PRotein Ontology (PRO) Release 40.1 (01-Apr-2014) There are 59198 PRO terms 54 terms are in the 'external' category. 342 terms are in the 'family' category. 23506 terms are in the 'gene' category. 1798 terms are in the 'sequence' category. 6630 terms are in the 'modification' category. 213 terms are in the 'complex' category. 9 terms are in the 'organism-family' category. 23741 terms are in the 'organism-gene' category. 914 terms are in the 'organism-sequence' category. 1411 terms are in the 'organism-modification' category. 352 terms are in the 'organism-complex' category. 21 terms are in the 'union' category. 2070 terms have some kind of annotation, codifying the information from 1326 papers. 3380 connections to GO (1201 PRO terms). 374 connections to MOD (331 PRO terms). 617 connections to Pfam (371 PRO terms). 338 connections to SO (317 PRO terms). 8 annotations of a phenotype (8 PRO terms). The ontology includes a subset of terms from other ontologies and resources that are used for logical definitions. _Current changes_ 1) Newly introduced PRO terms in the organism-sequence category (which are thus equivalent to alternative products in UniProtKB entries) have the PR: id become UniProtKB-derived id. Thus, PR:Q8R5G7-1 will be the ontological representation of UniProtKB:Q8R5G7-1. The OBO stanza is now like: [Term] id: PR:Q8R5G7-1 name: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1 (mouse) def: "An Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1 that is encoded in the genome of mouse." [PRO:HJD, PMID:15546919] comment: Category=organism-sequence. synonym: "mARAP3/iso:1" EXACT PRO-short-label [PRO:DNx] xref: UniProtKB:Q8R5G7-1 intersection_of: PR:000037352 ! Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1 intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus 2) OMIM terms in PAF file have been replaced by the corresponding controlled vocabulary in disease ontology (DO). 3) We have corrected some errors in parentage of several terms. _Forthcoming changes_ 1) Other existing PRO terms in the organism-sequence category (which are thus equivalent to alternative products in UniProtKB entries) will have the current PR: id become an alt_id to the UniProtKB-derived id. Thus, the new primary identifier for PR:000025481 (the ontological representation of UniProtKB:Q0QWG9-1) will be PR:Q0QWG9-1. The OBO stanza will thus have: [Term] id: PR:Q0QWG9-1 alt_id: PR:000025481 name: delphilin isoform 1 (mouse) def: "A delphilin isoform 1 that is encoded in the genome of mouse." [PRO:HJD] comment: Category=organism-sequence. synonym: "mGRID2IP/iso:1" EXACT PRO-short-label [PRO:DNx] xref: UniProtKB:Q0QWG9-1 intersection_of: PR:000025480 ! delphilin isoform 1 intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus _Ongoing_ 1) Continue to add shorthand labels to terms. 2) Continue to expand the set of mapped terms. 3) Resolve names and synonym duplicates.