ArticleJournal of biomedical semantics2010
Applying the functional abnormality ontology pattern to anatomical functions.
Article in Journal of biomedical semantics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models.Journal of biomedical semantics · 2014Article
- Evaluation of research in biomedical ontologies.Briefings in bioinformatics · 2013Article
- Ontology design patterns to disambiguate relations between genes and gene products in GENIA.Journal of biomedical semantics · 2011Article
- PhenomeNET: a whole-phenome approach to disease gene discovery.Nucleic acids research · 2011Article
- Integrating systems biology models and biomedical ontologies.BMC systems biology · 2011Article
- A common layer of interoperability for biomedical ontologies based on OWL EL.Bioinformatics (Oxford, England) · 2011Article
- Interoperability between phenotype and anatomy ontologies.Bioinformatics (Oxford, England) · 2010Article
- Relations as patterns: bridging the gap between OBO and OWL.BMC bioinformatics · 2010Article
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Authors and funding
3 authors.
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Abstract
backgroundSeveral biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions.Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately.
resultsWe provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions.
conclusionsOntological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities. AVAILABILITY: The source code and results of our analysis are available at http://bioonto.de.
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