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PRotein Ontology (PRO) Release 40.0, version 0
28-May-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 41.0 (28-May-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 41.0, version 0:

There are 59578 PRO terms in the pro.obo file
      54 terms are in the 'external' category.
     347 terms are in the 'family' category.
   23521 terms are in the 'gene' category.
    1844 terms are in the 'sequence' category.
    6632 terms are in the 'modification' category.
     214 terms are in the 'complex' category.
       9 terms are in the 'organism-family' category.
   23810 terms are in the 'organism-gene' category.
    1098 terms are in the 'organism-sequence' category.
    1447 terms are in the 'organism-modification' category.
     368 terms are in the 'organism-complex' category.
      23 terms are in the 'union' category.
2124 terms have some kind of annotation, codifying the information from 1353 papers.
    3501 connections to GO (1253 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) Other existing PRO terms in the organism-sequence category (which are thus equivalent to alternative products in UniProtKB entries) 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) is now PR:Q0QWG9-1.
The OBO stanza 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


_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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