PRotein Ontology (PRO) Release 35.0 (04-Jun-2013) 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 other ontologies and resources that are used for logical definitions. _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) 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