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Re: [Treebase-devel] [PhyloWS] Re: [CDAO-discuss] interoperability of resources using CDAO -- telecon Tuesday Aug 17
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From: Rutger V. <rut...@gm...> - 2010-08-17 03:06:16
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I am sorry I won't be able to call in. I'm looking forward to see the summary, though. Best wishes, Rutger On Tue, Aug 17, 2010 at 5:56 AM, Arlin Stoltzfus <ar...@um...> wrote: > As noted last week, a teleconference is scheduled for Tuesday at 11:00 am > EST (GMT -5). The agenda is to discuss steps to improve interoperability > among tools that use CDAO (see message below for details). > > To connect, > 1. call 1-213-289-0500 (this is a long-distance call to Los Angeles), then > 2. when prompted, enter 375259 > > After the telecon is over, I will post a summary somewhere accessible. > > Arlin > > On Aug 13, 2010, at 12:35 PM, Arlin Stoltzfus wrote: > >> Dear CDAO developers and users-- >> >> For the past 2 years, CDAO has been an experimental project done in >> our spare time. Last summer, we reached our first big milestones with >> an initial ontology version and a publication. This summer, we are >> poised for another milestone where CDAO mediates interoperability >> between real tools developed for use by researchers. TreeBase2 >> (phylo database used by systematists), CDAOstore (experimental >> triplestore by CDAO developers), and Nexplorer3 (phylogenetic data >> viewer developed and used at NIAID) are open-source projects that have >> made recent efforts to support CDAO encodings for import or export or >> internal representation. They were presented at the 2010 "iEvoBio" >> satellite meeting at Evolution 2010 in Portland this summer. >> >> * TreeBase2 claims to deliver CDAO instance files (RDF-XML) in >> response to phylows URLs >> * Both CDAOstore and Nexplorer3 claim to be able to consume CDAO >> instance files via a URL. >> * CDAOstore also has a translator, so that a user can upload a NEXUS >> or phylip file, and translate it into CDAO >> >> Thus, in principle, CDAOstore can be used as a query interface to a >> TreeBase2 data entry by giving it a phyloWS URL like this: >> >> http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF >> >> and loading the result into the triplestore. Likewise, in principle, >> Nexplorer3 can be used as an interface to visualize a TreeBase2 data >> entry via its phyloWS URL. Or we could translate a NEXUS file (e.g., >> from TreeBase2) using CDAO-store's online translator, then view the >> result in Nexplorer3. To achieve this kind of interoperability would >> fulfill the hopes of the NESCent evolutionary informatics working >> group (2006-2009), from whose members sprang the CDAO, phyloWS and >> nexml projects. >> >> But we aren't there yet. Having tried all of the pairwise >> interoperations listed above, I found that none of them actually >> works. But I'm not discouraged by that, and neither are the TreeBase, >> CDAO-store and Nexplorer3 developers. Now that we have actual >> concrete targets for interoperability, we can focus on finding >> problems and solving them. >> >> We have planned an initial teleconference on this issue Tuesday, the >> 17th at 11:00 am Eastern (GMT -5). Details will be provided later. >> >> Arlin >> ------- >> 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 >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by >> >> Make an app they can't live without >> Enter the BlackBerry Developer Challenge >> http://p.sf.net/sfu/RIM-dev2dev >> _______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > ------- > 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 > "PhyloWS" group. > To post to this group, send email to ph...@go.... > To unsubscribe from this group, send email to > phy...@go.... > For more options, visit this group at > http://groups.google.com/group/phylows?hl=en. > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
