]> Creative Commons - By Attribution [http://creativecommons.org/licenses/by/3.0/]. https://github.com/BioInterchange/Ontologies 1.0.18 An ontology that describes the Genome Variation Format Version 1 (GVF) by Karen Eilbeck, Paul Flicek, Gabor Marth, Martin Reese, Lincoln Stein and Mark Yandell (http://www.sequenceontology.org/resources/gvf.html). The ontology was inspired by previous work of Robert Hoehndorf's RDF2OWL (http://code.google.com/p/rdf2owl). Begum Durgahee Chris Mungall Erick Antezana Genomic Variation Format Version 1 Ontology (GVF1O) Joachim Baran Joachim Baran Karen Eilbeck Michel Dumontier Robert Hoehndorf seqid Establishes the landmark (e.g. a chromosome) on which a feature is located. strand Strand of the feature. attributes Tag name/value pair attributes of a feature. parent Link out to the parent feature. contains Relationship that describes which features belong to a feature set. region FALDO "Region" instance replacement for a feature's start, stop, strand properties. species NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set. variant Specific information about the variant(s) of a feature. individual Links to information about an individual. zygosity Zygosity of a variant. effect An effect of a particular feature variant. sequence_variant Effect of a sequence alteration on a sequence feature. feature_type A term that is describing the sequence feature that is being affected. start_range A coordinate range for ambiguous start coordinates. end_range A coordinate range for ambiguous start coordinates. chromosome Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism. genotype Determines the genotype as observed in an individual. feature_properties Properties that are directly associated with Feature class instances. sequencedindividual_properties Properties that are directly associated with SequencedIndividual class instances. set_properties Properties that are directly associated with Set class instances. variant_properties Properties that are directly associated with Variant class instances. effect_properties Properties that are directly associated with Effect class instances. seqid Link to the landmark that establishes the coordinate system for the breakpoint. breakpoint_properties Properties that are directly associated with Breakpoint class instances. dbxref A database cross-reference to associate a sequence alteration to its representation in another database. region FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties. breakpoint Potential source or destination of zero-length sequence alterations. strand Strand of the breakpoint. target_properties Properties that are directly associated with Target class instances. region FALDO "Region" instance replacement for a target's start, stop, strand properties. strand Strand of a target -- if applicable. technologyplatform_properties Properties that are directly associated with TechnologyPlatform class instances. datasource_properties Properties that are directly associated with DataSource class instances. dbxref A database cross-reference to associate a structured pragma to a representation in another database. structuredpragma_properties Properties describing structured pragma properties. read_type Types of reads produced by the platform. data_type Datatype of this data source. technology_platform Technology platform that was used to derive the feature. data_source