================================================
PRotein Ontology (PRO) Release 36.0, version 0
03-July-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 36.0 (03-July-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 36.0, version 0:

There are 36085 PRO terms
     335 terms are in the 'family' category.
   23703 terms are in the 'gene' category.
    1713 terms are in the 'sequence' category.
    6587 terms are in the 'modification' category.
     179 terms are in the 'complex' category.
       4 terms are in the 'organism-family' category.
     953 terms are in the 'organism-gene' category.
     747 terms are in the 'organism-sequence' category.
    1343 terms are in the 'organism-modification' category.
     308 terms are in the 'organism-complex' category.
      16 terms are in the 'union' category.
1992 terms have some kind of annotation, codifying the information from 1281 papers.
    3141 connections to GO (1123 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) Please note that this release still contains a number of duplicate names and synonyms. These will be resolved in upcoming releases.
2) In the PAF.txt file, we changed 'TaxID:' prefix to 'NCBITaxon:'
3) The has_part relationship used for complexes changed to has_component
4) "Flag=automatic" were removed. The evidence field  instead indicates this (as it already does, with DNx and CNx).
5) In the promapping.obo file, UniProtKB entries are prefixed with
PR: instead of UniProtKB: so that the ontology terms can be linked to and viewed within the PRO hierarchy. Links to the UniProtKB database remain in the xref field, and the accessions used are not changed.

_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.


For next Release

4) In pro.obo, PRO terms in the organism-gene category (which are thus equivalent to UniProtKB terms) will 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) will be PR:P40336. The OBO stanza will thus have:

[Term]
id: PR:P40336
alt_id: PR:000025484
<other stuff>
xref: UniProtKB:P40336

9) When 8) is implemented the pro_reasoned.obo file will be generated with the ELK reasoner within the OORT release manager tool. The "implied link automatically realized !" comment will not be present. 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
 
 will become

[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 ! 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

================================================