotating the codon sequence)n/a
Collectionn/an/asee subclasses "Contig" and "Catalog" and "Scaffold" for applicationssee subclasses "Contig" and "Catalog" and "Scaffold" for applications
Commentcomment lines (beginning with a single "#"; linkage via GFVO properties "isAfter"/"isBefore")comment lines (beginning with a single "#"; linkage via GFVO properties "isAfter"/"isBefore")"Comment" attribute; comment lines (beginning with a single "#"; linkage via GFVO properties "isAfter"/"isBefore")n/a
ConditionalGenotypeQualityn/an/an/a"GQ" additional information
Contign/an/a"sequencing-scope" pragma (for use with targeted sequencing)"contig" information field (see also GFVO class "Landmark")
Coveragen/an/asee GFVO class "AverageCoverage""DP" additional information
DNAMicroarrayn/an/a"data-source" structured pragman/a
DNASequence"FASTA" annotationn/a"sequencing-scope" pragma (for use with targeted sequencing)n/a
DNASequencingn/an/a"data-source" structured pragman/a
Exomen/an/a"sequencing-scope" pragman/a
ExperimentalMethod"source" column"source" column"source" column; "capture-method" pragma (for use with exome and targeted sequencing)"CHROM" column; "VALIDATED" additional information (GFVO class instance does not need to be further annotated)
ExternalReference"Dbxref" attribute; "genome-build" pragma"source" column"Dbxref" attribute; "genome-build" pragma; "source-method" structured pragma; "attribute-method" structured pragma; "phenotype-description" structured pragma (see also GFVO class "Phenotype"); "phased-genotypes" structured pragma"assembly" information field (encouraged to include the linked FASTA file contents; compare to GVF FASTA annotations); "pedigreeDB" information field; "DB" additional information (link to dbSNP via GFVO property "hasEvidence"); "H2" additional information and "H3" additional information (link to HapMap via GFVO property "hasEvidence"); "1000G" additional information (link to 1000 Genomes via GFVO property "hasEvidence")
Featurerows with 9-tab delimiters (see "Description of the Format")every line (see "Fields")rows with 9-tab delimiters (see "Column Descriptions"); "Variant_effect" attribute (see also GFVO’s "is_affected_by" property)data lines (see section 1.4 of the specification)
Femalen/an/a"sex" pragman/a
Filen/an/a"reference_fasta" pragma and "feature-gff3" pragma (it is encouraged to load and encode for the referenced file contents)n/a
ForwardReferenceSequenceFrameshift"Target" attributen/a"Target" attribute; utilized by "sequence-alignment" pragmautilized by "CIGAR" additional information
FragmentReadPlatformn/an/a"technology-platform-read-type" pragman/a
FunctionalSpecificationsee GFVO subclass "Genotype" for applicationssee GFVO subclass "Genotype" for applicationssee GFVO subclass "Genotype" for applicationssee GFVO subclass "Genotype" for applications
GameticPhasen/an/a"Phase" attribute"GT" additional information (see also GFVO class "Genotype"); "PS" additional information (see also GFVO class "Haplotype")
Genome"genome-build" pragman/a"genome-build" pragma; "sequencing-scope" pragma"Genomes" key/value property in information field ("SAMPLE" information field); "PEDIGREE" information field (relationships via GFVO properties "isAfter"/"isBefore"; labels encoded via GFVO property "hasAttribute" and class "Label")
GenomeAnalysisn/an/an/a"FILTER" information field (applicable if GFVO classes "Genotyping" and "VariantCalling" are not applicable; see also GFVO property "isRefutedBy")
GenomicAscertainingMethodn/an/aparent class to classes used with the "data-source" structured pragman/a
Genotypen/an/a"Genotype" attribute"GT" additional information (see also GFVO class "GameticPhase")
Genotypingn/an/an/a"FILTER" information field (see also GFVO property "isRefutedBy")
GermlineCelln/an/a"genomic-source" pragman/a
Haplotypen/an/an/a"HQ" additional information (see also GFVO class "PhredScore")
HelixStructuresee GFVO subclasses "CircularHelix" and "WatsonCrickHelix" for applicationsn/asee GFVO subclasses "CircularHelix" and "WatsonCrickHelix" for applicationsn/a
Hemizygousn/an/a"Zygosity" attributenot explicitly specified; can be applied to genotypes (see GFVO class "Genotype")
Heritagen/an/asee GFVO subclasses "MaternalHeritage" and "PaternalHeritage"see GFVO subclasses "MaternalHeritage" and "PaternalHeritage"
Hermaphroditen/an/aunspecified; potential future use with "sex" pragman/a
Heterozygousn/an/a"Zygosity" attributenot explicitly specified; can be applied to genotypes (see GFVO class "Genotype")
Homozygousn/an/a"Zygosity" attributenot explicitly specified; can be applied to genotypes (see GFVO class "Genotype")
Identifier"seqid" column; "ID" attribute"seqname" column"seqid" column; "ID" attribute; "individual-id" pragma; "technology-platform-machine-id" pragma"CHROM" column; "ID" key/value property
InformationContentEntityn/an/an/a"FORMAT" information field
Labeln/an/an/a"PEDIGREE" information field (see also GFVO class "Genome")
Landmark"seqid" column; "sequence-region" pragma; "FASTA" annotation"seqname" column; "DNA" "##"-line type and "RNA" "##"-line type and "Protein" "##"-line type"seqid" column; "sequence-region" pragma; "FASTA" annotation"CHROM" column; "contig" information field (see also GFVO class "Contig")
Likelihoodn/an/an/a"GL" additional information; "GP" additional information (use with GFVO property "isSupportedBy" and GFVO class "ExperimentalMethod" or its descendants)
LikelihoodOfHeterogeneousPloidyn/an/an/a"GLE" additional information
Locus"start" column; "end" column; "strand" column"start" column; "end" column; "strand" column"start" column; "end" column; "strand" column; "Start_range" attribute; "End_range" attribute"POS" column
Malen/an/a"sex" pragman/a
MappingQualityn/an/an/a"MQ" information field
Match"Target" attributen/a"Target" attribute; utilized by "sequence-alignment" pragmautilized by "CIGAR" additional information
MaterialEntitysee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
MaternalHeritagen/an/aunspecified; potential use in phased genotypesunspecified; potential use in phased genotypes
Name"genome-build" pragma"feature" column"genome-build" pragma; "population" pragma; "technology-platform-name" pragman/a
Noten/an/a"sample-description" pragma; "Comment" key/value pairs in structured attributes"Description" key/value property in information fields; "SB" information field (chosen due to ambiguous definition of strand bias)
NumberOfReadsn/an/a"Variant_reads" attribute"MQ0" attribute (with GFVO property "hasQuality" and GFVO class "MappingQuality" instance with value 0)
Objectsee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
PairedEndReadPlatformn/an/a"technology-platform-read-type" pragman/a
PaternalHeritagen/an/aunspecified; potential use in phased genotypesunspecified; potential use in phased genotypes
PeptideSequence"FASTA" annotationn/a"FASTA" annotationn/a
Phenotypen/an/a"phenotype-description" structured pragma (see also GFVO class "Phenotype")n/a
PhredScoren/an/a"score" column"QUAL" column; "PL" additional information (linked to GFVO class "Genotype"); "HQ" additional information (see also GFVO class "Haplotype"); "PQ" additional information (see also GFVO "GameticPhase")
PrenatalCelln/an/a"genomic-source" pragma (deprecated class; meaning questioned in the specification)n/a
Processsee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
ProteinSequencen/an/a"sequencing-scope" pragma (for use with targeted sequencing)n/a
Proteomen/an/a"sequencing-scope" pragma (anticipated future use)n/a
Qualitysee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
Quantitysee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
RNASequencingn/an/a"data-source" structured pragman/a
ReferenceSequencen/an/a"Reference_seq" attribute; "Sequence_context" attribute (see also GFVO properties "isBefore"/"isAfter")"REF" column
ReferenceSequenceGap"Target" attributen/a"Target" attribute; utilized by "sequence-alignment" pragmautilized by "CIGAR" additional information
ReverseReferenceSequenceFrameshift"Target" attributen/a"Target" attribute; utilized by "sequence-alignment" pragmautilized by "CIGAR" additional information
Samplen/an/a"sample-description" pragma"SAMPLE" information field
SampleCountn/an/an/a"NS" additional information
SampleMixturen/an/an/a"Mixture" key/value property in information fields ("SAMPLE" information field)
Scaffoldn/an/a"sequencing-scope" pragma (for use with targeted sequencing)n/a
Score"score" column"score" column"score" column; "score-method" structured pragmauses subclasses of "Score" (see GFVO classes "Phred Score" and "Conditional Genotype Quality")
Sequencesee subclasses for applicationsn/a""sequencing-scope" pragma (for use with targeted sequencing) see subclasses for further applications"n/a
SequenceAlignment"Target" attributen/a"Target" attribute; "sequence-alignment" pragma"CIGAR" additional information
SequenceAlignmentOperationsee subclasses for applicationssee subclasses for applicationssee subclasses for applicationssee subclasses for applications
SequenceVariantn/an/a"Variant_seq" attribute"ALT" column; "ALT" information field (with SO annotation)
SequencedIndividualn/an/a"Individual" attribute; "multi-individual" pragmanot within specification; but could be applied by data providers (see GFVO class "Haplotype")
SequencingTechnologyPlatformn/an/a"technology-platform-class" pragma; composite for aggregating "technology-platform-name" pragma and "technology-platform-version" pragma and "technology-platform-machine-id" pragma and "technology-platform-read-length" pragma and "technology-platform-read-type" pragma and "technology-platform-read-pair-span" pragma and "technology-platform-average-coverage" pragma; "technology-platform" structured pragman/a
Sexn/an/a"sex" pragman/a
SomaticCelln/an/a"genomic-source" pragma"SOMATIC" additional information (use with GFVO property "refersTo")
Spanfor use with "SequenceAlignmentOperation"n/afor use with "SequenceAlignmentOperation"; "technology-platform-read-length" pragma and "technology-platform-read-pair-span" pragman/a
TargetSequenceGap"Target" attributen/a"Target" attribute; utilized by "sequence-alignment" pragmautilized by "CIGAR" additional information
TotalNumberOfAllelesn/an/an/a"AN" additional information
TotalNumberOfReadsn/an/a"Total_reads" attribute"DP" additional information
VariantCallingn/an/a"variant-calling" pragma"FILTER" information field (see also GFVO property "isRefutedBy")
Version"gff-version" pragma"gff-version" "##"-line type"gvf-version" pragma; "file-version" pragma; "technology-platform-version" pragma"fileformat" meta-information line
WatsonCrickHelix"Is_circular" attribute (see also GFVO class "CircularHelix")n/a"Is_circular" attribute (see also GFVO class "CircularHelix")n/a
Zygosityn/an/asee specific GFVO classes "Heterozygous" and "Homozygous" and "Hemizygous"see specific GFVO classes "Heterozygous" and "Homozygous" and "Hemizygous"