Data source origin of the feature. score_method Used scoring method. source_method Further information about the algorithm/methodologies used. phenotype_description Further information about an individual's phenotype. Applies only to single individual sets. attribute_method Further information about the associated attribute(s). attribute_method Further information about the associated attribute(s). attribute_properties Properties about Attribute instances. attribute_method Further information about the associated attribute(s). attribute_method Further information about the associated attribute(s). attribute_method Further information about the associated attribute(s). sex Denotes the sex of the sequenced individual for single-individual sets. genomic_source Denotes the source of genomic data (on a cell-type level). feature_ontology Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies. attributes Tag name/value pair attributes that are not captured by the GVF specification. target Identifies the target that the features aligns to. source A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name. 1 type Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO). http://www\.sequenceontology\.org/miso/current_release/term/.+ start Start coordinate of the feature on the seqid landmark. 1 end End coordinate of the feature on the seqid landmark. 1 score Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features. tag Tag name of a feature attribute. 1 gvf_version Version of the GVF specification that defines the feature set contents. 1 2 build Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'. 1 variant_seq All sequence variations at a locus -- including the reference sequence when appropriate (for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates. ([ACGTUWSMKRYBDHVN\-]+|\~[0-9]*|\.|!|\^) id A unique identifier for the feature within the feature set. 1 alias Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (e.g. dbSNP, OMIM) which should use the dbxref property. 1 reference_seq Sequence from the reference genome. ([ACGTUWSMKRYBDHVN\-]+|\~[0-9]*|\.) variant_reads Number of reads that are supporting this variant. total_reads Total number of reads. variant_freq Frequency of a variant in a population. feature Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier. 1 start A coordinate that defines the start of an ambiguous coordinate range. 1 end A coordinate that defines the end of an ambiguous coordinate range. 1 phased Unclear from GVF specification. 1 variant_codon Describes the codon that overlaps this variant. ([ACGT]{3})+ reference_codon Describes the codon from the reference sequence whose coordinates overlap with this variant. ([ACGT]{3})+ variant_aa Amino acid that overlaps with the variant. [A-Z] reference_aa Amino acid in the reference genome that overlaps with a variant's genome coordinates. [A-Z] feature_properties Properties that are directly associated with Feature class instances. variant_properties Properties that are directly associated with Variant class instances. range_properties Properties that are directly associated with Range class instances. set_properties Properties that are directly associated with Set class instances. attribute_properties Properties that are directly associated with Attribute class instances. sequencedindividual_properties Properties that are directly associated with SequencedIndividual class instances. breakpoint_properties Properties that are directly associated with Breakpoint class instances. start Start coordinate of the feature on the seqid landmark. 