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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

The full printed program is also available.
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Thursday, June 29 • 15:40 - 17:00
P05: The EDAM ontology and its integration into Galaxy

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Poster (doi: 10.7490/f1000research.1114336.1)


Hervé Ménager 1, Jon Ison 2, Matúš Kalaš 3, Veit Schwaemmle 4, Edam Contributors

1 : Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur, Paris, France
2 : Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark
3 : Computational Biology Unit (CBU), University of Bergen
4 : Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark

EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations, and topics. EDAM has a simple structure, and comprises a set of concepts with terms, synonyms, definitions, relations, links, and some additional information (especially for data formats).

7 consecutive stable versions of EDAM have been released since July 2015 (version 1.10), with version 1.17 being the current one at the time of the abstract submission. EDAM is developed in a participatory and transparent fashion, with a growing community of contributors. EDAM is used by multiple bioinformatics projects, including Debian Med[1] and the Common Workflow Language[2].  

Thanks to the Galaxy community, it has been integrated with Galaxy through recent modifications:
  • the annotation of Galaxy datatypes with their corresponding EDAM data and format terms,
  • the possibility to specify EDAM topics and operations in Galaxy tool definitions.
This allows for an easier integration of Galaxy and other EDAM-compatible systems, including the ELIXIR bio.tools registry of bioinformatics tools and services, for which a direct application of this mapping enables the automated registration in bio.tools of Galaxy services[3], and the semi-automated creation of Galaxy tool definitions using bio.tools metadata[4].

[1] http://debian.org/devel/debian-med
[2] http://commonwl.org/
[3] https://github.com/c3bi-pasteur-fr/regate
[4] https://github.com/bio-tools/ToolDog

avatar for Hervé Ménager

Hervé Ménager

Research Engineer, Institut Pasteur
Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur

Thursday June 29, 2017 15:40 - 17:00 CEST
Le Corum Le Corum

Attendees (3)