Relations in biomedical ontologies
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* Corresponding author: Barry Smith phismith@buffalo.edu
Genome Biology 2005, 6:R46 doi:10.1186/gb-2005-6-5-r46
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BioMed Central: 51 citations
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Research
A semantic web framework to integrate cancer omics data with biological knowledge Matthew E Holford, James P McCusker, Kei-Hoi Cheung, Michael Krauthammer BMC Bioinformatics 2012, 13(Suppl 1):S10 (25 January 2012) |
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Research
Populous: a tool for building OWL ontologies from templates Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens BMC Bioinformatics 2012, 13(Suppl 1):S5 (25 January 2012) |
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Research article
A unified framework for managing provenance information in translational research Satya S. Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth BMC Bioinformatics 2011, 12:461 (29 November 2011) |
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Research article
Unintended consequences of existential quantifications in biomedical ontologies Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz BMC Bioinformatics 2011, 12:456 (24 November 2011) Almost a quarter of all existential restrictions in the Open Biomedical Ontologies (OBO) Foundry contain assertions that do not properly describe the underlying biological reality, suggesting that a restriction to fewer, well-defined, relation types is needed.
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Research
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology Yu Lin, Zuoshuang Xiang, Yongqun He Journal of Biomedical Semantics 2011, 2:9 (31 October 2011) The first reported bacterial infectious disease ontology, that provides a brucellosis knowledge-base and supports brucellosis data integration and automated reasoning.
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Database
The representation of protein complexes in the Protein Ontology (PRO) Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu BMC Bioinformatics 2011, 12:371 (19 September 2011) ProComp is a component of the Protein Ontology (PRO) database for implementing a logical and consistent representation of protein complexes, and facilitates robust annotation of variations in composition and function contexts within and between species
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Research
Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm Journal of Biomedical Semantics 2011, 2:6 (13 September 2011) |
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Short Report
Bernard de Bono, Robert Hoehndorf , Sarala Wimalaratne, George Gkoutos, Pierre Grenon BMC Research Notes 2011, 4:313 (30 August 2011) |
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Methodology article
Integrating systems biology models and biomedical ontologies Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook, Georgios V Gkoutos BMC Systems Biology 2011, 5:124 (11 August 2011) |
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Proceedings
Johannes Röhl, Ludger Jansen Journal of Biomedical Semantics 2011, 2(Suppl 4):S4 (9 August 2011) |
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Proceedings
Grains, components and mixtures in biomedical ontologies Ludger Jansen, Stefan Schulz Journal of Biomedical Semantics 2011, 2(Suppl 4):S2 (9 August 2011) |
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Research article
Sabina Leonelli, Alexander D Diehl, Karen R Christie, Midori A Harris, Jane Lomax BMC Bioinformatics 2011, 12:325 (5 August 2011) |
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Proceedings
Integration and publication of heterogeneous text-mined relationships on the Semantic Web Adrien Coulet, Yael Garten, Michel Dumontier, Russ B Altman, Mark A Musen, Nigam H Shah Journal of Biomedical Semantics 2011, 2(Suppl 2):S10 (17 May 2011) |
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Proceedings
Representation of research hypotheses Larisa N Soldatova, Andrey Rzhetsky Journal of Biomedical Semantics 2011, 2(Suppl 2):S9 (17 May 2011) |
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Proceedings
Developing a kidney and urinary pathway knowledge base Simon Jupp, Julie Klein, Joost Schanstra, Robert Stevens Journal of Biomedical Semantics 2011, 2(Suppl 2):S7 (17 May 2011) |
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Proceedings
Scalable representations of diseases in biomedical ontologies Stefan Schulz, Kent Spackman, Andrew James, Cristian Cocos, Martin Boeker Journal of Biomedical Semantics 2011, 2(Suppl 2):S6 (17 May 2011) |
