PRotein Ontology (PRO) Release 50.0, version 0 22-Sept-2016 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 50.0 (22-Sept-2016). PRO describes the relationships of proteins and protein evolutionary classes, delineates the multiple protein forms of a gene locus (ontology for protein forms), protein complexes, and interconnects existing ontologies. Further information is available at http://www.proteininformationresource.org/pro/. In PRO Release 50.0, version 0: There are 208290 PRO terms in the Protein Ontology. Those representing individual proteins are mapped to 127734 UniProtKB sequences. 57 terms are in the 'external' category. 403 terms are in the 'family' category. 23560 terms are in the 'gene' category. 8323 terms are in the 'sequence' category. 6677 terms are in the 'modification' category. 212 terms are in the 'complex' category. 34 terms are in the 'organism-family' category. 93389 terms are in the 'organism-gene' category. 68413 terms are in the 'organism-sequence' category. 6420 terms are in the 'organism-modification' category. 384 terms are in the 'organism-complex' category. 117 terms are in the 'union' category. 2513 terms have some kind of annotation, codifying the information from 1673 papers. 4416 connections to GO (1710 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 GO, MOD, CHEBI, 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. _Current changes_ 1) From this release on the default download of PRO (http://purl.obolibrary.org/obo/pr.obo) will point to the reasoned version (called pro_reasoned.obo). The previous default (pro.obo), that has not had prior reasoning applied, can be obtained via ftp (ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo). 2) A new relation has been added "non-covalently_bound_to". Example: PR:000037031 represents the class of GTP-binding protein rho3 in its GTP-bound form [Typedef] id: non-covalently_bound_to name: non-covalently_bound_to def: "A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions. Such entities will, at all times of the interaction, colocalize with each other." [PRO:DAN] domain: CHEBI:24431 ! chemical entity range: CHEBI:24431 ! chemical entity is_symmetric: true 3) We introduced a new standard comment, "Status=unreviewed.", to indicate proteoforms that have been automatically generated based on data integrated from external resources but have not yet been reviewed by a curator. Example:PR:000046210 [Term] id: PR:000046210 name: heterogeneous nuclear ribonucleoprotein A0 phosphorylated 1 (mouse) def: "A heterogeneous nuclear ribonucleoprotein A0 (mouse) that has been post-translationally modified to include phosphorylation at a position equivalent to Ser-84 of the amino acid sequence represented by UniProtKB:Q9CX86. UniProtKB:Q9CX86, Ser-84, MOD:00046." [PMID:12456657, iPTMnet:Q9CX86] comment: Category=organism-modification. Evidence=(ECO:0000006, based on PMID:12456657). Status=unreviewed. synonym: "mHNRNPA0/Phos:1" EXACT PRO-short-label [PRO:DNx] is_a: PR:Q9CX86 ! heterogeneous nuclear ribonucleoprotein A0 (mouse) relationship: has_part MOD:00046 ! O-phospho-L-serine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus _Forthcoming changes_ ================================================