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

Research output: Contribution to journal › Article › peer-review

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. © 2013 The Author. Published by Oxford University Press. All rights reserved.

Original language	English
Pages (from-to)	1325-1332
Number of pages	7
Journal	Bioinformatics
Volume	29
Issue number	10
DOIs	https://doi.org/10.1093/bioinformatics/btt113
Publication status	Published - 15 May 2013

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10.1093/bioinformatics/btt113

Enhancing RDM in Galaxy by integrating RO-Crate
De Geest, P., Coppens, F., Soiland-reyes, S., Eguinoa, I. & Leo, S., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e95164.
Research output: Contribution to journal › Conference article › peer-review

Open Access

Cite this

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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. {\textcopyright} 2013 The Author. Published by Oxford University Press. All rights reserved.",

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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

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EP - 1332

JO - Bioinformatics

JF - Bioinformatics

IS - 10

ER -

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

Abstract

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Research output

Enhancing RDM in Galaxy by integrating RO-Crate

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