Examples

Examples are provided in Turtle syntax. All examples are archived and downloadable as the file "gfvo_examples.ttl" of the ontologies' GitHub repository.

Example 1: Loci and Basic Genomic Feature Annotation of a Gene and its Transcription Factor Binding Site

Encoding loci and basic genomic feature annotations. The example covers lines 0-3 of the example gene description given in the GFF3 specification.

@prefix : <http://www.biointerchange.org/gfvo#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix faldo: <http://biohackathon.org/resource/faldo#> .
@prefix so: <http://purl.bioontology.org/ontology/SO/SO> .

#################################################################
#
#    Example 1
#
#    Encoding loci and basic genomic feature annotations. The
#    example covers lines 0-3 of the example gene description
#    given in the GFF3 specification.
#           (http://www.sequenceontology.org/resources/gff3.html)
#
#    Please note that this seemingly verbose data representation
#    is slighly misleading. The reuse of non-literals as well as
#    binary RDF encodings such as RDF/HDT permits a more concise
#    representation of the same data.
#
#    This example also avoids blank nodes, so that this file can
#    be conveniently viewed using the Protege ontology editor.
#    Using blank nodes, the line
#
#        :hasIdentifier :ExampleSet1Feature1Identifier ;
#
#    can be substituted with
#
#        :hasIdentifier [
#            a :Identifier ;
#            :hasValue "gene00001" ;
#        ]
#
#################################################################

# This example is representing the contents of a GFF3 file, version 3.
:Example1Version a :Version ;
                 :hasValue "gff-version 3" .

# Two genomic features are described in the file, where an extra comment
# was added to clarify the provenance of this example representation.
:ExampleSet1 a :File ;
             :hasIdentifier :Example1Version ;
             :hasMember :ExampleSet1Feature1 ,
                        :ExampleSet1Feature2 ;
             rdfs:comment "A simple example of a hierarchical genomic feature dependency. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .

# Features in this example are placed on a single langmark, which has
# an identifier associated with it (it cannot be anonymous in GFF3, even
# though GFVO permits landmarks without explicit identifier), and it
# has a range of sequence positions it covers (expressed by a separate
# pragma statement in GFF3).
:ExampleSet1Landmark a :Landmark ;
                     :hasIdentifier :ExampleSet1LandmarkIdentifier ;
                     :hasAttribute :ExampleSet1LandmarkRegion .

:ExampleSet1LandmarkIdentifier a :Identifier ;
                               :hasValue "ctg123" .

:ExampleSet1LandmarkRegion a faldo:Region ;
                           faldo:begin :ExampleSet1LandmarkStartPosition ;
                           faldo:end :ExampleSet1LandmarkEndPosition .

:ExampleSet1LandmarkStartPosition a faldo:ExactPosition ;
                                  faldo:position "1" .

:ExampleSet1LandmarkEndPosition a faldo:ExactPosition ;
                                faldo:position "1497228" .

# GFF3, GTF and GVF make use of named attributes. There are predefined (reserved)
# names, but users can also freely contribute their own attributes. In this example,
# only one labeled attribute is used, whose name we define upfront.
#
# Note: It might be a bit confusing that the label "Name" is applied to an attribute
#       of type "Name". This is just an artifact of the chosen example and it is of
#       course possible to label a "Name" attribute arbitrarily.
:ExampleSet1AttributeName a :Label ;
                          :hasValue "Name" .

# First feature of the GFF3 file (line 2): a gene.
:ExampleSet1Feature1 a :Feature ,
                       so:0000704 ;
                     :isLocatedOn :ExampleSet1Landmark ;
                     :hasPart :ExampleSet1Feature1Locus ;
                     :hasIdentifier :ExampleSet1Feature1Identifier ;
                     :hasAttribute :ExampleSet1Feature1Name .

:ExampleSet1Feature1Locus a :Locus ;
                          :hasAttribute :ExampleSet1Feature1Region .

:ExampleSet1Feature1Region a faldo:Region ;
                           faldo:begin :ExampleSet1FeatureStartPosition ;
                           faldo:end :ExampleSet1Feature1EndPosition .

# The start coordinate of both features is the same in this example. So this
# entity is used by both :ExampleSet1Feature1 and :ExampleSet1Feature2.
:ExampleSet1FeatureStartPosition a faldo:ExactPosition ;
                                 faldo:position "1000" .

:ExampleSet1Feature1EndPosition a faldo:ExactPosition ;
                                faldo:position "9000" .

:ExampleSet1Feature1Identifier a :Identifier ;
                               :hasValue "gene00001" .

:ExampleSet1Feature1Name a :Name ;
                         :hasAttribute :ExampleSet1AttributeName ;
                         :hasValue "EDEN" .

# Second feature of the GFF3 file (line 3): a transcription factor
# binding site.
# It references the first feature via a "Parent" attribute.
:ExampleSet1Feature2 a :Feature ,
                       so:0000235 ;
                     :isLocatedOn :ExampleSet1Landmark ;
                     :hasPart :ExampleSet1Feature2Locus ;
                     :hasIdentifier :ExampleSet1Feature2Identifier ;
                     :hasSource :ExampleSet1Feature1 .

