From: Hilmar L. <hl...@ne...> - 2012-02-09 14:58:33
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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 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 : =========================================================== |