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PRotein Ontology (PRO) Release 40.0, version 0
04-March-2014

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 40.0 (04-March-2014). 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 40.0, version 0:

There are 59198 PRO terms
      53 terms are in the 'external' category.
     342 terms are in the 'family' category.
   23506 terms are in the 'gene' category.
    1798 terms are in the 'sequence' category.
    6632 terms are in the 'modification' category.
     211 terms are in the 'complex' category.
       9 terms are in the 'organism-family' category.
   23741 terms are in the 'organism-gene' category.
     914 terms are in the 'organism-sequence' category.
    1411 terms are in the 'organism-modification' category.
     352 terms are in the 'organism-complex' category.
      21 terms are in the 'union' category.
2070 terms have some kind of annotation, codifying the information from 1326 papers.
    3380 connections to GO (1201 PRO terms).
     374 connections to MOD (331 PRO terms).
     617 connections to Pfam (371 PRO terms).
     338 connections to SO (317 PRO terms).
       8 annotations of a phenotype (8 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) Newly introduced PRO terms in the organism-sequence category (which are thus equivalent to alternative products in UniProtKB entries) have the PR: id become UniProtKB-derived id. Thus, PR:Q8R5G7-1 will be the ontological representation of UniProtKB:Q8R5G7-1.
The OBO stanza is now like:

[Term]
id: PR:Q8R5G7-1
name: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1 (mouse)
def: "An Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1 that is encoded in the genome of mouse." [PRO:HJD, PMID:15546919]
comment: Category=organism-sequence.
synonym: "mARAP3/iso:1" EXACT PRO-short-label [PRO:DNx]
xref: UniProtKB:Q8R5G7-1
intersection_of: PR:000037352 ! Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 isoform 1
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus


2) MIM terms in PAF file will be replaced by the corresponding controlled vocabulary in disease ontology (DO).

_Forthcoming changes_

1) Other existing PRO terms in the organism-sequence category (which are thus equivalent to alternative products in UniProtKB entries) will have the current PR: id become an alt_id to the UniProtKB-derived id. Thus, the new primary identifier for PR:000025481 (the ontological representation of UniProtKB:Q0QWG9-1) will be PR:Q0QWG9-1.
The OBO stanza will thus have:

[Term]
id: PR:Q0QWG9-1
alt_id: PR:000025481
name: delphilin isoform 1 (mouse)
def: "A delphilin isoform 1 that is encoded in the genome of mouse." [PRO:HJD]
comment: Category=organism-sequence.
synonym: "mGRID2IP/iso:1" EXACT PRO-short-label [PRO:DNx]
xref: UniProtKB:Q0QWG9-1
intersection_of: PR:000025480 ! delphilin isoform 1
intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus

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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