:ExampleSet1Feature2Locus a :Locus ;
                          :hasAttribute :ExampleSet1Feature1Region .

:ExampleSet1Feature2Region a faldo:Region ;
                           faldo:begin :ExampleSet1FeatureStartPosition ;
                           faldo:end :ExampleSet1Feature2EndPosition .

:ExampleSet1Feature2EndPosition a faldo:ExactPosition ;
                                faldo:position "1012" .

:ExampleSet1Feature2Identifier a :Identifier ;
                               :hasValue "tfbs00001" .

Example 2: Encoding of a Sequence Alignment

Encoding of a sequence alignment. This is part of the GFF3 specification, denoting the alignment between the reference sequence "chr3" and the target sequence "EST23".

@prefix : <http://www.biointerchange.org/gfvo#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix faldo: <http://biohackathon.org/resource/faldo#> .
@prefix so: <http://purl.bioontology.org/ontology/SO/SO> .

#################################################################
#
#    Example 2
#
#    Encoding of a sequence alignment. This is part of the GFF3
#    specification, denoting the alignment between the reference
#    sequence "chr3" and the target sequence "EST23".
#           (http://www.sequenceontology.org/resources/gff3.html)
#
#################################################################

:ExampleSet2 a :Collection ;
             :hasMember :ExampleSet2Feature1 ,
                        :ExampleSet2Feature2 ;
             rdfs:comment "An example of a sequence alignment. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .

:ExampleSet2Landmark a :Landmark ;
                     :hasIdentifier :ExampleSet2LandmarkIdentifier .

:ExampleSet2LandmarkIdentifier a :Identifier ;
                               :hasValue "chr3" .

# Reference sequence feature:
:ExampleSet2Feature1 a :Feature ;
                     :isLocatedOn :ExampleSet2Landmark ;
                     :hasIdentifier :ExampleSet2Feature1Identifier .

:ExampleSet1Feature1Identifier a :Identifier ;
                               :hasValue "Match1" .

# Target sequence feature:
:ExampleSet2Feature2 a :Feature ;
                       so:0000343 ;
                     :isLocatedOn :ExampleSet2Landmark ;
                     :hasIdentifier :ExampleSet2Feature2Identifier .

:ExampleSet1Feature2Identifier a :Identifier ;
                               :hasValue "EST23" .

# Description of the sequence alignment between :ExampleSet2Feature1
# and :ExampleSet2Feature2 (features "Match1" and "EST23").
:ExampleSet2SequenceAlignment a :SequenceAlignment ;
                              :hasAttribute :ExampleSet2AlignmentLocus ;
                              :hasSource :ExampleSet2Feature1 ;
                              :hasInput :ExampleSet2Feature2 ;
                              :hasFirstPart :ExampleSet2AlignmentOperation1 ;
                              :hasOrderedPart :ExampleSet2AlignmentOperation2 ,
                                              :ExampleSet2AlignmentOperation3 ,
                                              :ExampleSet2AlignmentOperation4 ;
                              :hasLastPart :ExampleSet2AlignmentOperation5 .

# The locus describes the region over which the alignment operation
# is being carried out.
:ExampleSet2AlignmentLocus a :Locus ;
                           :hasAttribute :ExampleSet2AlignmentRegion .

:ExampleSet2AlignmentRegion a faldo:Region ;
                            faldo:begin :ExampleSet2AlignmentStartPosition ;
                            faldo:end :ExampleSet2AlignmentEndPosition .

:ExampleSet2AlignmentStartPosition a faldo:ExactPosition ;
                                   faldo:position "1" .

:ExampleSet2AlignmentEndPosition a faldo:ExactPosition ;
                                 faldo:position "21" .

# Description of an actual alignment operation.
:ExampleSet2AlignmentOperation1 rdf:type :Match ;
                                :hasAttribute ::ExampleSet2AlignmentOperation1Span ;
                                :isBefore :ExampleSet2AlignmentOperation2 .

:ExampleSet2AlignmentOperation1Span a :Span ;
                                    :hasValue "8" .

:ExampleSet2AlignmentOperation2 rdf:type :TargetSequenceGap ;
                                :hasAttribute ::ExampleSet2AlignmentOperation2Span ;
                                :isAfter :ExampleSet2AlignmentOperation1 ;
                                :isBefore :ExampleSet2AlignmentOperation3 .

:ExampleSet2AlignmentOperation2Span a :Span ;
                                    :hasValue "3" .

:ExampleSet2AlignmentOperation3 rdf:type :Match ;
                                :hasAttribute ::ExampleSet2AlignmentOperation3Span ;
                                :isAfter :ExampleSet2AlignmentOperation2 ;
                                :isBefore :ExampleSet2AlignmentOperation4 .

:ExampleSet2AlignmentOperation3Span a :Span ;
                                    :hasValue "6" .

:ExampleSet2AlignmentOperation4 rdf:type :ReferenceSequenceGap ;
                                :hasAttribute ::ExampleSet2AlignmentOperation4Span ;
                                :isAfter :ExampleSet2AlignmentOperation3 ;
                                :isBefore :ExampleSet2AlignmentOperation5 .

:ExampleSet2AlignmentOperation4Span a :Span ;
                                    :hasValue "1" .

:ExampleSet2AlignmentOperation5 rdf:type :Match ;
                                :hasAttribute ::ExampleSet2AlignmentOperation5Span ;
                                :isAfter :ExampleSet2AlignmentOperation4 .

:ExampleSet2AlignmentOperation5Span a :Span ;
                                    :hasValue "6" .

Example 3: Phased and Unphased Genotype and its Sequence Variants

Encoding of a phased/unphased genotype and its sequence variants. This is part of the GVF specification, denoting two variants for two separate sequenced individuals: "Variant_seq=A,T;Genotype=0:1,1:1". See "Genotype" in the GVF specification.

@prefix : <http://www.biointerchange.org/gfvo#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

#################################################################
#
#    Example 3
#
#    Encoding of genotypes/sequence variants. This is part of the GVF
#    specification, denoting two variants for two separate
#    sequenced individuals: "Variant_seq=A,T;Genotype=0:1,1:1".
#    (See "Genotype" in the GVF specification at
#     http://www.sequenceontology.org/resources/gvf.html)
#
#################################################################

:ExampleSet3 a :Collection ;
             :hasMember :ExampleSet3Feature1 ;
             rdfs:comment "Encoding of genotypes/sequence variants. This example is part of the GVF specification, denoting two variants for two separate sequenced individuals (http://www.sequenceontology.org/resources/gvf.html)."@en .

# The individuals that were sequenced are represented by named, but otherwise
# unspecified, instances. This provides sufficient information to distinguish
# between the individuals that were sequenced.
:ExampleSet3SequencedIndividual1 rdf:type :SequencedIndividual .
:ExampleSet3SequencedIndividual2 rdf:type :SequencedIndividual .

# Genomic feature that captures the two described genotypes.
:ExampleSet3Feature1 a :Feature ;
                     :hasAttribute :ExampleSet3Genotype1 ,
                                   :ExampleSet3Genotype2 .

# Genotype for the first individual.
#
# The genotype's phased variants are linked via "hasFirstPart" and
# "hasLastPart" here, which are descendants of &qout;hasOrderedPart".
# The object properties "isBefore"/"isAfter" connect the phased variants.
#
# Note: for an unphased genotype, it is sufficient to use "hasPart" only.
:ExampleSet3Genotype1 a :Genotype ;
                      :hasParticipant :ExampleSet3SequencedIndividual1 ;
                      :hasQuality :Heterozygous ;
                      :hasAttribute :ExampleSet3Phase ;
                      :hasFirstPart :ExampleSet3ReferenceA_AT ;
                      :hasLastPart :ExampleSet3VariantT_AT .