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Proceedings
Automating generation of textual class definitions from OWL to English Robert Stevens, James Malone, Sandra Williams, Richard Power, Allan Third Journal of Biomedical Semantics 2011, 2(Suppl 2):S5 (17 May 2011) |
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Proceedings
An open annotation ontology for science on web 3.0 Paolo Ciccarese, Marco Ocana, Leyla Garcia Castro, Sudeshna Das, Tim Clark Journal of Biomedical Semantics 2011, 2(Suppl 2):S4 (17 May 2011) |
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Proceedings
Joanne S Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine K Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, Scott M Marshall, James P McCusker, Deborah L McGuinness, Chimezie Ogbuji, Elgar Pichler, Robert L Powers, Eric Prud’hommeaux, Matthias Samwald, Lynn Schriml, Peter J Tonellato, Patricia L Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier Journal of Biomedical Semantics 2011, 2(Suppl 2):S1 (17 May 2011) |
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Research
Mapping between the OBO and OWL ontology languages Syed Tirmizi, Stuart Aitken, Dilvan A Moreira, Chris Mungall, Juan Sequeda, Nigam H Shah, Daniel P Miranker Journal of Biomedical Semantics 2011, 2(Suppl 1):S3 (7 March 2011) |
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Methodology article
Relations as patterns: bridging the gap between OBO and OWL Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre BMC Bioinformatics 2010, 11:441 (31 August 2010) |
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Technical Note
OntoFox: web-based support for ontology reuse Zuoshuang Xiang, Mélanie Courtot, Ryan R Brinkman, Alan Ruttenberg, Yongqun He BMC Research Notes 2010, 3:175 (22 June 2010) OntoFox facilitates knowledge sharing by supporting extraction and reuse of user-defined subsets of terms from existing ontologies, enabling interoperability between projects through standardization of concepts and definitions.
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Proceedings
Modeling biomedical experimental processes with OBI Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jessica A Turner, Jie Zheng, Journal of Biomedical Semantics 2010, 1(Suppl 1):S7 (22 June 2010) |
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Proceedings
Matthias Samwald, Holger Stenzhorn Journal of Biomedical Semantics 2010, 1(Suppl 1):S5 (22 June 2010) |
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Proceedings
RKB: a Semantic Web knowledge base for RNA Jose Cruz-Toledo, Michel Dumontier, Marc Parisien, François Major Journal of Biomedical Semantics 2010, 1(Suppl 1):S2 (22 June 2010) |
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Research article
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base Jiye Ai, Barry Smith, David T Wong BMC Bioinformatics 2010, 11:302 (3 June 2010) |
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Research
Applying the functional abnormality ontology pattern to anatomical functions Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso Journal of Biomedical Semantics 2010, 1:4 (31 March 2010) |
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Method
Integrating phenotype ontologies across multiple species Christopher J Mungall, Georgios V Gkoutos, Cynthia L Smith, Melissa A Haendel, Suzanna E Lewis, Michael Ashburner Genome Biology 2010, 11:R2 (8 January 2010) A phenotypic ontology that can be used for the analysis of phenotype-genotype data across multiple species, paving the way for truly cross species translational research. |
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Research
BioGateway: a semantic systems biology tool for the life sciences Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper BMC Bioinformatics 2009, 10(Suppl 10):S11 (1 October 2009) |
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Software
Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009) A software resource for the analysis of cell cycle related molecular networks. |
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Proceedings
TGF-beta signaling proteins and the Protein Ontology Cecilia N Arighi, Hongfang Liu, Darren A Natale, Winona C Barker, Harold Drabkin, Judith A Blake, Barry Smith, Cathy H Wu BMC Bioinformatics 2009, 10(Suppl 5):S3 (6 May 2009) |
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Research article
An improved ontological representation of dendritic cells as a paradigm for all cell types Anna Masci, Cecilia N Arighi, Alexander D Diehl, Anne E Lieberman, Chris Mungall, Richard H Scheuermann, Barry Smith, Lindsay G Cowell BMC Bioinformatics 2009, 10:70 (25 February 2009) |
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Proceedings
