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PRotein Ontology (PRO) Release 12.0, version 0
21-July-2010

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 12.0 (21-July-2010). PRO describes the relationships of proteins and protein evolutionary classes, delineates the multiple protein forms of a gene locus (ontology for protein forms), and interconnects existing ontologies. In addition, PRO formally describes protein complexes. Further information is available at http://pir.georgetown.edu/pro/.

In PRO Release 12.0, version 0:

There are 25656 PRO terms
   277 terms are in the 'family' category.
   18182 terms are in the 'gene' category.
   1144 terms are in the 'sequence' category.
   5643 terms are in the 'modification' category.
   144 terms are in the 'organism-gene' category.
   107 terms are in the 'organism-sequence' category.
   33 terms are in the 'organism-modification' category.
   13 terms are in the 'complex' category.
   9 terms are in the 'organism-complex' category.
1436 terms have some kind of annotation, codifying the information from 926 papers.
  1995 connections to GO (685 PRO terms).
  361 connections to MOD (317 PRO terms).
  599 connections to Pfam (358 PRO terms).
  325 connections to SO (307 PRO terms).
  296 annotations of a phenotype (289 PRO terms). 

The ontology includes a subset of terms from 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.

_Changes from Release 11.0_

1) From this release on the promapping.txt file will consist of three tab-delimited columns: 

PRO ID 
Mapped ID 
exact|is_a|related 

The latter column indicates the equivalency of the mapped term to the PRO term in a hierarchical/categorical sense. For example, the entity represented by a UniProtKB accession is either organism-gene or organism-sequence, hence would be tagged as "exact" if the PRO term was such. "is_a" indicates that the mapped term belongs to a subcategory of the PRO term, while "related" indicates that the mapped term is either a superclass of the the indicated PRO class, or a non-child descendant (that is, grandchild or other). Currently "related" terms are not mapped, but may be done in the future. A preview of the format is available in the file promapping_newformat.txt. An explicit hierarchical view of that same information is provided in the file promapping.obo. 

The older format of the file has been renamed to promapping_oldformat.txt

2) PRO is now aligned with the Basic Formal Ontology (BFO), and therefore the root nodes changed from previous release. For example, "amino acid chain" and "protein complex" will be children of the BFO term "object" while "immature protein part" and "modified amino acid residue" will be children of "fiat_object_part" (both BFO terms are "material_entity").

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