ArticleBMC bioinformatics2008
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.Scientific reports · 2019Article
- The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.Database : the journal of biological databases and curation · 2019Article
- Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties.Frontiers in pharmacology · 2019Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
- Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier.Biodiversity data journal · 2018Article
- Discovery of Emerging Design Patterns in Ontologies Using Tree Mining.Semantic web · 2018Article
- Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.Journal of biomedical informatics · 2016Article
- Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.Journal of biomedical semantics · 2016Article
- Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.Journal of biomedical semantics · 2015Article
- The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.Journal of biomedical semantics · 2014Article
- Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.Journal of biomedical semantics · 2014Article
- Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV).NeuroImage · 2013Article
- Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.Journal of biomedical semantics · 2012Article
- Populous: a tool for building OWL ontologies from templates.BMC bioinformatics · 2012Article
- Applications of ontology design patterns in biomedical ontologies.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2012Article
- Predicting the extension of biomedical ontologies.PLoS computational biology · 2012Article
- Ontology design patterns to disambiguate relations between genes and gene products in GENIA.Journal of biomedical semantics · 2011Article
- Semi-automated ontology generation within OBO-Edit.Bioinformatics (Oxford, England) · 2010Article
- Applying the functional abnormality ontology pattern to anatomical functions.Journal of biomedical semantics · 2010Article
- The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.Genome biology · 2009Article
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4 authors.
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Abstract
backgroundBio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.
resultsAnalogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (http://odps.sourceforge.net/).
conclusionsOntology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.
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