# Ordering of the variants permits the expression of phased genotypes.
# It is recommended to use "isBefore", but the use of "isAfter" is optional.
:ExampleSet3ReferenceA_AT :isBefore :ExampleSet3VariantT_AT .
:ExampleSet3VariantT_AT :isAfter :ExampleSet3ReferenceA_AT .

# Genotype of the second individual.
:ExampleSet3Genotype2 a :Genotype ;
                      :hasParticipant :ExampleSet3SequencedIndividual2 ;
                      :hasQuality :Homozygous ;
                      :hasAttribute :ExampleSet3Phase ;
                      :hasFirstPart :ExampleSet3VariantT_TT ;
                      :hasLastPart :ExampleSet3VariantT_TT .

# As above: variant ordering to phase the genotype.
:ExampleSet3VariantT_TT :isBefore :ExampleSet3VariantT_TT ;
                        :isAfter :ExampleSet3VariantT_TT .

# Having an instance to denote the presence of phase information
# might appear redundant across data sets. On the other hand, it
# permits data providers to enrich their own or other providers'
# data set with additional information (annotations) about used
# protocols/equipment/tools.
:ExampleSet3Phase a :GameticPhase .

# For VCF data, the type can also be "ReferenceSequence", which
# denotes that the sequence is located on a reference genome. This
# would be indicated -- in a VCF file -- by a "0" in the GT field
# (e.g., "0|1" (phased) or "0/1" (unphased) to indicate a genotype
# whose first allele is on the reference genome and the second allele
# is an alternative allele).
:ExampleSet3ReferenceA_AT a :ReferenceSequence ;
                          :hasValue "A" .

:ExampleSet3VariantT_AT a :SequenceVariant ;
                        :hasValue "T" .

:ExampleSet3VariantT_TT a :SequenceVariant ;
                        :hasValue "T" .

Example 4: Encoding of a Phred Score

Encoding of a Phred score, which is part of the GVF specification, but more widely utilized in the VCF specification.

@prefix : <http://www.biointerchange.org/gfvo#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

#################################################################
#                                                                
#    Example 4                                                   
#                                                                
#    Encoding of a Phred score. GVF leaves it open how the       
#    "score" (column 6) should be interpreted, but recommends    
#    the use of Phred scores. If a data provider knows that      
#    a Phred score was utilized, then this can be represented    
#    via GFVO.                                                   
#    (See "Column Descriptions" in the GVF specification at      
#     http://www.sequenceontology.org/resources/gvf.html)        
#                                                                
#################################################################
                                                                 
:ExampleSet4 a :Collection ;                                     
             :hasMember :ExampleSet4Feature1 ;                   
             rdfs:comment "Encoding of a Phred score. This example is motivated by the GVF specification, which encourages -- but does not enforce -- the use of Phred scores (http://www.sequenceontology.org/resources/gvf.html)."@en .
                                                                 
# Interpreting "score" (column 6) of a GVF file as Phred score.  
:ExampleSet4Feature1 a :Feature ;                                
                     :hasAttribute :ExampleSet4Feature1Score .   
                                                                 
# Use of "PhredScore" instead of "Score" to denote the specific  
# type of score being used.
:ExampleSet4Feature1Score a :PhredScore ;                        
                          :hasValue 38 .

Ontology Reference

Ontology namespace "gfvo": http://www.biointerchange.org/gfvo#

Classes

Class "Alias"
Subclass of: Name
Label: Alias
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Pseudonym
GFF3GVF

Class "AlleleCount"
Subclass of: Quantity
Label: Allele Count
Comment:
Count of a specific allele in genotypes.
Encodes for "AC" additional information in VCF files.
VCF

Class "AlleleFrequency"
Subclass of: Quantity
Label: Allele Frequency
Comment:
Proportion of a particular gene allele in a gene pool or genotype.
Encodes for "AF" additional information in VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Allele_frequency
GVFVCF

Class "AminoAcid"
Subclass of: ChemicalEntity
Label: Amino Acid
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Amino_acid
External class equivalences: SO_0001237SIO_010074
GVF

Class "AncestralSequence"
Subclass of: ReferenceSequence
Label: Ancestral Sequence
Comment:
Denotes an ancestral allele of a feature.
May be used to denote the "ancestral allele" ("AA" additional information) of VCF formatted files.
Wikipedia reference: http://en.wikipedia.org/wiki/Ancestral_reconstruction
VCF

Class "ArrayComparativeGenomicHybridization"
Subclass of: GenomicAscertainingMethod
Label: Array Comparative Genomic Hybridization
Comment:
Feature provenance is based on array-comparative genomic hybridization.
Used by the "data-source" structured pragma in GVF.
GVF

Class "Attribute"
Label: Attribute
Comment:
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.
External class equivalence: SIO_000614

Class "AverageCoverage"
Subclass of: Coverage
Label: Average Coverage
Comment:
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).
Wikipedia reference: http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage
GVF

Class "BaseQuality"
Subclass of: Score
Label: Base Quality
Comment:
Root mean square base quality.
Accounts for "BQ" additional information in VCF files.
VCF

Class "BiologicalEntity"
Subclass of: MaterialEntity
Label: Biological Entity
Comment:
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.
External class equivalence: SIO_010046

Class "BiopolymerSequencing"
Subclass of: GenomicAscertainingMethod
Label: Biopolymer Sequencing
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Sequencing

Class "Breakpoint"
Subclass of: Locus
Label: Breakpoint
Comment:
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.
External class equivalence: SO_0000699
GVF

Class "Catalog"
Subclass of: Collection
Label: Catalog
Comment:
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.
External class equivalence: SIO_001241

Class "Cell"
Subclass of: BiologicalEntity
Label: Cell
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Cell_(biology)
External class equivalence: SIO_010001

Class "ChemicalEntity"
Subclass of: MaterialEntity
Label: Chemical Entity
Comment:
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.
External class equivalence: SIO_010004

Class "Chromosome"
Subclass of: ChemicalEntity
Label: Chromosome
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Chromosome
External class equivalences: SO_0000340SIO_000899
GVF

Class "CircularHelix"
Subclass of: HelixStructure
Label: Circular Helix
Comment:
A circular helix structure.
Can be used to indicate a true "Is_circular" attribute in GFF3 and GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Circular_DNA
GFF3GVF

Class "CodingFrameOffset"
Subclass of: Quality
Label: Coding Frame Offset
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Reading_frame
GTFGVF

Class "CodonSequence"
Subclass of: DNASequence
Label: Codon Sequence
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Codon
External class equivalence: SO_0000360
GVF

Class "Collection"
Subclass of: InformationContentEntity
Label: Collection
Comment:
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).
External class equivalence: SIO_000616
GFF3GTFGVFVCF

Class "Comment"
Subclass of: InformationContentEntity
Label: Comment
Comment:
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.
External class equivalence: SIO_001167

Class "ConditionalGenotypeQuality"
Subclass of: PhredScore
Label: Conditional Genotype Quality
Comment:
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.
VCF

Class "Contig"
Subclass of: Collection
Label: Contig
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Contig
External class equivalence: SO_0000149
GVFVCF

Class "Coverage"
Subclass of: Quantity
Label: Coverage
Comment:
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.
VCF

Class "DNAMicroarray"
Subclass of: GenomicAscertainingMethod
Label: DNA Microarray
Comment:
Feature information is based on DNA microarray probes.
Used by the "data-source" structured pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/DNA_microarray_experiment
External class equivalence: SIO_001076
GVF

Class "DNASequence"
Subclass of: Sequence
Label: DNA Sequence
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Dna_sequence
External class equivalence: SIO_010016
GFF3GTFGVFVCF

Class "DNASequencing"
Subclass of: BiopolymerSequencing
Label: DNA Sequencing
Comment:
Information about features and variants is based on DNA sequencing.
Used by the "data-source" structured pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/DNA_sequencing
GVF

Class "Exome"
Subclass of: BiologicalEntity
Label: Exome
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Exome
GVF

