PRotein Ontology (PRO) Release 56.0 (15-May-2018)

There are 215542 PRO terms in the Protein Ontology. Those representing individual proteins are mapped to 137401 UniProtKB sequences.
       27 terms are in the 'organism-genegroup' category.
       78 terms are in the 'external' category.
      154 terms are in the 'organism-seqgroup' category.
      417 terms are in the 'family' category.
    23532 terms are in the 'gene' category.
     8333 terms are in the 'sequence' category.
     5072 terms are in the 'modification' category.
      211 terms are in the 'complex' category.
       25 terms are in the 'organism-family' category.
    98475 terms are in the 'organism-gene' category.
    70056 terms are in the 'organism-sequence' category.
     6576 terms are in the 'organism-modification' category.
      390 terms are in the 'organism-complex' category.
       47 terms are in the 'union' category.
 2527 terms have some kind of annotation, codifying the information from 1691 papers.
     4446 connections to GO (1724 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) IDspaces added to header: 
   UniCarbFT
   GlyTouCan
   IUPHARfam
   IUPHARobj
   UniProtKB_VAR

2) New synonymtypedef added to header:
   NC-IUPHAR "Official label of the IUPHAR Nomenclature Committee"

3) New categories "genegroup" and "organism-genegroup" added. Terms in these categories are cases where specific subsets of gene-level (or organism-gene level) terms are collected. For example, flu virus subtypes based on neuraminidase antigenicity would have a genegroup for each of the subtypes (N1, N2, etc). 

4) Added xref to IUPHAR directly to the PRO file. Previously this information was found in a custom mapping file.

5) The synonyms of type PRO-proteoform-std and PRO-proteoform-ftid, which provide information about modified proteoforms using UniProtKB accessions, have been added to the promapping.txt file.

_Forthcoming changes_

1) We will phase out ftp as the default method for downloads, starting with release 57.0. All downloads should use PURLs, as described in https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+PURLs.
2) A new synonym type "PRO-org-label" will be added to appropriate terms. Currently the PRO-short-label synonyms use an orthology-based mechanism to identify related terms across species. The new synonym type will identify related terms based on the gene name in the given organism.