1 end End coordinate of the feature on the seqid landmark. 1 5'_context Sequence context (positive strand) of a feature on the 5' end. [ACGT]+ 3'_context Sequence context (positive strand) of a feature on the 3' end. [ACGT]+ gff_version Version of the GFF specification that defines the feature set contents apart from GVF related definitions. 3 4 file_date Creation date of the GVF file that this set stems from. target_properties Properties that are directly associated with Target class instances. target_id ID or accession of the target alignment. 1 start Start coordinate of the target. 1 end End coordinate of the target. 1 ontology_term A cross-reference to an ontology term that is associated with a feature. http://www\.ncbi\.nlm\.nih\.gov/entrez/viewer\.fcgi\?val=.+|http://www\.gramene\.org/db/qtl/qtl_display\?qtl_accession_id=.+|http://www\.gramene\.org/db/protein/protein_search\?acc=[A-Z][0-9][A-Z0-9]{3}[0-9]|http://www\.biolws1\.york\.ac\.uk/echobase/Gene\.cfm\?recordID=EB[0-9]{4}|http://www\.ncbi\.nlm\.nih\.gov/Structure/cdd/cddsrv\.cgi\?uid=.+|http://www\.ecogene\.org/geneInfo\.php\?eg_id=EG[0-9]{5}|http://umbbd\.msi\.umn\.edu/servlets/rule\.jsp\?rule=.+|http://www\.riken\.jp/SPD/[0-9]{2}/[0-9]{2}[A-Z][0-9]{2}\.html|http://www\.proconsortium\.org/cgi\-bin/pro/entry_pro\?id=PR:[0-9]{9}|http://img\.jgi\.doe\.gov/cgi\-bin/pub/main\.cgi\?section=GeneDetail&page=geneDetail&gene_oid=.+|http://dictybase\.org/db/cgi\-bin/dictyBase/reference/reference\.pl\?refNo=.+|http://www\.gramene\.org/db/genes/search_gene\?acc=.+|http://vega\.sanger\.ac\.uk/perl/searchview\?species=all&idx=All&q=.+|http://www\.sgn\.cornell\.edu/phenome/locus_display\.pl\?locus_id=.+|http://www\.neurolex\.org/wiki/.+|http://www\.nlm\.nih\.gov/cgi/mesh/2005/MB_cgi\?mode=&term=.+|http://www\.ebi\.ac\.uk/chebi/searchId\.do\?chebiId=CHEBI:[0-9]{1,6}|http://www\.theseed\.org/linkin\.cgi\?id=.+|http://www\.genome\.jp/dbget\-bin/www_bget\?rn:R[0-9]+|http://merops\.sanger\.ac\.uk/cgi\-bin/pepsum\?mid=.+|http://www\.expasy\.ch/cgi\-bin/nicezyme\.pl\?.+|http://www\.maizegdb\.org/cgi\-bin/displaylocusresults\.cgi\?term=[A-Za-z][A-Za-z0-9]*|http://gowiki\.tamu\.edu/wiki/index\.php/.+|http://www\.uniprot\.org/keywords/.+|http://www\.ensemblgenomes\.org/id/.+|http://www\.proteinatlas\.org/antibody_info\.php\?antibody_id=.+|http://www\.ncbi\.nlm\.nih\.gov/COG/new/release/coglist\.cgi\?pathw=.+|http://song\.sourceforge\.net/SOterm_tables\.html#SO:[0-9]{7}|http://db\.yeastgenome\.org/cgi\-bin/locus\.pl\?locus=.+|http://pubchem\.ncbi\.nlm\.nih\.gov/assay/assay\.cgi\?aid=.+|http://amigo\.geneontology\.org/cgi\-bin/amigo/term\-details\.cgi\?term=GO:[0-9]{7}|http://medicago\.jcvi\.org/cgi\-bin/medicago/search/shared/ORF_infopage\.cgi\?orf=.+|http://www\.informatics\.jax\.org/accession/MGI:[0-9]{5,}|http://www\.wormbase\.org/db/get\?class=Protein;name=WP:.+|http://rgd\.mcw\.edu/generalSearch/RgdSearch\.jsp\?quickSearch=1&searchKeyword=[0-9]{4,7}|http://biocyc\.org/ECOLI/reference\.html\?type=CITATION\-FRAME&object=.+|http://www\.ncbi\.nlm\.nih\.gov/sites/entrez\?cmd=Retrieve&db=gene&list_uids=[0-9]+|http://www\.genome\.jp/dbget\-bin/www_bget\?cpd:C[0-9]{5}|http://www\.expasy\.ch/cgi\-bin/prosite\-search\-ac\?.