Class "ExperimentalMethod"
Subclass of: Process
Label: Experimental Method
Comment:
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.
External class equivalence: SIO_000999
GFF3GTFGVFVCF

Class "ExternalReference"
Subclass of: InformationContentEntity
Label: External Reference
Comment:
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.
External class equivalence: SIO_001171
GFF3GTFGVFVCF

Class "Feature"
Subclass of: InformationContentEntity
Label: Feature
Comment:
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.
External class equivalences: SO_0000110SIO_010065
GFF3GTFGVFVCF

Class "Female"
Subclass of: Sex
Label: Female
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Female
External class equivalence: SIO_010052
GVF

Class "File"
Subclass of: Collection
Label: File
Comment:
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.
External class equivalence: SIO_000396
GFF3GTFGVFVCF

Class "ForwardReferenceSequenceFrameshift"
Subclass of: SequenceAlignmentOperation
Label: Forward Reference Sequence Frameshift
Comment:
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.
GFF3GVFVCF

Class "FragmentReadPlatform"
Subclass of: SequencingTechnologyPlatform
Label: Fragment Read Platform
Comment:
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.
GVF

Class "FunctionalSpecification"
Subclass of: InformationContentEntity
Label: Functional Specification
Comment:
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.
External class equivalence: SIO_000315

Class "GameticPhase"
Subclass of: Quality
Label: Gametic Phase
Comment:
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.
Wikipedia reference: http://en.wikipedia.org/wiki/Gametic_phase
GVFVCF

Class "Genome"
Subclass of: BiologicalEntity
Label: Genome
Comment:
Representation of a genome. Genomic features that constitute the genome may be linked via one or more Collection, Catalog, Contig, Scaffold or File instances.
Genome can be used for describing data contents of the "genome-build" and "sequencing-scope" pragmas in GVF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Genome
External class equivalences: SO_0001026SIO_000984
GVFVCF

Class "GenomeAnalysis"
Subclass of: ExperimentalMethod
Label: Genome Analysis
Comment:
A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly.
Genome Analysis can be instantiated for cases where an application of "FILTER" in VCF cannot be linked to Genotyping or Variant Calling, which are subclasses of Genome Analysis. If possible, further annotation should be provided to indicate the actually utilized filter type.
Wikipedia reference: http://en.wikipedia.org/wiki/Genomics#Genome_analysis
VCF

Class "GenomicAscertainingMethod"
Subclass of: ExperimentalMethod
Label: Genomic Ascertaining Method
Comment:
Provides information about the source of data.
Subclasses of the class can be used to encode for the "data-source" structured pragma in GVF.
GVF

Class "Genotype"
Subclass of: FunctionalSpecification
Label: Genotype
Comment:
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.
A genotype is denoted by a string of slash-separated list of alleles (has value property). The length of the list is dependent on the ploidy of the studied species as well as sequencing technique used.
Example: "A/G" denotes a genotype with alleles "A" and "G".
Encodes for the Genotype attribute in GVF and "GT" additional information in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Genotype
External class equivalences: SO_0001027SIO_001079
GVFVCF

Class "Genotyping"
Subclass of: GenomeAnalysis
Label: Genotyping
Comment:
Genotyping is the process of determining the genetics of an individual or sample. The genotype itself is expressed as the difference of genetic mark-up compared to a reference genome.
Applicable to the "FILTER" information field in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Genotyping
VCF

Class "GermlineCell"
Subclass of: Cell
Label: Germline Cell
Comment:
The germline feature class captures information about genomic sequence features arising from germline cells.
VCF files permit the explicit annotation with Somatic Cell via "SOMATIC" additional information. The absence of that field does not imply the presence of germine cell material though. Describes the "genomic-source" pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Germline
GVF

Class "Haplotype"
Subclass of: Catalog
Label: Haplotype
Comment:
A Haplotype is a collection of Genotype or Sequence Variant instances. It can imply that a set of genes is inherited as a group, or alternatively, that the set of genotypes or sequence variance has a biological function when acting together (e.g., there exists a disease association).
Haplotype instances should only catalog a single type, i.e. either Genotype or Sequence Variant instances; they should not mix both types (see also Catalog).
Encodes for "HQ" additional information in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Haplotype
External class equivalence: SO_0001024
VCF

Class "HelixStructure"
Subclass of: Quality
Label: Helix Structure
Comment:
Helix Structure denotes the physical shape of biopolymers.
The subclasses Circular Helix and Watson-Crick Helix can be used to for encoding the "Is_circular" attribute in GFF3 and GVF files.
Wikipedia reference: http://en.wikipedia.org/wiki/DNA_helix

Class "Hemizygous"
Subclass of: Zygosity
Label: Hemizygous
Comment:
A sequence alteration with hemizygous alleles.
This quality can be used to directly encode for the Zygosity attribute in GVF files and it indirectly describes genotypes in VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Zygosity#Hemizygous
GVF

Class "Heritage"
Subclass of: Quality
Label: Heritage
Comment:
Heritage denotes the passing of traits from parents or ancestors. Passed traits may not be visible as a phenotype, but instead, might only manifest as genetic inheritance.
Wikipedia reference: http://en.wikipedia.org/wiki/Heredity

Class "Hermaphrodite"
Subclass of: Sex
Label: Hermaphrodite
Comment:
Denoting sex of an individual that contains both male and female gametes.
Wikipedia reference: http://en.wikipedia.org/wiki/Hermaphrodite
External class equivalence: SIO_000784

Class "Heterozygous"
Subclass of: Zygosity
Label: Heterozygous
Comment:
A sequence alteration with heterozygous alleles.
This quality can be used to directly encode for the Zygosity attribute in GVF files and it indirectly describes genotypes in VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Zygosity#Heterozygous
GVF

Class "Homozygous"
Subclass of: Zygosity
Label: Homozygous
Comment:
A sequence alteration with homozygous alleles.
This quality can be used to directly encode for the Zygosity attribute in GVF files and it indirectly describes genotypes in VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Zygosity#Homozygous
GVF

Class "Identifier"
Subclass of: Label
Label: Identifier
Comment:
An identifier labels an entity with preferably a single term that is interpreted as an accession. An accession labels entities that are part of a collection of similar type. More generic naming of entities can be achieved using the Label class.
Encodes for the "seqid" column in GFF3 and GVF; encodes for the "seqname" column in GTF and "CHROM" column in VCF. Captures the "ID" attribute in GFF3 and GVF. Suitable for expression values of "individual-id" and "technology-platform-machine-id" pragmas in GVF. Encodes for the "ID" key/value property in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Identifier
External class equivalence: SIO_000115
GFF3GTFGVFVCF

Class "InformationContentEntity"
Subclass of: Object
Label: Information Content Entity
Comment:
An information content entity is a data structure or data type that requires background information or specific domain knowledge to be interpreted correctly. Information content entities can be of simple structure, such as Label that only requires the application of has value to be meaningful, or, they can be of complex structure such as Locus which becomes meaningful with multiple FALDO annotations.
External class equivalence: SIO_000015

Class "Label"
Subclass of: InformationContentEntity
Label: Label
Comment:
A label is a term or short list of terms that describe an entity for the purpose of distinguishing it from entities of similar type. It should be considered to utilize the Identifier class, if labels of entities are sufficiently unique to actually identify them.
Encodes for the "PEDIGREE" information field in VCF.
External class equivalence: SIO_000179
VCF

Class "Landmark"
Subclass of: Identifier
Label: Landmark
Comment:
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.
To annotate a landmark with a biological type, it is encouraged to use terms of the Sequence Ontology, but not the classes Chromosome, Scaffold and Contig. The latter classes are used for describing ploidy within a dataset as well as offering means of data aggregation.
Encodes for the "seqid" column in GFF3 and GVF; encodes for the "seqname" column in GTF and "CHROM" column in VCF. Captures the "sequence-region" pragma in in GFF3 and GVF as well as their "FASTA" annotation. Encodes for "DNA", "RNA" and "Protein" "##"-lines in GTF. Captures the "contig" information field in VCF.
GFF3GTFGVFVCF

