PRotein Ontology (PRO) Release 51.0 (23-Dec-2016)

There are 209540 PRO terms in the Protein Ontology.
   59 terms are in the 'external' category.
    6 terms are in the 'seqgroup' category.
   112 terms are in the 'organism-seqgroup' category.
   397 terms are in the 'family' category.
  23567 terms are in the 'gene' category.
  8325 terms are in the 'sequence' category.
  6676 terms are in the 'modification' category.
   212 terms are in the 'complex' category.
   15 terms are in the 'organism-family' category.
  94253 terms are in the 'organism-gene' category.
  68685 terms are in the 'organism-sequence' category.
  6430 terms are in the 'organism-modification' category.
   385 terms are in the 'organism-complex' category.
   117 terms are in the 'union' category.
2514 terms have some kind of annotation, codifying the information from 1674 papers.
  4419 connections to GO (1711 PRO terms).
   292 connections to MOD (255 PRO terms).
   616 connections to Pfam (369 PRO terms).
   338 connections to SO (317 PRO terms).
   349 annotations of a phenotype (342 PRO terms).

The ontology includes a subset of terms from other ontologies and resources that are used for logical definitions.

_Current changes_

1) Two new synonymtypedef declarations have been added to the header, namely

synonymtypedef: PRO-proteoform-std "Synonyms for proteoforms based on use of UniProtKB accession, subsequence range, and positions and types of modifications or variations" EXACT

synonymtypedef: PRO-proteoform-ftid "Synonyms for proteoforms based on use of UniProtKB feature identifier (FTId) and positions and types of modifications or variations" EXACT

Therefore two new synonyms lines have been added to modification terms. Examples:

synonym: "cow-CSN1S1/SigPep-" EXACT PRO-short-label [PRO:DNx]
synonym: "PRO_0000004446" EXACT PRO-proteoform-ftid [PRO:DNx]

2) PRO terms of use has been added as a remark in the header: “The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details.”

3) A new Category pair "seqgroup" and "organism-seqgroup" has been added to indicate related sequences from a single gene. For, example the different flu hemagglutinin sequences of H1 type vs H2 type.

4) The identifiers for relations have been changed to their correct identifiers. For example, part_of is BFO:0000050.

5)Terms that are logically defined by gene, such as PR:Q9USM5, which were defined like so:

intersection_of: PR:000000001 ! protein
intersection_of: has_gene_template PomBase:SPCC16A11.12c ! ubp1 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:284812 ! Schizosaccharomyces pombe 972h-

Will now be defined like so:

intersection_of: PR:000000001 ! protein
intersection_of: only_in_taxon NCBITaxon:284812 ! Schizosaccharomyces pombe 972h-
intersection_of: has_gene_template PomBase:SPCC16A11.12c ! ubp1 (Schizosaccharomyces pombe)

This is because the gene used is sometimes defined for a broader taxon than the one under consideration (as in the pombe case), so the intersection with taxon is required.