PRotein Ontology (PRO) Release 36.0 (03-Jul-2013)

There are 36085 PRO terms
   335 terms are in the 'family' category.
  23703 terms are in the 'gene' category.
  1713 terms are in the 'sequence' category.
  6587 terms are in the 'modification' category.
   179 terms are in the 'complex' category.
    4 terms are in the 'organism-family' category.
   953 terms are in the 'organism-gene' category.
   747 terms are in the 'organism-sequence' category.
  1343 terms are in the 'organism-modification' category.
   308 terms are in the 'organism-complex' category.
   16 terms are in the 'union' category.
1992 terms have some kind of annotation, codifying the information from 1281 papers.
  3141 connections to GO (1123 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) Please note that this release still contains a number of duplicate names and synonyms. These will be resolved in upcoming releases.
2) The has_part relationship used for complexes changed to has_component
3) "Flag=automatic" was removed. The evidence field instead indicates this (as it already does, with DNx and CNx).
4) In the promapping.obo file, UniProtKB entries are 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 remain in the xref field, and the accessions used are not changed.

_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.

For next Release

4) 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
<other stuff>
xref: UniProtKB:P40336