Class "Likelihood"
Subclass of: Quantity
Label: Likelihood
Comment:
A Likelihood is a probability of a certain even occurring.
For use with "GL" and "GP" additional information in VCF files.
External class equivalence: SIO_001243
VCF

Class "LikelihoodOfHeterogeneousPloidy"
Subclass of: Likelihood
Label: Likelihood of Heterogeneous Ploidy
Comment:
Likelihood of Heterogeneous Ploidy expresses the likelihood of genotypes in absence of copy number data.
Specifically designed to encode for values of "GLE" additional information in VCF files.
VCF

Class "Locus"
Subclass of: InformationContentEntity
Label: Locus
Comment:
A locus refers to a position within a designated genomic landmark. Actual locus coordinates should be provided using classes of the Feature Annotation Location Description Ontology.
The class encodes for the "start", "end" and "strand" columns in GFF3, GTF, and GVF and for the "POS" column in VCF. It also encodes the "Start_range" and "End_range" attributes in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Locus_(genetics)
External class equivalence: SIO_000056
GFF3GTFGVFVCF

Class "Male"
Subclass of: Sex
Label: Male
Comment:
Denoting sex of a male individual, who is defined as an individual producing spermatozoa.
This quality can be used to encode for the "sex" pragma in GVF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Male
External class equivalence: SIO_010048
GVF

Class "MappingQuality"
Subclass of: Score
Label: Mapping Quality
Comment:
Root mean square mapping quality.
Encodes values of the "MQ" additional information in VCF files.
VCF

Class "Match"
Subclass of: SequenceAlignmentOperation
Label: Match
Comment:
Denotes a match between the reference sequence and target 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.
GFF3GVFVCF

Class "MaterialEntity"
Subclass of: Object
Label: Material Entity
Comment:
A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc.
Material Entity should not be instantiated as such, instead, it is suggested that its subclasses Genome, DNA Sequence, Sample Count, etc. are appropriated.
External class equivalence: SIO_000004

Class "MaternalHeritage"
Subclass of: Heritage
Label: Maternal Heritage
Comment:
Maternal heritage is the passing of traits from a female to her ancestors.
Currently ununsed but might be applicable to phased genotypes in GVF and VCF files; included for future use.
Wikipedia reference: http://en.wikipedia.org/wiki/Maternal_effect

Class "Name"
Subclass of: Label
Label: Name
Comment:
A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity. Unlike an Identifier, a name should not be considered unique.
Encodes for the "feature" column in GTF. Captures the "genome-build" pragma in GFF3 and GVF. Captures the "population", "technology-platform-name" pragmas in GVF.
External class equivalence: SIO_000116
GFF3GTFGVF

Class "Note"
Subclass of: InformationContentEntity
Label:
Comment:
A note is a short textual description about an entity. It provides a formal or semi-formal description of an entity, as opposed to a Comment.
Encodes for the "sample-description" pragma and Comment key/value pairs in structured attributes in GVF. Captures "Description" key/value pairs in information fields and "SB" information field in VCF.
External class equivalence: SIO_000152
GVFVCF

Class "NumberOfReads"
Subclass of: Quantity
Label: Number of Reads
Comment:
Number of reads supporting a particular feature or variant.
Can encode for "MQ0" additional information in VCF files, if additional annotations are provided to denote a mapping quality of zero for the given count. In GVF files, the class accounts for the "Variant_reads" attribute.
GVFVCF

Class "Object"
Label: Object
Comment:
An object is a concrete entity that realizes a concept and encapsulates data associated with said concept. Objects are typically representing tangible entities, such as Chromosome, DNA Sequence, but also objects such as Identifier, Average Coverage or other computational or mathematical entities.
Since an object describes a large body of entities, its use is discouraged. Where applicable, one of its subclasses should be used instead.
External class equivalence: SIO_000776

Class "PairedEndReadPlatform"
Subclass of: SequencingTechnologyPlatform
Label: Paired End Read Platform
Comment:
Details about the paired-end read sequencing technology used to gather the data in a set.
Encodes for the "technology-platform-read-type" pragma in GVF.
GVF

Class "PaternalHeritage"
Subclass of: Heritage
Label: Paternal Heritage
Comment:
Paternal heritage is the passing of traits from a male to his ancestors.
Currently ununsed but might be applicable to phased genotypes in GVF and VCF files; included for future use.
Wikipedia reference: http://en.wikipedia.org/wiki/Maternal_effect#Paternal_effect_genes

Class "PeptideSequence"
Subclass of: Sequence
Label: Peptide Sequence
Comment:
A peptide sequence is an ordered sequence of amino acid residues, but which may not necessarily be a protein sequence. For encoding sequences of proteins, the subclass Protein Sequence should be used.
Encodes for "FASTA" annotation in GFF3 and GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Peptide_sequence
External class equivalence: SO_0000104
GFF3GVF

Class "Phenotype"
Subclass of: Quality
Label: Phenotype
Comment:
A phenotype description represents additional information about a sequenced individual's phenotype. A sequenced individual is represented by instances of the Sequenced Individual class.
Encodes for the "phenotype-description" structured pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Phenotype
External class equivalence: SIO_010056
GVF

Class "PhredScore"
Subclass of: Score
Label: Phred Score
Comment:
The Phred score can be used to assign quality scores to base calls of DNA sequences.
GVF supports the use of Phred scores in the "score" column, but this information needs to be obtained/given by the data provider. In VCF files, the "QUAL" column and "PL", "HQ", and "PQ" additional information carries Phred scores that can be encoded as Phred Score.
GFVO's Score and Phred Score cannot be defined as equivalent to the Sequence Ontology terms "score" (SO:0001685) and "quality_value" (SO:0001686) due to differences in inheritance between the two ontology implementations. GFVO defines Phred Score as a subclass of Score, but the Sequence Ontology defines "score" as a sibling of "quality_value".
Wikipedia reference: http://en.wikipedia.org/wiki/Phred_score
GVFVCF

Class "PrenatalCell"
Subclass of: Cell
Label: Prenatal Cell
Comment:
A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive "##genomic-source", but does not describe its semantics and the referenced Logical Observation Identifiers Names and Codes (LOINC, http://loinc.org), do not define the meaning or intended usage of the term "prenatal" either.
Wikipedia reference: http://en.wikipedia.org/wiki/Prenatal
GVF

Class "Process"
Label: Process
Comment:
A process denotes a temporally dependent entity. It can be thought of as a function, where input data is transformed by an algorithm to produce certain output data.
Since a process describes a large number of entities, its direct use is discouraged. At least Experimental Method or one of its subclasses should be used instead.
External class equivalence: SIO_000006

Class "ProteinSequence"
Subclass of: PeptideSequence
Label: Protein Sequence
Comment:
A protein sequence is a peptide sequence which represents the primary structure of a protein.
Encodes for "sequencing-scope" pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Peptide_sequence
External class equivalence: SIO_010015
GVF

Class "Proteome"
Subclass of: BiologicalEntity
Label: Proteome
Comment:
Representation of a proteome. Features that constitute or contribute to the proteome may be linked via one or more Collection, Catalog, Contig, Scaffold or File instances.
It is envisioned that Proteome could be used for describing data contents of the "sequencing-scope" pragma in GVF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Proteome

Class "Quality"
Subclass of: Attribute
Label: Quality
Comment:
Quality is a specific attribute that is strongly associated with an entity, but whose values are varying and disjunct. Qualities are finite enumerations, such as sex (Female, Male, Hermaphrodite), heritage ("Maternal", "Paternal"), but they also make use of the has value datatype property such as Coding Frame Offset (either "0", "1" or "2").
For encoding numerical qualities, see Base Quality and Mapping Quality, or, Phred Score and Conditional Genotype Quality, which are sub-classes of Score.
External class equivalence: SIO_000005

Class "Quantity"
Subclass of: Object
Label: Quantity
Comment:
A property of a phenomenon, body, or substance, where the property has a value that can be expressed by means of a number. This class is typically not directly instantiated, but instead, its subclasses Allele Frequency, Average Coverage, etc. are used.
External class equivalence: SIO_000052

