title: Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
abstract: 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.
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA dan5@georgetown.edu.
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Cecilia N
authors.initials: CN
authors.lastname: Arighi
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors.forename: Judith A
authors.identifier: 0000-0001-8522-334X
authors.initials: JA
authors.lastname: Blake
authors.affiliation: Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY 14214, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Bona
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Chuming
authors.initials: C
authors.lastname: Chen
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Sheng-Chih
authors.initials: SC
authors.lastname: Chen
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors.forename: Karen R
authors.initials: KR
authors.lastname: Christie
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Cowart
authors.affiliation: Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: D'Eustachio
authors.affiliation: Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA.
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Diehl
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors.forename: Harold J
authors.initials: HJ
authors.lastname: Drabkin
authors.affiliation: Roswell Park Cancer Institute, Buffalo, NY 14203, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA.
authors.forename: William D
authors.initials: WD
authors.lastname: Duncan
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Hongzhan
authors.initials: H
authors.lastname: Huang
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Jia
authors.initials: J
authors.lastname: Ren
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Ross
authors.affiliation: Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY 14214, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Ruttenberg
authors.affiliation: Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
authors.forename: Veronica
authors.initials: V
authors.lastname: Shamovsky
authors.affiliation: National Center for Ontological Research, University at Buffalo, Buffalo, NY 14214, USA.
authors.forename: Barry
authors.initials: B
authors.lastname: Smith
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Abdelrahman
authors.initials: A
authors.lastname: El-Sayed
authors.affiliation: Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.|Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D064878:Web Browser
chemical_list: D011506:Proteins