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, Peter Rice

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

187 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1325-1332
Number of pages8
Issue number10
StatePublished - May 15 2013
Externally publishedYes

Bibliographical note

Funding Information:
Funding: This work was partially supported by the European Commission (FP6 grant LHSG-CT-2004-512092, EMBRACE; FP7-INFRA-2007-211601, ELIXIR; FP7 Capacities Specific Programme grant 284209, BioMedBridges, the latter to J.I.), BBSRC (grant BB/G02264X/1 EMBOSS-BBR, EMBOSS, to J.I. and P.R.) and the Research Council of Norway (grant 178885/V30, eSysbio; 183438, FUGE Bioinformatics platform; 208481, ELIXIR.NO; all to M.K.).

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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