PRotein Ontology (PRO) Release 54.0 (27-Oct-2017) There are 214812 PRO terms in the Protein Ontology. 79 terms are in the 'external' category. 158 terms are in the 'organism-seqgroup' category. 410 terms are in the 'family' category. 23556 terms are in the 'gene' category. 8329 terms are in the 'sequence' category. 5063 terms are in the 'modification' category. 211 terms are in the 'complex' category. 142 terms are in the 'organism-family' category. 97903 terms are in the 'organism-gene' category. 69887 terms are in the 'organism-sequence' category. 6550 terms are in the 'organism-modification' category. 389 terms are in the 'organism-complex' category. 47 terms are in the 'union' category. 2526 terms have some kind of annotation, codifying the information from 1690 papers. 4445 connections to GO (1723 PRO terms). 292 connections to MOD (255 PRO terms). 616 connections to Pfam (369 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) Araport has replaced TAIR as the authoritative source for Arabidopsis thaliana gene information. 2) A subset of sequence variants have been defined by referencing CHEBI to identify the changed amino acid residue. For example, PR:000036782 (tumor necrosis factor ligand superfamily member 6 isoform FasL sequence variant F273L (human)) has the usual phenylalanine resideu at position 273 replaced by a leucine residue (CHEBI:30006). 3) Proteolytic cleavage products have been logically defined in terms of output of protein processing (RO:0002353, GO:0016485). The net effect is that terms thus defined will fit within the is_a hierarchy of their respective gene-level parent instead of being derived_from those parents. _Forthcoming changes_ 1) We will phase out ftp as default method for downloads, switching instead to http. Downloads that use PURLs (such as http://purl.obolibrary.org/obo/pr.owl, which is the preferred method) will not be affected, as the target file and method will update automatically.