Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
| Author(s) | Natale, Darren A. | |
| Author(s) | Arighi, Cecilia N. | |
| Author(s) | Blake, Judith A. | |
| Author(s) | Bona, Jonathan | |
| Author(s) | Chen, Chuming | |
| Author(s) | Chen, Sheng-Chih | |
| Author(s) | Christie, Karen R. | |
| Author(s) | Cowart, Julie | |
| Author(s) | D’Eustachio, Peter | |
| Author(s) | Diehl, Alexander D. | |
| Author(s) | Drabkin, Harold J. | |
| Author(s) | Duncan, William D. | |
| Author(s) | Huang, Hongzhan | |
| Author(s) | Ren, Jia | |
| Author(s) | Ross, Karen | |
| Author(s) | Ruttenberg, Alan | |
| Author(s) | Shamovsky, Veronica | |
| Author(s) | Smith, Barry | |
| Author(s) | Wang, Qinghua | |
| Author(s) | Zhang, Jian | |
| Author(s) | El-Sayed, Abdelrahman | |
| Author(s) | Wu, Cathy H. | |
| Ordered Author | Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D’Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed and Cathy H. Wu | |
| UD Author | Arighi, Cecilia N. | en_US |
| UD Author | Chen, Chuming | en_US |
| UD Author | Chen, Sheng-Chih | en_US |
| UD Author | Cowart, Julie | en_US |
| UD Author | Huang, Hongzhan | en_US |
| UD Author | Ren, Jia | en_US |
| UD Author | Wang, Qinghua | en_US |
| UD Author | Wu, Cathy H. | en_US |
| Date Accessioned | 2018-08-09T13:12:35Z | |
| Date Available | 2018-08-09T13:12:35Z | |
| Copyright Date | Copyright © The Author(s) 2016. | en_US |
| Publication Date | 2016-11-28 | |
| Description | Publisher's PDF | en_US |
| Abstract | The Protein Ontology (PRO; http://purl.obolibrary. org/obo/pr) formally defines and describes taxonspecific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and proteincontaining 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-translationalmodification 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. | en_US |
| Department | University of Delaware. Center for Bioinformatics & Computational Biology. | en_US |
| Citation | Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H. Wu; Protein Ontology (PRO): enhancing and scaling up the representation of protein entities, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D339–D346, https://doi.org/10.1093/nar/gkw1075 | en_US |
| DOI | 10.1093/nar/gkw1075 | en_US |
| ISSN | 1362-4962 | en_US |
| URL | http://udspace.udel.edu/handle/19716/23668 | |
| Language | en_US | en_US |
| Publisher | Oxford University Press | en_US |
| dc.rights | Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. | en_US |
| dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | en_US |
| dc.source | Nucleic acids Research | en_US |
| dc.source.uri | https://academic.oup.com/nar | en_US |
| Title | Protein Ontology (PRO): enhancing and scaling up the representation of protein entities | en_US |
| Type | Article | en_US |
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