The Experimental Factor Ontology

An application ontology of experimental variables from the EBI

The EFO Project

The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and Gene Expression Atlas.

We have also involed in the SWORD project to develop a Software Ontology for resource description.

We have performed a semi-automated transformation of the Coriell cell line catalogue to create an OWL ontology of over 27,000 classes.


Publications on EFO

Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 2010, 26(8):1112-1118 PDF

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