Re: [CDAO-discuss] EDAM ontology

[Rutger V. <rut...@gm...>]

>
> 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 :)


> On Feb 9, 2012, at 9:46 AM, Karen Cranston wrote:
>
> > 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.
> >
> > On Thu, Feb 9, 2012 at 8:27 AM, Arlin Stoltzfus <ar...@um...> wrote:
> >> 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
> >>
> >> On Feb 9, 2012, at 7:55 AM, Rutger Vos wrote:
> >>
> >> 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
> >> --
> >> Dr. Rutger A. Vos
> >> Bioinformaticist
> >> NCB Naturalis
> >> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the
> >> Netherlands
> >> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
> >> http://rutgervos.blogspot.com
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> >> Groups "MIAPA" group.
> >> For more options, visit this group at
> >> http://groups.google.com/group/miapa-discuss?hl=en
> >>
> >>
> >> -------
> >> Arlin Stoltzfus (ar...@um...)
> >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> >> IBBR, 9600 Gudelsky Drive, Rockville, MD
> >> tel: 240 314 6208; web: www.molevol.org
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> >> Groups "MIAPA" group.
> >> For more options, visit this group at
> >> http://groups.google.com/group/miapa-discuss?hl=en
> >
> >
> >
> > --
> > ~~~~~~~~~~~~~~~~~~~~~~~
> > kar...@gm...
> > ~~~~~~~~~~~~~~~~~~~~~~~
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "MIAPA" group.
> > For more options, visit this group at
> > http://groups.google.com/group/miapa-discuss?hl=en
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "MIAPA" group.
> For more options, visit this group at
> http://groups.google.com/group/miapa-discuss?hl=en
>



-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the
Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com