Framework for a protein ontology
Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu
BMC Bioinformatics 8 (Suppl 9):S1 (2007)
Abstract
Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway.Author Profiles
My notes
Similar books and articles
Concept of immunomics: A new frontier in the battle for Gene function?Jan Klysik - 2001 - Acta Biotheoretica 49 (3):191-202.
Protein folding and evolution are driven by the Maxwell demon activity of proteins.Alejandro Balbín & Eugenio Andrade - 2004 - Acta Biotheoretica 52 (3):173-200.
Structure, function, and protein taxonomy.William Goodwin - 2011 - Biology and Philosophy 26 (4):533-545.
The Unified Medical Language System and the Gene Ontology: Some critical reflections.Anand Kumar & Barry Smith - 2003 - In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence. Berlin: Springer. pp. 135-148.
Support vector machines for predicting apoptosis proteins types.Jing Huang & Feng Shi - 2005 - Acta Biotheoretica 53 (1):39-47.
Analytical background and discussion of the chaperone model of prion diseases.J. P. Liautard - 1999 - Acta Biotheoretica 47 (3-4):219-238.
Finding the Meaning in Images: Annotation and Image Markup.Daniel L. Rubin - 2011 - Philosophy, Psychiatry, and Psychology 18 (4):311-318.
On the probability of the emergence of a protein with a particular function.Paul Erbrich - 1985 - Acta Biotheoretica 34 (1):53-80.
Analytics
Added to PP
2009-07-06
Downloads
308 (#38,976)
6 months
30 (#42,097)
2009-07-06
Downloads
308 (#38,976)
6 months
30 (#42,097)
Historical graph of downloads
Author Profiles
Citations of this work
Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base.Jiye Ai, Barry Smith & David Wong - 2010 - BMC Bioinformatics 11 (1):302.
References found in this work
Relations in Biomedical Ontologies.Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse - 2005 - Genome Biology 6 (5):R46.
Referent Tracking: The Problem of Negative Findings.Werner Ceusters, Peter Elkin & Barry Smith - 2006 - Studies in Health Technology and Informatics 124:741-46.