PRotein Ontology (PRO) Release 67.0 (08-Aug-2022)

There are 232123 PRO terms in the Protein Ontology. Those representing individual proteins are mapped to 142990 UniProtKB sequences.
      520 terms are in the 'family' category.
    23989 terms are in the 'gene' category.
       25 terms are in the 'seqgroup' category.
     8067 terms are in the 'sequence' category.
     4974 terms are in the 'modification' category.
      221 terms are in the 'complex' category.
       43 terms are in the 'organism-family' category.
   100671 terms are in the 'organism-gene' category.
      202 terms are in the 'organism-seqgroup' category.
    71694 terms are in the 'organism-sequence' category.
    15680 terms are in the 'organism-modification' category.
      497 terms are in the 'organism-complex' category.
       24 terms are in the 'union' category.
       72 terms are in the 'external' category.
 2265 terms have some kind of annotation, codifying the information from 1644 papers.
     4436 connections to GO (1721 PRO terms).
       27 connections to SO (24 PRO terms).
      610 annotations of a phenotype (585 PRO terms).

The ontology includes a subset of terms from other ontologies and resources that are used for logical definitions.

_Current changes_

1) Relations used in the PAF file have been updated to conform to those currently in use in the GO Consortium's GAF file:
   participates_in --> acts_upstream_of_or_within
   capable_of      --> enables

2) Lines in the PAF file with has_part annotations have been removed. These were (a) incompletely applied; (b) potentially misleading; and (c) more properly, if needed, should be part of a term's definition.

_Forthcoming changes_

1) A new upper-level term, "protein-containing material entity", will be introduced with release 68.0. This term will serve as an umbrella for proteins, protein complexes, and protein aggregates.
2) A new synonym type "PRO-org-label" will be added to appropriate terms. Currently the PRO-short-label synonyms use an orthology-based mechanism to identify related terms across species. The new synonym type will identify related terms based on the gene name in the given organism.
3) The use of both EXACT and NARROW PRO-proteoform synonyms will be systematically implemented.
4) We will switch the only_in_taxon relation to in_taxon, in anticipation of the likely deprecation of the former in favor of the latter.