PRotein Ontology (PRO) Release 43.0 (26-Sep-2014) There are 219118 PRO terms in the Protein Ontology. 54 terms are in the 'external' category. 352 terms are in the 'family' category. 23523 terms are in the 'gene' category. 8298 terms are in the 'sequence' category. 6649 terms are in the 'modification' category. 214 terms are in the 'complex' category. 15 terms are in the 'organism-family' category. 113050 terms are in the 'organism-gene' category. 64846 terms are in the 'organism-sequence' category. 1503 terms are in the 'organism-modification' category. 372 terms are in the 'organism-complex' category. 26 terms are in the 'union' category. 2400 terms have some kind of annotation, codifying the information from 1575 papers. 4348 connections to GO (1526 PRO terms). 374 connections to MOD (330 PRO terms). 621 connections to Pfam (374 PRO terms). 338 connections to SO (317 PRO terms). 349 annotations of a phenotype (342 PRO terms). The ontology includes a subset of terms from other ontologies and resources that are used for logical definitions. _Current changes_ 1) The content from the promapping.obo file has been merged with the pro.obo file. 2) Changes in the annotation file (PAF): a) the relation used for disease terms has been replaced. Instead of agent_in we now use 'associated_with_disease_progression' or 'associated_with_disease_suppression'. Note however that the relation may change in the future as progress on this field occurs. b) the column Equivalent_Form has been removed as it is not longer maintained in this file. 3) Starting from this release the promapping.obo file will no longer be provided as it is now included in the main ontology file (pro_nonreasoned.obo). _Ongoing_ 1) Continue to add shorthand labels to terms. 2) Continue to expand the set of mapped terms. 3) Resolve names and synonym duplicates.