+|http://www\.maizegdb\.org/cgi\-bin/id_search\.cgi\?id=.+|http://mips\.gsf\.de/genre/proj/corum/complexdetails\.html\?id=.+|http://research\.calacademy\.org/research/ichthyology/catalog/getref\.asp\?id=.+|http://viralzone\.expasy\.org/all_by_protein/.+\.html|http://purl\.obolibrary\.org/obo/RO_.+|http://pantree\.org/node/annotationNode\.jsp\?id=.+|http://umbbd\.msi\.umn\.edu/servlets/pageservlet\?ptype=r&reacID=.+|http://purl\.obolibrary\.org/obo/UBERON_[0-9]{7}|http://arabidopsis\.org/servlets/TairObject\?accession=locus:[0-9]{7}|http://www\.agbase\.msstate\.edu/cgi\-bin/getEntry\.pl\?db_pick=.+&uid=.+|http://www\.genenames\.org/data/hgnc_data\.php\?hgnc_id=HGNC:.+|http://cmr\.jcvi\.org/cgi\-bin/CMR/shared/GenomePropDefinition\.cgi\?prop_acc=GenProp[0-9]{4}|http://vbrc\.org/query\.asp\?web_id=VBRC:.+|http://agro\.vbi\.vt\.edu/public/servlet/GeneEdit\?&Search=Search&level=2&genename=.+|http://www\.unimod\.org/modifications_view\.php\?editid1=.+|http://www\.gdb\.org/gdb\-bin/genera/accno\?accessionNum=GDB:.+|http://us\.expasy\.org/unirules/.+|http://arsa\.ddbj\.nig\.ac\.jp/arsa/ddbjSplSearch\?KeyWord=.+|http://www\.grenoble\.prabi\.fr/obiwarehouse/unipathway/upa\?upid=.+|http://supfam\.cs\.bris\.ac\.uk/SUPERFAMILY/cgi\-bin/scop\.cgi\?ipid=SSF.+|http://db\.yeastgenome\.org/cgi\-bin/locus\.pl\?dbid=S[0-9]{9}|http://s59\.cas\.albany\.edu/RNAmods/cgi\-bin/rnashow\.cgi\?.+|http://www\.gramene\.org/db/searches/browser\?search_type=All&RGN=on&query=.+|http://dictybase\.org/gene/DDB_G[0-9]{7}|http://www\.aspergillusgenome\.org/cgi\-bin/locus\.pl\?locus=.+|http://mips\.gsf\.de/cgi\-bin/proj/funcatDB/search_advanced\.pl\?action=2&wert=.+|http://salilab\.org/modbase/searchbyid\?databaseID=.+|http://purl\.obolibrary\.org/obo/BFO_.+|http://www\.wormbase\.org/db/misc/paper\?name=.+|http://www\.ncbi\.nlm\.nih\.gov/Taxonomy/Browser/wwwtax\.cgi\?id=.+|http://www\.ensembl\.org/id/ENSP[0-9]{9,16}|http://flybase\.org/reports/FBgn[0-9]{7}\.html|http://www\.genome\.jp/dbget\-bin/www_bget\?ec:[0-9](\.[0-9]{1,2}){2}\.[0-9]{1,3}|http://www\.genedb\.org/genedb/Search\?organism=leish&name=LmjF\.[0-9]+\.[0-9]+|http://www\.ebi\.ac\.uk/ena/data/view/([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})|http://zfin\.org/cgi\-bin/ZFIN_jump\?record=ZDB-(GENE|GEN|MRPHLNO)-[0-9]{6}-[0-9]+|http://www\.reactome\.org/cgi\-bin/eventbrowser_st_id\?ST_ID=.+|http://www\.plantontology\.org/amigo/go\.cgi\?action=query&view=query&search_constraint=terms&query=PO:[0-9]{7}|http://pir\.georgetown\.edu/cgi\-bin/ipcSF\?id=.+|http://patric\.vbi\.vt\.edu/gene/overview\.php\?fid=.+|http://www\.candidagenome\.org/cgi\-bin/locus\.pl\?locus=.+|http://purl\.obolibrary\.org/obo/CL_[0-9]{7}|http://www\.iuphar\-db\.org/DATABASE/ObjectDisplayForward\?objectId=.+|http://www\.pharmgkb\.org/do/serve\?objId=.+|http://www\.proteinatlas\.org/tissue_profile\.php\?antibody_id=.+|http://seeds\.nottingham\.ac\.uk/NASC/stockatidb\.lasso\?code=.+|http://www\.ncbi\.nlm\.nih\.gov/projects/SNP/snp_ref\.cgi\?rs=[0-9]+|http://www\.ensembl\.org/id/ENS[A-Z0-9]{10,17}|http://www\.uniprot\.org/uniprot/[A-Z][0-9][A-Z0-9]{3}[0-9]((-([0-9]+)|:PRO_[0-9]{10}))?|http://www\.tcdb\.org/tcdb/index\.php\?tc=.+|http://www\.ncbi\.nlm\.nih\.gov/entrez/query\.fcgi\?CMD=search&DB=pccompound&term=[0-9]+|http://prodom\.prabi\.fr/prodom/current/cgi\-bin/request\.pl\?question=DBEN&query=.+|http://www\.ncbi\.nlm\.nih\.gov/COG/new/release/cow\.cgi\?cog=.