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

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2013 Mar 13

PMID 23479348

Citations 105

Authors

Jon Ison

Matus Kalas

Inge Jonassen

Dan Bolser

Mahmut Uludag

Hamish McWilliam

James Malone

Rodrigo Lopez

Steve Pettifer

Peter Rice

Affiliations

Soon will be listed here.

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.

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