]> 1.0.12 Begum Durgahee Creative Commons - By Attribution [http://creativecommons.org/licenses/by/3.0/]. https://github.com/BioInterchange/Ontologies An ontology that describes the Generic Feature Format Version 3 (GFF3) by Lincoln Stein (http://www.sequenceontology.org/resources/gff3.html). The ontology was inspired by previous work of Robert Hoehndorf's RDF2OWL (http://code.google.com/p/rdf2owl). Chris Mungall Erick Antezana Generic Feature Format Version 3 Ontology (GFF3O) 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 that are not covered by object-/data-properties of the ontology. Tags that are represented as object-/data-properties are: ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular 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. set_properties Properties that are directly associated with Set class instances. feature_properties Properties that are directly associated with Feature class instances. target Identifies the target that the features aligns to. target_properties Properties that are directly associated with Target class instances. strand Strand of a target -- if applicable. derives_from Describes a temporal relationship between two features, where the object denotes the subjects origin. region FALDO "Region" instance replacement for a target's start, stop, strand properties. 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. 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. phase Phase for "CDS" features. It indicates where the feature begins with reference to the reading frame. For forward strand features, phase is counted from the start field, whilst for reverse strand features, phase is counted from the end field. 0 2 tag Tag name of a feature attribute. 1 version Version of the GFF3 specification that defines the feature set contents. 4 3 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'. set_properties Properties that are directly associated with Set class instances. feature_properties Properties that are directly associated with Feature class instances. attribute_properties Properties that are directly associated with Attribute class instances. dbxref A database cross-reference to associate a sequence alteration to its representation in another database. 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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=.+ name Name of a feature, which can be used for display purposes. The name is not a unique property among features. 1 alias An alternative name for a feature. This can be another descriptive name of a feature, such as a locus name or accession number. 1 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 gap Gap describing the feature/target alignment if the sequences are not collinear. The formal description of this property has been lost due to a dead link in the GFF3 specification. 1 note A free text note. is_circular Describes whether a feature is circular or not. 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 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\*\-]+ Set Set of genomic sequence features, whose identifiers are unique within the set. Feature 0 1 1 1 1 1 1 0 1 1 0 0 1 A genomic sequence feature. Attribute Describes additional feature attributes besides ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular. Strand Class describing a genomic strand. Instances of the class (individuals) are used to denote forward-/reverse-strands, etc. Target Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. Landmark A landmark that establishes the coordinate system for features. 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.