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PRotein Ontology (PRO) Release 11.0, version 0
08-June-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 11.0 (08-June-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 11.0, version 0:

There are 25570 PRO terms
   13 terms are in the 'organism-modification' category.
   92 terms are in the 'organism-sequence' category.
   1131 terms are in the 'sequence' category.
   7 terms are in the 'complex' category.
   18182 terms are in the 'gene' category.
   5627 terms are in the 'modification' category.
   139 terms are in the 'organism-gene' category.
   276 terms are in the 'family' category.
1410 terms have some kind of annotation, codifying the information from
917 papers.
  1964 connections to GO (669 PRO terms).
  360 connections to MOD (316 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, MI, 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 10.0_

1) The has_modification and lacks_modification relations have been obsoleted

2) The logical definition for PRO terms for unmodified form has been revised as follows: 
   the line 
intersection_of: lacks_modification PRO:000002967 ! post-translational protein modification 
   has been replaced with 
intersection_of: has_part PRO:000021935 ! immature protein part 
intersection_of: lacks_part PRO:0000255513 ! modified amino acid chain residue 
disjoint_from: PRO:000018264 ! proteolytic cleavage product 

3) Terms for modified protein residues have been revised to reflect the fact that protein is_a amino acid chain. For example, "post-translationally modified protein residue" has become "post-translationally modified amino acid chain residue." Also, a unifying term "modified amino acid chain residue" has been introduced." 

4) There are two additional mapping files, promapping.obo is the mapping file in OBO format, and the promapping_newformat.txt is the mapping file in the upcoming new format (see upcoming changes below).

_Important upcoming changes for Release 12.0_

1) Starting with release 12, 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. 

2) Also in release 12 PRO will be aligned with the Basic Formal Ontology (BFO), and therefore the root nodes will change. 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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