+|http://www\.wormbase\.org/db/gene/gene\?name=WB(Gene|Var)[0-9]{8}|http://www\.uniprot\.org/uniprot/.+|http://www\.sgn\.cornell\.edu/chado/publication\.pl\?pub_id=.+|http://sabio\.villa\-bosch\.de/reacdetails\.jsp\?reactid=.+|http://www\.bioinf\.manchester\.ac\.uk/cgi\-bin/dbbrowser/sprint/searchprintss\.cgi\?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=.+|http://www\.pombase\.org/spombe/result/S[0-9a-zA-Z_]+(\.)?[0-9a-zA-Z_]+(\.)?|http://www\.h\-invitational\.jp/hinv/spsoup/locus_view\?hix_id=.+|http://www\.ncbi\.nlm\.nih\.gov/entrez/viewer\.fcgi\?val=[0-9]{6,}|http://www\.ebi\.ac\.uk/intact/search/do/search\?searchString=.+|https://sourceforge\.net/tracker/index\.php\?func=detail&aid=.+&group_id=76834&atid=835555|http://biocyc\.org/META/NEW\-IMAGE\?type=PATHWAY&object=.+|http://www\.candidagenome\.org/cgi\-bin/locus\.pl\?dbid=(CAL|CAF)[0-9]{7}|http://www\.gramene\.org/db/literature/pub_search\?ref_id=.+|http://my\.linkbaton\.com/get\?lbCC=q&nC=q&genre=book&item=.+|http://search\.jcvi\.org/search\?p&q=.+|http://www\.broad\.mit\.edu/annotation/genome/magnaporthe_grisea/GeneLocus\.html\?sp=S.+|http://www\.ncbi\.nlm\.nih\.gov/entrez/viewer\.fcgi\?db=nucleotide&val=[A-Z]{2}[0-9]{6}|http://www\.uniprot\.org/locations/.+|http://db\.yeastgenome\.org/cgi\-bin/reference/reference\.pl\?dbid=.+|http://rfam\.sanger\.ac\.uk/family/.+|http://v2\.pseudomonas\.com/getAnnotation\.do\?locusID=.+|http://www\.sanger\.ac\.uk/cgi\-bin/Pfam/getacc\?.+|http://www\.geneontology\.org/cgi\-bin/references\.cgi#GO_REF:[0-9]{7}|http://www\.genome\.jp/dbget\-bin/www_bget\?path:.+|http://merops\.sanger\.ac\.uk/cgi\-bin/famsum\?family=.+|http://scotland\.fgl\.ncsu\.edu/cgi\-bin/adHocQuery\.cgi\?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional\+Categorization\+of\+MGG\+GO\+Annotation&P_KeyWord=.+|http://umbbd\.msi\.umn\.edu/servlets/pageservlet\?ptype=ep&enzymeID=.+|http://www\.ncbi\.nlm\.nih\.gov/COG/grace/shokog\.cgi\?fun=.+|http://www\.ensembl\.org/id/ENST[0-9]{9,16}|http://www\.arabidopsis\.org:1555/ARA/NEW\-IMAGE\?type=NIL&object=.+|http://biocyc\.org/META/NEW\-IMAGE\?type=NIL&object=.+|http://db\.ciliate\.org/cgi\-bin/locus\.pl\?locus=.+|http://www\.ncbi\.nlm\.nih\.gov/entrez/viewer\.fcgi\?val=(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_[0-9]+|http://biocyc\.org/ECOLI/NEW\-IMAGE\?type=PATHWAY&object=EG[0-9]{5}|http://www\.expasy\.org/enzyme/.+|http://www\.h\-invitational\.jp/hinv/spsoup/transcript_view\?acc_id=.+|http://www\.dkfz\.de/LIFEdb/LIFEdb\.aspx\?ID=.+|http://flybase\.org/cgi\-bin/fbcvq\.html\?query=FBbt:.+|https://asap\.ahabs\.wisc\.edu/annotation/php/feature_info\.php\?FeatureID=.+|http://pir\.georgetown\.edu/cgi\-bin/pirwww/nbrfget\?uid=[A-Z]{1}[0-9]{5}|http://www\.ecogene\.org/geneInfo\.php\?eck_id=ECK[0-9]{4}|http://old\.genedb\.org/genedb/Search\?organism=pombe&name=SP[A-Z0-9]+\.[A-Za-z0-9]+|http://www\.ncbi\.nlm\.nih\.gov/pubmed/.+|http://www\.ebi\.ac\.uk/cgi\-bin/emblfetch\?style=html&Submit=Go&id=([A-Z]{1}[0-9]{5})|([A-Z]{2}[0-9]{6})|([A-Z]{4}[0-9]{8,9})|http://mged\.sourceforge\.net/ontologies/MGEDontology\.php#.+|http://www\.ebi\.ac\.uk/compneur\-srv/biomodels\-main/publ\-model\.do\?mid=.+|http://www\.uniprot\.org/uniparc/.+|http://research\.calacademy\.org/research/ichthyology/catalog/getname\.asp\?rank=Species&id=1979|http://www\.aspergillusgenome\.org/cgi\-bin/reference/reference\.pl\?dbid=.