EDAM ontology

[Rutger Vos]

Hi all,

just to bring this to your attention: the EDAM ontology is amazingly extensive, including terms for all the file formats we all love, tree annotation (for which the concept has been aligned with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, terms for reconstruction methods, etc. Maybe you knew all this, but I was quite amazed to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM

Rutger

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Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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http://rutgervos.blogspot.com

[Arlin Stoltzfus]

Is there a GSOC project here?  Take the MIAPA checklist: 

 http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist

plus some kind of ontology-aware forms interface-- can ISA-tools do this?--

  http://isatab.sourceforge.net/

and EDAM, and create a tool that can be used to satisfy a small set of test-cases. The test-cases would be phylogenetic reports (with some associated data files for tree, alignment, etc) that can be rendered as MIAPA reports, which is what we are aiming at here: 

  http://www.evoio.org/wiki/MIAPA/PhyloWays

although this needs more work.  

Arlin

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Arlin Stoltzfus (ar...@umd.edu)

Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST

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[Karen Cranston]

Nice find, Rutger! I didn't know about this. I like the idea of a GSoC
project, and I think using ISA-tools is the way to go.

NESCent will be announcing this year's request for PhyloSoC ideas shortly.

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[Hilmar Lapp]

Yes indeed, a GSoC project on polishing / customizing an ISA-tools-based annotation tool was one of the follow-up actions that we discussed at the MIAPA workshop at TDWG in October.

I've known EDAM for quite a while, in fact it came up in CDAO discussions some time ago. The EBI has been using it to index their microarray and other databases.

-hilmar

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: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
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[Rutger Vos]

I've known EDAM for quite a while, in fact it came up in CDAO discussions some time ago. The EBI has been using it to index their microarray and other databases.

I'd known of it (because it was one of the stars at the biohackathons) but the extent of it was amazing. The EDAM people actually made the effort to make terms for things such as "the NeXML file format", "a TreeBASE identifiers", "a CDAO annotation". Makes you feel that you're not actually working in a complete vacuum :)