Journal Article

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Jon Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer and Peter Rice

in Bioinformatics

Volume 29, issue 10, pages 1325-1332
Published in print May 2013 | ISSN: 1367-4803
Published online March 2013 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btt113

Show Summary Details

Preview

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.

Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations.

Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl.

Contact: jison@ebi.ac.uk

Journal Article.  5465 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.