+|http://www\.candidagenome\.org/cgi\-bin/reference/reference\.pl\?dbid=.+|http://www\.genedb\.org/genedb/Search\?organism=tryp&name=Tb[0-9]+\.[0-9]+\.[0-9]+|http://omim\.org/entry/.+|http://www\.ebi\.ac\.uk/ontology\-lookup/\?termId=MOD:.+|http://www\.genedb\.org/genedb/Search\?organism=malaria&name=SP[A-Z0-9]+\.[A-Za-z0-9]+|http://vmd\.vbi\.vt\.edu/cgi\-bin/browse/browserDetail_new\.cgi\?gene_id=.+|http://www\.ncbi\.nlm\.nih\.gov/UniGene/clust\.cgi\?ORG=.+&CID=.+|http://research\.calacademy\.org/research/ichthyology/catalog/getname\.asp\?rank=Species&id=.+|http://arabidopsis\.org/servlets/TairObject\?type=locus&name=AT[MC0-5]G[0-9]{5}(\.[0-9]{1})?|http://www\.geneontology\.org/gene\-associations/submission/paint/.+/.+\.txt|http://cmr\.jcvi\.org/cgi\-bin/CMR/shared/GenePage\.cgi\?locus=.+|http://www\.nmpdr\.org/linkin\.cgi\?id=.+|http://www\.genenames\.org/data/hgnc_data\.php\?app_sym=.+|http://www\.iuphar\-db\.org/DATABASE/FamilyMenuForward\?familyId=.+|http://www\.ensembl\.org/id/ENSG[0-9]{9,16}|http://www\.ebi\.ac\.uk/interpro/IEntry\?ac=IPR[0-9]{6}|http://en\.wikipedia\.org/wiki/.+|http://www\.genedb\.org/genedb/Search\?organism=glossina&name=.+|http://cmr\.jcvi\.org/cgi\-bin/CMR/EgadSearch\.cgi\?search_string=.+|http://gene3d\.biochem\.ucl\.ac\.uk/superfamily/\?accession=.+|http://www\.cazy\.org/(CE|GH|GT|PL)[0-9]+\.html|http://www\.aspergillusgenome\.org/cgi\-bin/locus\.pl\?dbid=.+|http://db\.ciliate\.org/cgi\-bin/reference/reference\.pl\?dbid=.+|http://rebase\.neb\.com/rebase/enz/.+\.html|http://www\.ncbi\.nlm\.nih\.gov/entrez/query\.fcgi\?CMD=search&DB=pcsubstance&term=[0-9]{4,}|http://dictybase\.org/gene/.+|http://umbbd\.msi\.umn\.edu/.+/.+_map\.html|http://smart\.embl\-heidelberg\.de/smart/do_annotation\.pl\?BLAST=DUMMY&DOMAIN=.+|http://www\.ebi\.ac\.uk/rhea/reaction\.xhtml\?id=.+|http://www\.rcsb\.org/pdb/cgi/explore\.cgi\?pdbId=[A-Za-z0-9]{4}|http://research\.calacademy\.org/research/ichthyology/catalog/getname\.asp\?rank=Genus&id=.+|http://wiki\.plantontology\.org:8080/index\.php/PO_REF:.+|http://www\.ncbi\.nlm\.nih\.gov/sites/entrez\?db=pmc&cmd=search&term=.+|http://www\.plasmodb\.org/gene/.+|http://www\.ncbi\.nlm\.nih\.gov/entrez/viewer\.fcgi\?db=protein&val=[A-Z]{3}[0-9]{5}(\.[0-9]+)?|http://www\.informatics\.jax\.org/searches/AMA\.cgi\?id=MA:.+|http://www\.brenda\-enzymes\.info/php/result_flat\.php4\?ecno=.+|http://www\.ncbi\.nlm\.nih\.gov/sites/GDSbrowser\?acc=.+|http://dx\.doi\.org/DOI:.+|http://www\.jstor\.org/stable/.+|http://vmd\.vbi\.vt\.edu/cgi\-bin/browse/go_detail\.cgi\?gene_id=.+ phased Indicates whether this particular is phased. Used to encode ##phased-genotypes statements. comment An arbitrary comment. Free text. 1 platform_class Type of technology used to gather the variant data. Unrestricted range due to open specification. 1 technologyplatform_properties Properties that are directly associated with TechnologyPlatform class instances. platform_name Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification. 1 structuredpragma_properties Properties describing structured pragma properties. read_length Undocumented in GVF specification. 0 read_pair_span Undocumented in GVF specification. 0 average_coverage Undocumented in GVF specification. 0 landmark_properties Properties that are directly associated with Landmark class instances. id ID that uniquely establishes the Landmark's identity within a Set. ([a-zA-Z0-9\.:\^\*\$@!