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meeting record: BioRDF 25 Jun 2007

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 26 Jun 2007 12:06:41 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20070626160641.GA4964@w3.org>

http://www.w3.org/2007/06/25-BioRDF-minutes

Note action items:
   [NEW] ACTION: alanr and Susie to contact useful LSID users and get them
   on board with what we do [recorded in
   [26]http://www.w3.org/2007/06/25-BioRDF-irc]
   [NEW] ACTION: ericp to add navigation to wiki pages [recorded in
   [27]http://www.w3.org/2007/06/25-BioRDF-irc]
   [NEW] ACTION: Scott review Requirements URL (in IRC) [recorded in
   [28]http://www.w3.org/2007/06/25-BioRDF-irc]


                                     BioRDF

25 Jun 2007

   See also: [2]IRC log

Attendees

   Present
          Don_Doherty, Scott_Marshall, susie, Kerstin_Forsberg,
          John_Barkley, EricP, BillBug, Eric_Neumann, Kei, Matthias,
          Kersten, JonathanR, AlanR, Olivier_Bodenreider

   Regrets

   Chair
          Susie Stevens

   Scribe
          mscottm

Contents

     * [3]Topics
     * [4]Summary of Action Items
     __________________________________________________________________

   Susie: focus of today's call URI work that we are proposing to do

   <alanr> where is ericn

   <alanr> can someone ping him?

   Susie: it would be nice to set a goal that we can reach by the end of
   the charter

   <BillBug>
   [5]http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practi
   ces/Recommendations

   Jonathan: the number of approaches being proposed is difficult to
   manage at the moment, especially those that do not refer to origins and
   related work

   <BillBug> URI Best Practices:

   <BillBug>
   [6]http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practi
   ces

   <ericP> eneumann: suggest take top 3 or 4 items off the todo list

   EricN: what are things that can be achieved - let's take the top few
   items with time constraints in mind

   <ericP> alanr: suggest drafting Mark Wilkinson as he has experience
   with LSID apps

   <ericP> BillBug: taxonomic WG and an informatics program out of EBI are
   both using LSID

   <alanr> uniprot is *not* using LSID

   Bill: applications are using LSID's such as one out of EBI and the
   taxonomic WG

   <jar286> the issue is LSID *in the semantic web*

   Jonathan: tricky isn't LSID's as there were meant but their use in the
   semweb

   <eneumann> however, I believe uniprot is using a form of URN's...

   <matthiassamwald> Projects are only 'using LSIDs' if they actually
   resolve to anything useful. If they do not, they are just arbitrary
   strings.

   <alanr> +1

   1+

   <Zakim> BillBug, you wanted to discuss current LSID applications and to

   <ericP> oops!

   <alanr> oxymoron

   Susie: maybe we should focus on what we want to do if the consensus is
   to use web architecture

   <alanr> lsids/best practices

   <alanr> solicit wikinson + goble for requirements

   <alanr> we won

   :)

   <jar286> lsid supporters have not wanted to talk to us

   <matthiassamwald> (I agree)

   <Zakim> ericP, you wanted to suggest forgetting LSIDs until we have a
   strong sense we need them

   All agreed: we move on from LSID's and consult people not present in
   email

   <ericP> ACTION: alanr and Susie to contact useful LSID users and get
   them on board with what we do [recorded in
   [7]http://www.w3.org/2007/06/25-BioRDF-irc]

   <ericP>
   [8]http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practi
   ces/Recommendations

   Taverna uses versioning

   Alan: ontology that describes the contract with regard to versioning

   <eneumann> Alan, can you draft a minimum core list of "URI contract"
   items for any HCLS URI?

   <matthiassamwald> Is versioning actually an issue of URIs? I see it
   more as an issue of ontologies, and out of scope for this discussion.

   Jonathan: all of the problems have solutions but we lack a structure
   for the current set of solutions

   <jar286>
   [9]http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practi
   ces/Recommendations/RequirementsTalk

   <scribe> ACTION: Scott review Requirements URL (in IRC) [recorded in
   [10]http://www.w3.org/2007/06/25-BioRDF-irc]

   <jar286> [11]http://wiki.neurocommons.org/CommonNaming

   <alanr> ACTION: ericp to add navigation to wiki pages [recorded in
   [12]http://www.w3.org/2007/06/25-BioRDF-irc]

   <ericP> note header of
   [13]http://www.w3.org/2005/05/22-SPARQL-MySQL/XTech , has navigation
   bar that promotes a set of documents to consider as being at one level

   <ericP> plus it has those cooool numers

   Susie: push local caching to second tier priority?

   <alanr> cooool numbers?

   Susie: what is the status of the versioning topic?

   somebody will take something to do with version up as an action item
   (still)?

   Jonathan: wondering about the plan to contact stakeholders

   <matthiassamwald> I propose to start with reviewing the PURL-based
   Banff URIs. It is much easier to start with a concrete proposal, than
   from a completely white sheet.

   +1

   <alanr> [14]http://www.w3.org/2001/sw/hcls/charter mentions URIs?

   <alanr> can't see it

   EricN: many 'outside' (i.e. non-HCLS) are very interested in the URI
   problem and we should report in a way that is accessible to them.
   ... one of the first questions is "What happens if I put the URI in the
   browser?"

   <MarcAlexandre_Bio> it should return the corresponding RDF document

   EricN: I will ping some of these people and try to involve them in the
   process.

   <alanr> should return the corresponding RDF document only if the URI
   denotes an RDF document.

   <alanr> if you ask for html you get html. If you ask for a protein you
   get some indication that you can't "GET" one of those on the web

   <eneumann> alan, see Guidelines and Best Practices for Resource
   Identification:

   <alanr> actually, I suggest MarcAlexandre reads said. I have.

