Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
By D. Natale, C. Arighi, Judith A. Blake, Jonathan P. Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie E. Cowart, P. D’Eustachio, A. Diehl and 12 more. 2016
98 citations recorded by the source corpus.
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.
Subfields: Molecular Biology
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In Molecular Biology
- Gene Ontology Consortium
- Paul D. Thomas
- Huaiyu Mi
- Dustin Ebert
- Tremayne Mushayahama
- Pascale Gaudet
- Anushya Muruganujan
- Judith A. Blake
Citations in the corpus
- The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
- The Gene Ontology knowledgebase in 2023 (2023, background): “2019), PATO (Gkoutos, Schofield and Hoehndorf 2018), and Protein Ontology (Natale et al. 2017).”