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PRotein Ontology (PRO) Release 18.0, version 0
25-April-2011

The Protein Ontology Consortium--Protein Information Resource, The Jackson Laboratory, Reactome, and the Department of Philosophy at the State University of New York at Buffalo--is pleased to announce PRO Release 18.0 (25-April-2011). PRO describes the relationships of proteins and protein evolutionary classes, delineates the multiple protein forms of a gene locus (ontology for protein forms), protein complexes, and interconnects existing ontologies. Further information is available at http://pir.georgetown.edu/pro/.

In PRO Release 18.0, version 0:

There are 26879 PRO terms
     304 terms are in the 'family' category.
   18201 terms are in the 'gene' category.
    1343 terms are in the 'sequence' category.
    5896 terms are in the 'modification' category.
      44 terms are in the 'complex' category.
     342 terms are in the 'organism-gene' category.
     343 terms are in the 'organism-sequence' category.
     192 terms are in the 'organism-modification' category.
      93 terms are in the 'organism-complex' category.
       9 terms are in the 'union' category.
1545 terms have some kind of annotation, codifying the information from 1032 papers.
    2282 connections to GO (774 PRO terms).
     374 connections to MOD (327 PRO terms).
     604 connections to Pfam (362 PRO terms).
     338 connections to SO (317 PRO terms).
     306 annotations of a phenotype (299 PRO terms).

The ontology includes a subset of terms from GO, MOD, CHEBI, and SO ontologies that are used for logical definitions.  If using OBO Edit to view PRO, please turn on the reasoner in order to display the hierarchy.


_Current changes_
-Format changes-
1) The header contains a new line indicating the identity of the ontology "ontology: pr" 
2) The id for taxonomy space have changed format. Instead of taxon:TAXID, it is now NCBITaxon:TAXID.
Example:"intersection_of: only_in_taxon taxon:10090 ! Mus musculus" is now "intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus" 

-New File-
1) There is a new file called pro_reasoned.obo which contains the ontology with implied links realized, then no reasoner is needed to view the ontology. The reasoned terms will contain the statement "implied link automatically realized" in the created is_a relation.
Example:
in pro.obo
[Term]
id: PR:000025257
name: heat shock protein 105 kDa (mouse)
def: "A heat shock protein 105 kDa that is encoded in the genome of mouse." [PRO:DAN]
comment: Category=organism-gene.
xref: UniProtKB:Q61699
intersection_of: PR:000003410 ! heat shock protein 105 kDa
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus

in pro_reasoned.obo
[Term]
id: PR:000025257
name: heat shock protein 105 kDa (mouse)
def: "A heat shock protein 105 kDa that is encoded in the genome of mouse." [PRO:DAN]
comment: Category=organism-gene.
xref: UniProtKB:Q61699
is_a: PR:000003410 ! implied link automatically realized ! heat shock protein 105 kDa
intersection_of: PR:000003410 ! heat shock protein 105 kDa
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus

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