ArticleBioinformatics (Oxford, England)2011
A common layer of interoperability for biomedical ontologies based on OWL EL.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Literature-Based Enrichment Insights into Redox Control of Vascular Biology.Oxidative medicine and cellular longevity · 2019Review
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Integrating phenotype ontologies with PhenomeNET.Journal of biomedical semantics · 2017Article
- Neuro-symbolic representation learning on biological knowledge graphs.Bioinformatics (Oxford, England) · 2017Article
- Using AberOWL for fast and scalable reasoning over BioPortal ontologies.Journal of biomedical semantics · 2016Article
- The role of ontologies in biological and biomedical research: a functional perspective.Briefings in bioinformatics · 2015Article
- Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.BMC medical informatics and decision making · 2015Article
- Aber-OWL: a framework for ontology-based data access in biology.BMC bioinformatics · 2015Article
- An ontology approach to comparative phenomics in plants.Plant methods · 2015Article
- Thematic series on biomedical ontologies in JBMS: challenges and new directions.Journal of biomedical semantics · 2014Review
- PhenoDigm: analyzing curated annotations to associate animal models with human diseases.Database : the journal of biological databases and curation · 2013Article
- Computational tools for comparative phenomics: the role and promise of ontologies.Mammalian genome : official journal of the International Mammalian Genome Society · 2012Review
- Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.Journal of biomedical semantics · 2012Article
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.Bioinformatics (Oxford, England) · 2012Article
- Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis.BMC medical informatics and decision making · 2012Article
- Mouse genetic and phenotypic resources for human genetics.Human mutation · 2012Review
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.Journal of biomedical semantics · 2012Article
- Uberon, an integrative multi-species anatomy ontology.Genome biology · 2012Article
- The Units Ontology: a tool for integrating units of measurement in science.Database : the journal of biological databases and curation · 2012Article
- Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases.PloS one · 2012Article
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Authors and funding
7 authors.
Funding
Abstract
motivationOntologies are essential in biomedical research due to their ability to semantically integrate content from different scientific databases and resources. Their application improves capabilities for querying and mining biological knowledge. An increasing number of ontologies is being developed for this purpose, and considerable effort is invested into formally defining them in order to represent their semantics explicitly. However, current biomedical ontologies do not facilitate data integration and interoperability yet, since reasoning over these ontologies is very complex and cannot be performed efficiently or is even impossible. We propose the use of less expressive subsets of ontology representation languages to enable efficient reasoning and achieve the goal of genuine interoperability between ontologies.
resultsWe present and evaluate EL Vira, a framework that transforms OWL ontologies into the OWL EL subset, thereby enabling the use of tractable reasoning. We illustrate which OWL constructs and inferences are kept and lost following the conversion and demonstrate the performance gain of reasoning indicated by the significant reduction of processing time. We applied EL Vira to the open biomedical ontologies and provide a repository of ontologies resulting from this conversion. EL Vira creates a common layer of ontological interoperability that, for the first time, enables the creation of software solutions that can employ biomedical ontologies to perform inferences and answer complex queries to support scientific analyses. AVAILABILITY AND IMPLEMENTATION: The EL Vira software is available from http://el-vira.googlecode.com and converted OBO ontologies and their mappings are available from http://bioonto.gen.cam.ac.uk/el-ont.
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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.