PRotein Ontology (PRO) Release 60.0 (22-Apr-2020)

There are 217558 PRO terms in the Protein Ontology. Those representing individual proteins are mapped to 134297 UniProtKB sequences.
      516 terms are in the 'family' category.
    23479 terms are in the 'gene' category.
       10 terms are in the 'seqgroup' category.
     8029 terms are in the 'sequence' category.
     4970 terms are in the 'modification' category.
      211 terms are in the 'complex' category.
       32 terms are in the 'organism-family' category.
    99635 terms are in the 'organism-gene' category.
       27 terms are in the 'organism-genegroup' category.
      154 terms are in the 'organism-seqgroup' category.
    70907 terms are in the 'organism-sequence' category.
     6648 terms are in the 'organism-modification' category.
      422 terms are in the 'organism-complex' category.
       25 terms are in the 'union' category.
       72 terms are in the 'external' category.
 2586 terms have some kind of annotation, codifying the information from 1656 papers.
     4442 connections to GO (1724 PRO terms).
      616 connections to Pfam (369 PRO terms).
       27 connections to SO (24 PRO terms).
      611 annotations of a phenotype (586 PRO terms).

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

_Current changes_

1) Implemented a change to the PRO-short-labels, definitions, PRO-proteoform-std, and PRO-proteoform-ftid to account for cases when the cardinality of a specific type of unknown-position modification is known to be equal to or more than some number. The minimum cardinality is indicated in parentheses, along with a plus sign. In the following example (from PR:000046934), there are at least three 4-hydroxy-L-prolines (4HyPro; MOD:00039):
synonym: "hCOL5A1/SigPep-/3HyPro4HyPro(3+)" EXACT PRO-short-label [PRO:DNx]
synonym: "UniProtKB:P20908, 38-1838, MOD:00038|MOD:00039(3+)" EXACT PRO-proteoform-std [PRO:DNx]
2) Implemented a periodic check using Bpforms software (https://www.bpforms.org/) to verify proteoforms. Changes to canonical sequences (for example, a different start position is selected, or a different isoform structure is used) over time will cause position-based information to go stale. Using the Bpforms package allows such cases to be found and corrected.
3) Added a new synonym type "Reactome-displayName" to indicate the name of the corresponding entity in Reactome.
4) Added idspace 'VectorBase'

_Forthcoming changes_

1) 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.
2) The PRO-proteoform-std and -ftid will be revamped to allow 'group' modifications. These are needed whenever a particular modification requires a precision not afforded by PSI-MOD terms. For example, though PSI-MOD allows one to indicate glycosylation at a particular residue, it does not allow one to indicate the precise glycan present there.
3) In cases when a proteoform is defined with respect to a canonical sequence, we will create both EXACT and NARROW PRO-proteoform-std and -ftid synonyms. This will enhance the ability to find specific proteoforms when searching using these synonym types. 
4) We will switch the only_in_taxon relation to in_taxon, in anticipation of the likely deprecation of the former in favor of the latter.