PRotein Ontology (PRO) Release 37.0 (30-Aug-2013)

There are 35101 PRO terms
   340 terms are in the 'family' category.
  23576 terms are in the 'gene' category.
  1725 terms are in the 'sequence' category.
  6607 terms are in the 'modification' category.
   181 terms are in the 'complex' category.
    8 terms are in the 'organism-family' category.
  23719 terms are in the 'organism-gene' category.
   765 terms are in the 'organism-sequence' category.
  1359 terms are in the 'organism-modification' category.
   310 terms are in the 'organism-complex' category.
   17 terms are in the 'union' category.
2009 terms have some kind of annotation, codifying the information from 1293 papers.
  3196 connections to GO (1140 PRO terms).
   374 connections to MOD (331 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) In pro.obo, PRO terms in the organism-gene category (which are thus equivalent to UniProtKB terms) 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) is PR:P40336. The OBO stanza thus has:
[Term]
id: PR:P40336
alt_id: PR:000025484
<other stuff>
xref: UniProtKB:P40336

_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.

4) The relationship between an organism-gene class and the gene coding
for proteins of that class will be made explicit using the
has_gene_template relation. For example:

[Term]
id: PR:P51946
alt_id: PR:000027293
name: cyclin-H (human)
def: "A cyclin-H that is encoded in the genome of human." [PRO:DNx]
comment: Category=organism-gene.
synonym: "hCCNH" EXACT PRO-short-label [PRO:DNx]
xref: UniProtKB:P51946
intersection_of: PR:000005130 ! cyclin-H
intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens
relationship: has_gene_template HGNC ! CCNH

This will initially apply only to those organisms with a dedicated model
organism database that curates genes and gene nomenclature.