PRotein Ontology (PRO) Release 6.0, version 1 Note
22-June-2009


The Protein Ontology Consortium-- Protein Information Resource, The Jackson Laboratory, and the Department of Philosophy, State University of New York at Buffalo--is pleased to announce PRO Release 6.0 (1-June-2009). 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. Further information is available at http://pir.georgetown.edu/pro/.

PRO Release 6.0, version 1 consists of 2941 terms with their respective definitions, comprising the families and translation products for 1045 genes. 

--Changes from previous version--
1- Update of some protein primary names.
2- Minor editing of some definitions.

--Changes from previous release (from release 5)--
To the obo file:

1- We have revised the description of the Category=modification which now refers to the protein products derived from a single mRNA species that differ because of some change (or lack thereof) that occurs after the initiation of translation (co- and post-translational). This includes sequence differences due to cleavage and chemical changes to one or more amino acid residues. For example, the long isoform of smad2 can either be unmodified or be post-translationally modified to contain phosphorylated residues. As a result we introduced the term unmodified form as a sibling of the post-translationally modified forms. 
2- We have started to introduce logical definitions (cross-products in OBO edit) for many terms in the Category=modification.
Example: 
[Term]
id: PRO:000000197
name: TGF-beta receptor type-2 isoform 1 cleaved form
def: "A TGF-beta receptor type-2 isoform 1 that has been processed by proteolytic cleavage." [PRO:CNA]
comment: Category=modification.
intersection_of: PRO:000000048 ! TGF-beta receptor type-2 isoform 1
intersection_of: has_modification MI:0570 ! protein cleavage

We use the term lacks_modification to define the unmodified form as follows

[Term]
id: PRO:000002463
name: TGF-beta receptor type-2 isoform 1 unmodified form
def: "A TGF-beta receptor type-2 isoform 1 that has not been subjected to any co- or post-translational residue modification or peptide bond cleavage." [PRO:DAN]
comment: Category=modification.
intersection_of: PRO:000000048 ! TGF-beta receptor type-2 isoform 1
intersection_of: lacks_modification PRO:000002967 ! post-translational protein modification

If you open the obo file in obo edit, please turn on the reasoner in order to display the hierarchy.

Now the ontology includes a subset of terms from MOD and MI ontologies that has been used for the logical definitions.  


To the PAF file:

1- A new column named Relative_to has been added to indicate the reference entity when using the modifiers increased, decreased or altered. This column has been placed between columns 7 and 8 in the PAF file. The PAF column order and  description are available in the PAF guidelines ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/PAF_guidelines.pdf
2- Due to the introduction of the unmodified forms, the annotation that was in the previous release under the isoform nodes in Category=sequence level, now is correctly reassigned to the unmodified form terms.