Formal representation of complex SNOMED CT expressions Stefan Schulz, Kornél Markó, Boontawee Suntisrivaraporn BMC Medical Informatics and Decision Making 2008, 8(Suppl 1):S9 (27 October 2008) |
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Proceedings
Ontological analysis of SNOMED CT Gergely Héja, György Surján, Péter Varga BMC Medical Informatics and Decision Making 2008, 8(Suppl 1):S8 (27 October 2008) |
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Software
OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology Kieran O'Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson, Henning Hermjakob BMC Bioinformatics 2008, 9:437 (16 October 2008) |
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Research
Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura, Akihiko Konagaya BMC Bioinformatics 2008, 9(Suppl 6):S11 (28 May 2008) |
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Proceedings
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens BMC Bioinformatics 2008, 9(Suppl 5):S1 (29 April 2008) |
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Research
RDFScape: Semantic Web meets Systems Biology Andrea Splendiani BMC Bioinformatics 2008, 9(Suppl 4):S6 (25 April 2008) |
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Research
Ontology-based, Tissue MicroArray oriented, image centered tissue bank Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano Milanesi BMC Bioinformatics 2008, 9(Suppl 4):S4 (25 April 2008) |
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Methodology article
An anatomy ontology to represent biological knowledge in Dictyostelium discoideum Pascale Gaudet, Jeffery G Williams, Petra Fey, Rex L Chisholm BMC Genomics 2008, 9:130 (18 March 2008) |
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Methodology article
Defining functional distances over Gene Ontology Angela del Pozo, Florencio Pazos, Alfonso Valencia BMC Bioinformatics 2008, 9:50 (25 January 2008) |
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Research article
Corpus annotation for mining biomedical events from literature Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii BMC Bioinformatics 2008, 9:10 (8 January 2008) A new semantic enrichment technique that highlights biomedical events in the literature has been used to produce a large, high-quality annotated corpus, which will be valuable for Natural Language Processing-based text mining.
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Proceedings
Framework for a Protein Ontology Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H Wu BMC Bioinformatics 2007, 8(Suppl 9):S1 (27 November 2007) |
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Method
Simplified ontologies allowing comparison of developmental mammalian gene expression Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide Genome Biology 2007, 8:R229 (25 October 2007) The Developmental eVOC ontologies presented are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy. |
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Methodology article
Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre BMC Bioinformatics 2007, 8:377 (9 October 2007) The problem of interoperability of fixed anatomy ontologies with the more flexible phenotype ontologies can be solved by treating canonical information as the default that can be modified when more information is available.
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Research article
Spatial location and its relevance for terminological inferences in bio-ontologies Stefan Schulz, Kornél Markó, Udo Hahn BMC Bioinformatics 2007, 8:134 (20 April 2007) |
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Commentary
Mikel Aranguren, Sean Bechhofer, Phillip Lord, Ulrike Sattler, Robert Stevens BMC Bioinformatics 2007, 8:57 (20 February 2007) |
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Proceedings
A critical review of PASBio's argument structures for biomedical verbs K Bretonnel Cohen, Lawrence Hunter BMC Bioinformatics 2006, 7(Suppl 3):S5 (24 November 2006) |
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Methodology article
Alexander Castro, Philippe Rocca-Serra, Robert Stevens, Chris Taylor, Karim Nashar, Mark A Ragan, Susanna-Assunta Sansone BMC Bioinformatics 2006, 7:267 (25 May 2006) A novel method for building biological ontologies introduces the use of concept maps during the knowledge acquisition phase to assist collaborative development and to formalize the methodology.
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Methodology article
Quality control for terms and definitions in ontologies and taxonomies Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith BMC Bioinformatics 2006, 7:212 (19 April 2006) |