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Journal Articles Bioinformatics Year : 2010

Modeling sample variables with an Experimental Factor Ontology.

James Malone
  • Function : Author
Ele Holloway
  • Function : Author
Tomasz Adamusiak
  • Function : Author
Jie Zheng
  • Function : Author
Nikolay Kolesnikov
  • Function : Author
Anna Zhukova
Alvis Brazma
  • Function : Author
Helen Parkinson
  • Function : Author


MOTIVATION: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users. RESULTS: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way. AVAILABILITY:

Dates and versions

hal-00721833 , version 1 (30-07-2012)



James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, et al.. Modeling sample variables with an Experimental Factor Ontology.. Bioinformatics, 2010, 26 (8), pp.1112-8. ⟨10.1093/bioinformatics/btq099⟩. ⟨hal-00721833⟩
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