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PRotein Ontology (PRO) Release 38.0, version 0
15-October-2013

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 38.0 (15-October-2013). 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 38.0, version 0:

There are 58980 PRO terms
      55 terms are in the 'external' category.
     341 terms are in the 'family' category.
   23575 terms are in the 'gene' category.
    1734 terms are in the 'sequence' category.
    6620 terms are in the 'modification' category.
     181 terms are in the 'complex' category.
       9 terms are in the 'organism-family' category.
   23775 terms are in the 'organism-gene' category.
     787 terms are in the 'organism-sequence' category.
    1368 terms are in the 'organism-modification' category.
     321 terms are in the 'organism-complex' category.
      19 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 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) The relationship between an organism-gene class and the gene coding
for proteins of that class is 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 applies only to those organisms with a dedicated model
organism database that curates genes and gene nomenclature.

_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.




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