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

doi:10.1093/bioinformatics/btt113

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 journal › Article › peer-review

196 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1325-1332
Number of pages	8
Journal	Bioinformatics
Volume	29
Issue number	10
DOIs	https://doi.org/10.1093/bioinformatics/btt113
State	Published - May 15 2013
Externally published	Yes

ASJC Scopus subject areas

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

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10.1093/bioinformatics/btt113

Cite this

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title = "EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics and formats",

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.",

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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.).",

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AU - Ison, Jon

AU - Kalaš, Matúš

AU - Jonassen, Inge

AU - Bolser, Dan

AU - Uludag, Mahmut

AU - McWilliam, Hamish

AU - Malone, James

AU - Lopez, Rodrigo

AU - Pettifer, Steve

AU - Rice, Peter

N1 - 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.).

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

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ASJC Scopus subject areas

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