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PRotein Ontology (PRO) Release 23.0, version 0
29-September-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 23.0 (29-September-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 23.0, version 0:

There are 27624 PRO terms
       4 terms are in the 'organism-family' category.
     309 terms are in the 'family' category.
   18226 terms are in the 'gene' category.
    1387 terms are in the 'sequence' category.
    6052 terms are in the 'modification' category.
     100 terms are in the 'complex' category.
     466 terms are in the 'organism-gene' category.
     406 terms are in the 'organism-sequence' category.
     373 terms are in the 'organism-modification' category.
     178 terms are in the 'organism-complex' category.
      11 terms are in the 'union' category.
1574 terms have some kind of annotation, codifying the information from 1066 papers.
    2347 connections to GO (804 PRO terms).
     374 connections to MOD (327 PRO terms).
     604 connections to Pfam (361 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_

1) To comply with the standard set by the Human Genome Nomenclature Committee, we replaced the word "antigen" with "molecule" for terms related to cell differentiation (CD). For example, CD9 antigen (PR:000005178) became CD9 molecule.
2) PRO terms at Category=gene received shorthand labels. These labels are meant to facilitate the ability to view the terms using software such as Cytoscape, where space is limited.
3) Synonyms have been sorted according to tag type (in the order EXACT, RELATED, BROAD, NARROW), followed by alphabetical order. 
4) PRO introduced inferred complexes. Inferred complexes are those that lack experimental evidence in an organism even though that organism is known to contain orthologs (or ortho-isoforms/ortho-modified forms) of every component of the complex found in another organism. Such complexes will be flagged with the evidence code ECO:0000088 ("Biological system reconstruction").


_Forthcoming changes_

1) Continue to add shorthand labels to terms.
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