Class "RNASequencing"
Subclass of: BiopolymerSequencing
Label: RNA Sequencing
Comment:
Information about features and variants is based on RNA sequencing.
Used by the "data-source" structured pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/RNA-Seq
GVF

Class "ReferenceSequence"
Subclass of: DNASequence
Label: Reference Sequence
Comment:
Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the "Variant" class.
Encodes for the "Reference_seq" and "Sequence_context" attributes in GVF and the "REF" column in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Reference_sequence
GVFVCF

Class "ReferenceSequenceGap"
Subclass of: SequenceAlignmentOperation
Label: Reference Sequence Gap
Comment:
Denotes a gap in the reference sequence for an alignment.
Encodes for the "Target" attribute in GFF3, encodes for "Target" attribute and "sequence-alignment" pragma in GVF, and, encodes "CIGAR" additional information in VCF.
GFF3GVFVCF

Class "ReverseReferenceSequenceFrameshift"
Subclass of: SequenceAlignmentOperation
Label: Reverse Reference Sequence Frameshift
Comment:
Denotes a frameshift backwards (reverse) 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.
GFF3GVFVCF

Class "Sample"
Subclass of: ChemicalEntity
Label: Sample
Comment:
A sample is a limited quantity of a chemical entity, which is typically used (destructively/non-desctructively) in a scientific analysis or test.
It can be applied to describe contents of the "sample-description" pragma in GVF files or the "SAMPLE" information field in VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Sample_(material)
External class equivalence: SIO_001050
GVFVCF

Class "SampleCount"
Subclass of: Quantity
Label: Sample Count
Comment:
Number of samples in the dataset.
Encodes for "NS" additional information in VCF files.
VCF

Class "SampleMixture"
Subclass of: Quantity
Label: Sample Mixture
Comment:
Sample mixture determines the proportion of various tissues/cell types in a biological sample that has been taken as part of a biopsy. The sum of various sample mixtures belonging to the same sample should equal 1.
Expresses the "Mixture" key/value pair in "SAMPLE" fields in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Biopsy
VCF

Class "Scaffold"
Subclass of: Collection
Label: Scaffold
Comment:
A scaffold is the aggregation of multiple contigs to form a larger continuous sequencing region. Scaffold is a specialization of a Collection and should be used to aggregate features, but not for indicating that a Landmark is representing a scaffold. It is encouraged that the latter is annotated by a term of the Sequence Ontology.
Encodes for "sequencing-scope" in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Contig
External class equivalence: SO_0000148
GVF

Class "Score"
Subclass of: Object
Label: Score
Comment:
A measure that permits the ranking of entities.
Directly encodes for the "score" column in GFF3, GTF and GVF files; if the actual scoring algorithm is known, then Phred Score might be used to encode for the values of the "score" column in GVF files. The class can encapsule information of the "score-method" pragma in GVF files. For VCF files, the subclasses Phred Score and Conditional Genotype Quality should be used.
GFVO's Score and Phred Score cannot be defined as equivalent to the Sequence Ontology terms "score" (SO:0001685) and "quality_value" (SO:0001686) due to differences in inheritance between the two ontology implementations. GFVO defines Phred Score as a subclass of Score, but the Sequence Ontology defines "score" as a sibling of "quality_value".
Wikipedia reference: http://en.wikipedia.org/wiki/Score_(statistics)
GFF3GTFGVFVCF

Class "Sequence"
Subclass of: ChemicalEntity
Label: Sequence
Comment:
A sequence provides information about any biopolymer sequences. Specialized subclasses are provided to denote specialized instances of sequences, such as Codon Sequence, Reference Sequence, Protein Sequence, etc.
Can be used to encode for the "sequencing-scope" pragma in GVF files. See subclasses for applications in both GFF3 and GVF files.
External class equivalences: SO_0000001SIO_000030
GFF3GTFGVFVCF

Class "SequenceAlignment"
Subclass of: Object
Label: Sequence Alignment
Comment:
A sequence alignment denotes the congruence of two sequences.
In GFF3/GVF, a sequence alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide alignment (see "The Gap Attribute", http://sequenceontology.org/resources/gff3.html). "Alignment Operation" class instances denote the actual steps that the constitute the sequence alignment.
Encodes for the "Target" attribute in GFF3/GVF files as well as the "sequence-alignment" pragma in GVF files. Can encode "CIGAR" additional information of VCF files.
Wikipedia reference: http://en.wikipedia.org/wiki/Sequence_alignment
GFF3GVFVCF

Class "SequenceAlignmentOperation"
Subclass of: ExperimentalMethod
Label: Sequence Alignment Operation
Comment:
A sequence alignment operation captures the type of alignment (see Sequence Alignment) between a reference sequence and target sequence. Note that a Sequence Alignment Operation is situated in a linked list, where the order of the alignment operations is of significance.
Its subclasses are used to encode for the "Target" attribute and "sequence-alignment" pragma in GVF, and, they encode "CIGAR" additional information in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Sequence_alignment

Class "SequenceVariant"
Subclass of: DNASequence
Label: Sequence Variant
Comment:
Describing specific sequence alterations of a genomic feature. A variant is related to "Reference" class instances, which denote the sequence that serves as a basis for sequence alteration comparisons.
Encodes for the "Variant_seq" attribute in GVF. Captures the "ALT" column and "ALT" information field in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Mutation
External class equivalence: SO_0001060
GVFVCF

Class "SequencedIndividual"
Subclass of: BiologicalEntity
Label: Sequenced Individual
Comment:
An abstract representation of a particular individual for representing aggregated sequencing information. Sequenced Individual can also be used to denote complex heritage relationships in genomic samples.
Encodes for the "individual" attribute and "multi-individual" pragma in GVF.
External class equivalence: SIO_010000
GVF

Class "SequencingTechnologyPlatform"
Subclass of: GenomicAscertainingMethod
Label: Sequencing Technology Platform
Comment:
Details about the sequencing/microarray technology used to gather the data in a set.
Encodes for the "technology-platform-class" pragma and is composite for aggregating information of the pragma statements "technology-platform-name", "technology-platform-version", "technology-platform-machine-id", "technology-platform-read-length", "technology-platform-read-type", "technology-platform-read-pair-span", "technology-platform-average-coverage", as well as the structured pragma "technology-platform" in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Read_(Biology)
GVF

Class "Sex"
Subclass of: Quality
Label: Sex
Comment:
Biological sex of a sequenced individual. Subclasses Female and Male can be used to encode for the "sex" pragma in GVF files. The subclass Hermaphrodite is included for potential future use cases.
Wikipedia reference: http://en.wikipedia.org/wiki/Sex
External class equivalence: SIO_010029

Class "SomaticCell"
Subclass of: Cell
Label: Somatic Cell
Comment:
The somatic feature class captures information about genomic sequence features arising from somatic cells.
Encodes for "genomic-source" pragma in GVF and "SOMATIC" additional information in VCF.
Wikipedia reference: http://en.wikipedia.org/wiki/Somatic
GVFVCF

Class "Span"
Subclass of: Quantity
Label: Span
Comment:
A span is an attribute denoting the number of nucleotides or peptides that an entity covers.
This is directly used in conjunction with Sequence Alignment Operation subclasses to express the number of nucleotides a sequence alignment match ranges over, which can be used in conjunction with GFF3/GVF files. The class also covers "technology-platform-read-length" and "technology-platform-read-pair-span" pragmas in GVF files.
GFF3GVF

Class "TargetSequenceGap"
Subclass of: SequenceAlignmentOperation
Label: Target Sequence Gap
Comment:
Denotes a gap in the target sequence for an alignment.
Encodes for the "Target" attribute in GFF3, encodes for "Target" attribute and "sequence-alignment" pragma in GVF, and, encodes "CIGAR" additional information in VCF.
GFF3GVFVCF

