Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu
BMC Bioinformatics 12 (371):1-11 (2011)
Authors |
|
Abstract |
Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and
modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/.
|
Keywords | proteomics protein complexes Gene Ontology |
Categories | (categorize this paper) |
Options |
![]() ![]() ![]() ![]() |
Download options
References found in this work BETA
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel & Suzanna Lewis - 2007 - Nature Biotechnology 25 (11):1251--1255.
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.
The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
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 - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge.Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Misra Sima, Westerfield Monte, Ashburner Michael, Christopher G. Chute, Ida Sim, Harold Solbrig, M. A. Storey, Barry Smith, John D. Richter, Natasha Noy & Mark A. Musen - 2006 - Omics: A Journal of Integrative Biology 10 (2):185-198.
View all 6 references / Add more references
Citations of this work BETA
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.
Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
Similar books and articles
The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Natale Darren, A. Arighi, N. Cecilia, Barker Winona, C. Blake, A. Judith, Bult Carol, J. Caudy, Michael Drabkin, J. Harold, DâEustachio Peter, Evsikov Alexei, V. Huang & Hongzhan Others - 2011 - Nucleic Acids Research 39 (suppl 1):D539--D545.
The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
Protein Ontology: A Controlled Structured Network of Protein Entities.Natale Darren, A. Arighi, N. Cecilia, Blake Judith, A. Bult, J. Carol, Christie Karen, R. Cowart, Julie DâEustachio, Peter Diehl, D. Alexander, Drabkin Harold, J. Helfer & Olivia Others - 2013 - Nucleic Acids Research:gkt1173.
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.
TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
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 - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
Framework for a Protein Ontology.Darren Natale, Arighi A., N. Cecilia, Winona Barker, Blake C., Chang Judith, Hu Ti-Cheng, Liu Zhangzhi, Smith Hongfang, Wu Barry & H. Cathy - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
Investigating Protein-Protein Interfaces in Bacterial Transcription Complexes: A Fragmentation Approach.Patricia C. Burrows - 2003 - Bioessays 25 (12):1150-1153.
Protein‐Protein Interactions: Making Sense of Networks Via Graph‐Theoretic Modeling.Nataša Pržulj - 2011 - Bioessays 33 (2):115-123.
The Development of Non-Coding RNA Ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
After Fifty Years, Why Are Protein X-Ray Crystallographers Still in Business?Sandra D. Mitchell & Angela M. Gronenborn - 2015 - British Journal for the Philosophy of Science:axv051.
Parallel Dynamics and Evolution: Protein Conformational Fluctuations and Assembly Reflect Evolutionary Changes in Sequence and Structure.Joseph A. Marsh & Sarah A. Teichmann - 2014 - Bioessays 36 (2):209-218.
Metabolites as Global Regulators: A New View of Protein Regulation.Xiyan Li & Michael Snyder - 2011 - Bioessays 33 (7):485-489.
Could Those Rapidly Exchangeable Phosphoproteins Be Polyphosphate-Protein Complexes?Norman W. Gabel - 1972 - Perspectives in Biology and Medicine 15 (4):640-643.
The Endomembrane System: A Representation of the Extracellular Medium? [REVIEW]Mehmet Ozansoy & Yagmur Denizhan - 2009 - Biosemiotics 2 (3):255-267.
Analytics
Added to PP index
2017-04-28
Total views
104 ( #111,157 of 2,498,783 )
Recent downloads (6 months)
20 ( #42,703 of 2,498,783 )
2017-04-28
Total views
104 ( #111,157 of 2,498,783 )
Recent downloads (6 months)
20 ( #42,703 of 2,498,783 )
How can I increase my downloads?
Downloads