Modeling sample variables with an Experimental Factor Ontology

• DOI: 10.1093/bioinformatics/btq099
• Publication Date: 2010-03-04T01:18:36Z
• Authors: James Malone; Ele Holloway; Tomasz Adamusiak; Misha Kapushesky; Jie Zheng; Nikolay Kolesnikov; Anna Zhukova; Alvis Brazma; Helen Parkinson
• Keywords: Open Biomedical Ontologies; Ontology components

Abstract Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for investigations, multiple are needed represent data. These subject rapid change, often not interoperable and present complexities that a barrier resource users. Results: We Experimental Factor Ontology, designed meet cross-domain, application focused use cases gene expression describe our methodology open source tools used create ontology. include creating ontology mappings, views, detecting changes using in interfaces enhance querying. The reference data key problem, this work presents guidelines on how community can be presented an data-driven way. Availability: http://www.ebi.ac.uk/efo Contact: [e-mail] Supplementary information: available at Bioinformatics online.