Class "TotalNumberOfAlleles"
Subclass of: AlleleCount
Label: Total Number of Alleles
Comment:
Total number of alleles in called genotypes.
Encodes for "AN" additional information in VCF files.
VCF

Class "TotalNumberOfReads"
Subclass of: NumberOfReads
Label: Total Number of Reads
Comment:
Total number of reads covering a feature or variant.
Covers the "Total_reads" attribute in GVF files and the "DP" additional information field in VCF files.
GVFVCF

Class "VariantCalling"
Subclass of: GenomeAnalysis
Label: Variant Calling
Comment:
Denotes the technique of calling genomic feature variants in a genome assembly.
Applicable to the "FILTER" information field in VCF as well as the "variant-calling" pragma in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data
GVFVCF

Class "Version"
Subclass of: Identifier
Label: Version
Comment:
A Version names a release of a software, dataset, or other resource. Versions can follow the common "major.minor.patch" version format, but are not restricted in any way. The version can also incorporate the dataset name (e.g., "HGNC19").
Encodes for the "gff-version" and "gvf-version" pragma statements in GFF3 and GVF, respectively. Encodes for the "gff-version" "##"-line type in GTF. Captures the "fileformat" meta-information line in VCF. Encodes for "file-version" and "technology-platform-version" pragmas in GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Versioning
External class equivalence: SIO_000653
GFF3GTFGVFVCF

Class "WatsonCrickHelix"
Subclass of: HelixStructure
Label: Watson-Crick Helix
Comment:
Helical structure as first proposed by James Watson and Francis Crick, whose work was greatly influenced by discoveries of Rosalind Franklin and Maurice Wilkins.
Can be used to indicate a false "Is_circular" attribute in GFF3 and GVF.
Wikipedia reference: http://en.wikipedia.org/wiki/Non-helical_models_of_DNA_structure#Proposal_of_Watson.E2.80.93Crick_helical_structure
GFF3GVF

Class "Zygosity"
Subclass of: Quality
Label: Zygosity
Comment:
Zygosity denotes the similarities of a specific allele in the genome of an organism. Subclasses can be utilized to directly encode zygosity (e.g., Zygosity attribute in GVF files), or, encode zygosity indirectly by inferring it from genotype descriptions (case in VCF files).
Wikipedia reference: http://en.wikipedia.org/wiki/Zygosity

Object Properties

Object Property "describes"
Label: describes
Comment:
Links to an entity for which supportive information is being provided.
Semanticscience Integrated Ontology property equivalence: SIO_000563

Object Property "hasAnnotation"
Label: has annotation
Comment:
Links to additional annotations about an entity.
Semanticscience Integrated Ontology property equivalence: SIO_000255

Object Property "hasAttribute"
Label: has attribute
Comment:
Links out to aggregate information for an entity.
Semanticscience Integrated Ontology property equivalence: SIO_000008

Object Property "hasEvidence"
Label: has evidence
Comment:
References an entity or resource that provides supporting/refuting evidence.
Semanticscience Integrated Ontology property equivalence: SIO_000772

Object Property "hasFirstPart"
Label: has first part
Comment:
Denotes the first entity of an ordered part relationship.
Semanticscience Integrated Ontology property equivalence: SIO_000971

Object Property "hasIdentifier"
Label: has identifier
Comment:
Links out to an identifier.
Semanticscience Integrated Ontology property equivalence: SIO_000671

Object Property "hasInput"
Label: has input
Comment:
Links out to an entity that is the input of a Process subclass.
Semanticscience Integrated Ontology property equivalence: SIO_000230

Object Property "hasLastPart"
Label: has last part
Comment:
Denotes the last entity of an ordered part relationship.
Semanticscience Integrated Ontology property equivalence: SIO_000972

Object Property "hasMember"
Label: has member
Comment:
Denotes membership for Collection, Catalog and File instances.
Semanticscience Integrated Ontology property equivalence: SIO_000059

Object Property "hasOrderedPart"
Label: has ordered part
Comment:
Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning.
Semanticscience Integrated Ontology property equivalence: SIO_000974

Object Property "hasOutput"
Label: has output
Comment:
Links out to an entity that is the output of a Process subclass.
Semanticscience Integrated Ontology property equivalence: SIO_000229

Object Property "hasPart"
Label: has part
Comment:
Denotes a compositional relationship to other entities.
Semanticscience Integrated Ontology property equivalence: SIO_000028

Object Property "hasParticipant"
Label: has participant
Comment:
Denotes the participation of other entities in processes.
Semanticscience Integrated Ontology property equivalence: SIO_000132

Object Property "hasQuality"
Label: has quality
Comment:
Links out to an entity that provides qualitative information.
Semanticscience Integrated Ontology property equivalence: SIO_000217

Object Property "hasSource"
Label: has source
Comment:
Denotes information origin.
Semanticscience Integrated Ontology property equivalence: SIO_000253

Object Property "isAbout"
Label: is about
Comment:
References an entity about which information is provided for.
Semanticscience Integrated Ontology property equivalence: SIO_000332

Object Property "isAffectedBy"
Label: is affected by
Comment:
Denotes that an entity is affected by another entity.
Semanticscience Integrated Ontology property equivalence: SIO_001159

Object Property "isAfter"
Label: is after
Comment:
Denotes the trailing occurrence or succession of the subject in regards to the object.
Semanticscience Integrated Ontology property equivalence: SIO_000211

Object Property "isAttributeOf"
Label: is attribute of
Comment:
Denotes that an entity is an attribute of the entity that this property links out to.
Semanticscience Integrated Ontology property equivalence: SIO_000011

Object Property "isBefore"
Label: is before
Comment:
Denotes the leading occurrence or precedence of the subject in regards to the object.
Semanticscience Integrated Ontology property equivalence: SIO_000240

Object Property "isCreatedBy"
Label: is created by
Comment:
Denotes the process or method that created an entity.
Semanticscience Integrated Ontology property equivalence: SIO_000365

Object Property "isDescribedBy"
Label: is described by
Comment:
Provides a description of the subject via reference to an object that provides further information on the subject.
Semanticscience Integrated Ontology property equivalence: SIO_000557

Object Property "isLocatedOn"
Label: is located on
Comment:
Denotes the location of genomic feature on a landmark.
Semanticscience Integrated Ontology property equivalence: SIO_000061

Object Property "isPartOf"
Label: is part of
Comment:
Denotes that an entity is an intrinsic component of an encapsulating entity.
Semanticscience Integrated Ontology property equivalence: SIO_000068

Object Property "isParticipantIn"
Label: is participant in
Comment:
Denotes participation with another entity.
Semanticscience Integrated Ontology property equivalence: SIO_000062

Object Property "isRefutedBy"
Label: is refuted by
Comment:
References an entity or resource that provides refuting evidence.
Semanticscience Integrated Ontology property equivalence: SIO_000774

Object Property "isSourceOf"
Label: is source of
Comment:
Denotes that an entity is the source of the entity that this property links out to.
Semanticscience Integrated Ontology property equivalence: SIO_000219

Object Property "isSpatiotemporallyRelatedTo"
Label: is spatiotemporally related to
Comment:
Denotes spatio-temporal relations to other entities.
Semanticscience Integrated Ontology property equivalence: SIO_000322

Object Property "isSupportedBy"
Label: is supported by
Comment:
References an entity or resource that provides supporting evidence.
Semanticscience Integrated Ontology property equivalence: SIO_000206

Object Property "isTemporarilyPartOf"
Label: is temporarily part of
Comment:
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.
Semanticscience Integrated Ontology property equivalence:

Object Property "references"
Label: references
Comment:
References another entity or resource.
Semanticscience Integrated Ontology property equivalence: SIO_000631

Object Property "refersTo"
Label: refers to
Comment:
References an entity, where additional information is provided to augment the reference.
Semanticscience Integrated Ontology property equivalence: SIO_000628

Datatype Properties

Datatype Property "hasValue"
Label: has value
Comment:
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.
Semanticscience Integrated Ontology property equivalence: SIO_000300
GFF3GTFGVFVCF