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. 2013 May 15;29(10):1325-32.
doi: 10.1093/bioinformatics/btt113. Epub 2013 Mar 11.

EDAM: An Ontology of Bioinformatics Operations, Types of Data and Identifiers, Topics and Formats

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Free PMC article

EDAM: An Ontology of Bioinformatics Operations, Types of Data and Identifiers, Topics and Formats

Jon Ison et al. Bioinformatics. .
Free PMC article

Abstract

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.

Figures

Fig. 1.
Fig. 1.
Organization of the main EDAM sub-ontologies and the relations explicitly maintained between EDAM concepts
Fig. 2.
Fig. 2.
Sketches of information models for semantic annotations with EDAM. (a) A model for annotations of tools corresponding to the SAWSDL standard (Kopecky et al., 2007). Standardizing an information model of tool metadata is, at least so far, out of scope of EDAM. (b) A similar model for annotations of data resources, used within DRCAT. Note that a query has always (implicitly) the function of Data retrieval. Defining an information standard for database metadata is within scope of the BioDBCore initiative (Gaudet et al., 2011)

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