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Title: Protein Ontology (PRO)      
aggregation:
digital object
privacy:
not applicable
refinement:
uncurated
ID:
http://cloud4.proteininformationresource.org/sparql
storedIn:
Multiple: Amazon Web Services, IBM
availability:
Available
creators:
Protein Information Resource
keywords:
Database; Ontology, Proteins, Post-translational modification; SPARQL
description:
Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific (e.g. the entity representing all protein products of the human SMAD2 gene is described in PR:Q15796; one particular human SMAD2 protein form, phosphorylated on the last two serines of a conserved C-terminal SSxS motif is defined by PR:000025934). Here we provide a SPARQL end point server for retrieving data from Protein Ontology database.
types:
Computational
authors:
Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH
publicationVenue:
Nucleic Acids Research
description:
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.
ID:
https://doi.org/10.1093/nar/gkw1075
title:
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
dateReleased:
01-04-2017
name:
Creative Commons Attribution 4.0 International (CC BY 4.0)
landingPage: http://creativecommons.org/licenses/by/4.0/
identifier:
5R01GM080646-12
funders:
National Institutes of Health
count:
1
unit:
MB
ID:
SCR:016270
name:
CEDAR Workbench
abbreviation:
CEDAR
homePage: https://cedar.metadatacenter.org