================================================ PRotein Ontology (PRO) Release 35.0, version 0 04-June-2013 The Protein Ontology Consortium--Protein Information Resource, The Jackson Laboratory, Reactome, and the Department of Philosophy at the State University of New York at Buffalo--is pleased to announce PRO Release 35.0 (04-June-2013). PRO describes the relationships of proteins and protein evolutionary classes, delineates the multiple protein forms of a gene locus (ontology for protein forms), protein complexes, and interconnects existing ontologies. Further information is available at http://pir.georgetown.edu/pro/. In PRO Release 35.0, version 0: There are 35465 PRO terms 334 terms are in the 'family' category. 23700 terms are in the 'gene' category. 1691 terms are in the 'sequence' category. 6548 terms are in the 'modification' category. 177 terms are in the 'complex' category. 4 terms are in the 'organism-family' category. 953 terms are in the 'organism-gene' category. 722 terms are in the 'organism-sequence' category. 816 terms are in the 'organism-modification' category. 308 terms are in the 'organism-complex' category. 16 terms are in the 'union' category. 1875 terms have some kind of annotation, codifying the information from 1267 papers. 3090 connections to GO (1055 PRO terms). 374 connections to MOD (328 PRO terms). 617 connections to Pfam (371 PRO terms). 338 connections to SO (317 PRO terms). 344 annotations of a phenotype (337 PRO terms). The ontology includes a subset of terms from GO, MOD, CHEBI, and SO ontologies that are used for logical definitions. If using OBO Edit to view PRO, please turn on the reasoner in order to display the hierarchy. _Current changes_ 1) Please note that this release still contains a number of duplicate names and synonyms. These will be resolved in upcoming releases. _Forthcoming changes_ Ongoing 1) Continue to add shorthand labels to terms. 2) Continue to expand the set of mapped terms. 3) Resolve names and synonym duplicates. NEW in Release 36 4) In the PAF.txt file, we will change 'TaxID:' prefix to 'NCBITaxon:' 5) The has_part relationship used for complexes will change to has_component 6) "Flag=automatic" will disappear. The evidence field will instead indicate this (as it already does, with DNx and CNx). 7) In the promapping.obo file, UniProtKB entries will be prefixed with PR: instead of UniProtKB: so that the ontology terms can be linked to and viewed within the PRO hierarchy. Links to the UniProtKB database will remain in the xref field, and the accessions used will not change. NEW in Release 37 8) In pro.obo, PRO terms in the organism-gene category (which are thus equivalent to UniProtKB terms) will have the current PR: id become an alt_id to the UniProtKB-derived id. Thus, the new primary identifier for PR:000025484 (the ontological representation of UniProtKB:P40336) will be PR:P40336. The OBO stanza will thus have: [Term] id: PR:P40336 alt_id: PR:000025484 xref: UniProtKB:P40336 9) When 8) is implemented the pro_reasoned.obo file will be generated with the ELK reasoner within the OORT release manager tool. The "implied link automatically realized !" comment will not be present. Example: [Term] id: PR:000018266 name: TGF-beta receptor type-2, signal peptide removed form def: "A TGF-beta receptor type-2 that has had the signal peptide removed." [PRO:DNx] comment: Category=modification. Flag=automatic. synonym: "TGFBR2/SigPep-" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000005 ! implied link automatically realized ! TGF-beta receptor type-2 intersection_of: PR:000000005 ! TGF-beta receptor type-2 intersection_of: lacks_part SO:0000418 ! signal_peptide will become [Term] id: PR:000018266 name: TGF-beta receptor type-2, signal peptide removed form def: "A TGF-beta receptor type-2 that has had the signal peptide removed." [PRO:DNx] comment: Category=modification. Flag=automatic. synonym: "TGFBR2/SigPep-" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000005 ! TGF-beta receptor type-2 intersection_of: PR:000000005 ! TGF-beta receptor type-2 intersection_of: lacks_part SO:0000418 ! signal_peptide relationship: lacks_part SO:0000418 ! signal_peptide ================================================