ArticleJournal of biomedical semantics2011
Ontology design patterns to disambiguate relations between genes and gene products in GENIA.
Article in Journal of biomedical semantics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition.Bioinformatics (Oxford, England) · 2024Article
- The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.Journal of biomedical semantics · 2018Review
- Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.Journal of biomedical semantics · 2015Article
- Design patterns for the development of electronic health record-driven phenotype extraction algorithms.Journal of biomedical informatics · 2014Article
- Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.BMC bioinformatics · 2012Article
- Towards mature use of semantic resources for biomedical analyses.Journal of biomedical semantics · 2011Article
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Authors and funding
6 authors.
Funding
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Abstract
motivationAnnotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences.
resultsWe provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. AVAILABILITY: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.