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PRotein Ontology (PRO) Release 42.0, version 0
15-July-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 42.0 (15-July-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 42.0, version 0:

There are 60311 PRO terms in the pro.obo file
      54 terms are in the 'external' category.
     347 terms are in the 'family' category.
   23520 terms are in the 'gene' category.
    1840 terms are in the 'sequence' category.
    6631 terms are in the 'modification' category.
     214 terms are in the 'complex' category.
       9 terms are in the 'organism-family' category.
   23845 terms are in the 'organism-gene' category.
    1787 terms are in the 'organism-sequence' category.
    1459 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).
       3 annotations of a phenotype (3 PRO terms).
 
There are 142267 PRO terms in the promapping.obo file
   89844 terms are in the 'organism-gene' category.
   52423 terms are in the 'organism-sequence' category.


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_

None

_Forthcoming changes_

1) Changes in the annotation file (PAF):

 a) the relation used for disease terms will be replaced. Instead of agent_in we will use 'associated_with_disease_progression' or 'associated_with_disease_suppression'. Note however that the relation may change in the future as progress on this field occurs.

 b) the column Equivalent_Form will be removed as it is not longer maintained in this file.

2) The annotat

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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