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PRotein Ontology (PRO) Release 37.0, version 0
30-August-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 37.0 (23-August-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 37.0, version 0:

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 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) 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

2)pro_reasoned.obo file is now generated with the ELK reasoner within the OORT release manager tool. The "implied link automatically realized !" comment is not present any more. Example:

[Term]
id: PR:000018266
name: TGF-beta receptor type-2, signal peptide removed form
def: "A TGF-beta receptor type-2 that has had the signal peptide removed." [PRO:DNx]
comment: Category=modification. Flag=automatic.
synonym: "TGFBR2/SigPep-" EXACT PRO-short-label [PRO:DNx]
is_a: PR:000000005 ! implied link automatically realized ! TGF-beta receptor type-2
intersection_of: PR:000000005 ! TGF-beta receptor type-2
intersection_of: lacks_part SO:0000418 ! signal_peptide
 
is now

[Term]
id: PR:000018266
name: TGF-beta receptor type-2, signal peptide removed form
def: "A TGF-beta receptor type-2 that has had the signal peptide removed." [PRO:DNx]
comment: Category=modification.
synonym: "TGFBR2/SigPep-" EXACT PRO-short-label [PRO:DNx]
is_a: PR:000000005 ! TGF-beta receptor type-2
intersection_of: PR:000000005 ! TGF-beta receptor type-2
intersection_of: lacks_part SO:0000418 ! signal_peptide
relationship: lacks_part SO:0000418 ! signal_peptide

_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.


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