\+_\?\-|]|%[a-fA-F0-9][a-fA-F0-9])+ start Genomic start coordinate of the landmark. 1 end Genomic end coordinate of the landmark. 1 file_version Version of the GVF file that this set stems from. structuredattribute_properties Properties that are directly associated with StructuredAttribute class instances. tag Tag name of an user defined structured attribute. sequence Sequence associated with this feature, if it has been specified using a FASTA string. [A-Z\*\-]+ sequence Sequence associated with this feature, if it has been specified using a FASTA string. [A-Z\*\-]+ effect_properties Properties that are directly associated with Effect class instances. Set Set of genomic sequence features, whose identifiers are unique within the set. Feature 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 1 A genomic sequence feature. Attribute Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant. Strand Class describing a genomic strand. Instances of the class (individuals) are used to denote forward-/reverse-strands, etc. Variant Describing specific alterations of a feature. SequencedIndividual Aggregated sequencing information for a particular individual. Effect Describing the effect of a feature variant. Range Describe ambiguity in either start or end coordinates. Chromosome An abstract representation of a chromosome to represent ploidy. Breakpoint Describes the source or destination of a zero-length sequence alteration. Zygosity Denotes the zygosity of alleles. Target Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. TechnologyPlatform Details about the sequencing/microarray technology used to gather the data in a set. DataSource Provides information about the source of the data. For example, it can link out to actual sequences associated with the Feature individuals in a Set. Method Information about the used scoring algorithm or method. PhenotypeDescription Additional information about an individual's phenotype. ReadType Type of reads obtained for a given technology platform. DataType Determines the datatype of a variant sequence. Landmark A landmark that establishes the coordinate system for features. Sex For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (real-life) individuals. GenomicSource An enumerated class for determining the genomic source (cell type) of sequenced data. StructuredAttribute Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification. Positive Location on the positive (forward) strand. Negative Location on the negative (reverse) strand. UnknownStrand Strand was not determined, which leaves it open whether the location is on the positive (forward) or negative (reverse) strand. NotStranded Strand is not applicable. Heterozygous Denotes heterozygous alleles. Homozygous Denotes homozygous alleles. Hemizygous Denotes hemizygous alleles. Fragment Denotes reads that are fragments. Pair Denotes reads that are pairs. DNASequence Denotes a DNA sequence. RNASequence Denotes an RNA sequence. DNAMicroarray Denotes a DNA microarray probe. ArrayComparativeGenomicHybridization Denotes an array-comparative genomic hybridization. Female Denotes that a Set contains features of a female. Male Denotes that a Set contains features of a male. Prenatal Denotes that a set contains features of prenatal cells. Germline Denotes that a set contains features of germline cells. Somatic Denotes that a set contains features of somatic cells.