   <MarcAlexandre_Bio> true, if you ask the html page, you should receive
   the html page

   <BillBug> LSID Applications:

   <BillBug> * Tax Data WG - [15]http://www.tdwg.org/

   <BillBug> * just had an LSID Policy Workshop -
   [16]http://www.tdwg.org/homepage-news-item/article/lsid-policy-workshop
   /

   <BillBug> * BioMOBY:

   <BillBug> * Mark Wilkinson - iCAPTURE Pjt - application of BioMOBY -
   [17]http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml

   <BillBug> * BioMOBY home - [18]http://www.biomoby.org/

   <BillBug> * iCAPTURE LSID client resolver -
   [19]http://bioinfo.icapture.ubc.ca/ekawas/data/LSID_resolver.html

   <BillBug> * iCAPTURE LSID metadata resolver -
   [20]http://mobycentral.icapture.ubc.ca:8090/authority/lsid/ResolveLSID?
   lsid=urn:lsid:biomoby.org:objectclass:DNASequence

   <BillBug> * EBI

   <BillBug> * Carole Gobel - [21]http://www.cs.man.ac.uk/~carole/

   <BillBug> * Taverna & LSID - PPT by Carole -
   [22]http://twiki.mygrid.org.uk/twiki/pub/Mygrid/PresentationStore/GGFTa
   vernaOMII.ppt

   <BillBug> * Newcastle U. - Centre for Integrated Systems Biology of
   Ageing and Nutrition Data Portal

   <BillBug> * abstract -
   [23]http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016

   <BillBug> * home - [24]http://www.cisban.ac.uk/index.html

   Susie: maybe a F2F would help to move things along, shall we try to
   organize something in July

   <BillBug> Sorry - I must be off. I'll get back to Jonathan re: the PURL
   use in the Banff demo.

   Matthias: I think that we should base our discussion on concrete
   examples (such as comparing what was done in Banff to LSID's)

   <Zakim> ericP, you wanted to propose template header that limits scope
   of documents to read

   Jonathan (?): I think that the requirements should come from the
   applications

   <alanr> matthias is getting flack :(

   <alanr> I will do some figures for poster

   Matthias (about BioOntologies poster): if you have (better) ideas about
   a visualization, please send them.

   <alanr> maybe we can draft JAR for common naming for poster

   Susie: Let's talk more about the poster at next week's call.

   <alanr> do we know the date of the demo yet?

   EricN: considering additional touches to demo such as the ability to
   move images around

   <eneumann> no dates yet, but we should here by beginning of July

   Don: we're setting up a demo machine here

   Alan: still arranging the new server at Wright Univ via email

   <alanr> matthias - please send out ontology + query for review

   <matthiassamwald>
   [25]http://neuroscientific.net/res/kidb_to_obo/kidb070131.turtle

   Matthias: Datasources - incorporating KI sources, can link ligands with
   receptors from NeuronDB, can link to pubmed articles

   bye

   <MarcAlexandre_Bio> Bye

   <matthiassamwald> bye, marc.

Summary of Action Items

   [NEW] ACTION: alanr and Susie to contact useful LSID users and get them
   on board with what we do [recorded in
   [26]http://www.w3.org/2007/06/25-BioRDF-irc]
   [NEW] ACTION: ericp to add navigation to wiki pages [recorded in
   [27]http://www.w3.org/2007/06/25-BioRDF-irc]
   [NEW] ACTION: Scott review Requirements URL (in IRC) [recorded in
   [28]http://www.w3.org/2007/06/25-BioRDF-irc]

   [End of minutes]
     __________________________________________________________________


    Minutes formatted by David Booth's [29]scribe.perl version 1.128
    ([30]CVS log)
    $Date: 2007/06/26 15:59:18 $

References

   1. http://www.w3.org/
   2. http://www.w3.org/2007/06/25-BioRDF-irc
   3. http://mouni.local/2007/06/25-BioRDF-minutes#agenda
   4. http://mouni.local/2007/06/25-BioRDF-minutes#ActionSummary
   5. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations
   6. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices
   7. http://www.w3.org/2007/06/25-BioRDF-irc
   8. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations
   9. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/RequirementsTalk
  10. http://www.w3.org/2007/06/25-BioRDF-irc
  11. http://wiki.neurocommons.org/CommonNaming
  12. http://www.w3.org/2007/06/25-BioRDF-irc
  13. http://www.w3.org/2005/05/22-SPARQL-MySQL/XTech
  14. http://www.w3.org/2001/sw/hcls/charter
  15. http://www.tdwg.org/
  16. http://www.tdwg.org/homepage-news-item/article/lsid-policy-workshop/
  17. http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml
  18. http://www.biomoby.org/
  19. http://bioinfo.icapture.ubc.ca/ekawas/data/LSID_resolver.html
  20. http://mobycentral.icapture.ubc.ca:8090/authority/lsid/ResolveLSID?lsid=urn:lsid:biomoby.org:objectclass:DNASequence
  21. http://www.cs.man.ac.uk/~carole/
  22. http://twiki.mygrid.org.uk/twiki/pub/Mygrid/PresentationStore/GGFTavernaOMII.ppt
  23. http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016
  24. http://www.cisban.ac.uk/index.html
  25. http://neuroscientific.net/res/kidb_to_obo/kidb070131.turtle
  26. http://www.w3.org/2007/06/25-BioRDF-irc
  27. http://www.w3.org/2007/06/25-BioRDF-irc
  28. http://www.w3.org/2007/06/25-BioRDF-irc
  29. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  30. http://dev.w3.org/cvsweb/2002/scribe/
-- 
-eric

office: +1.617.258.5741 NE43-344, MIT, Cambridge, MA 02144 USA
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Received on Tuesday, 26 June 2007 16:07:00 GMT

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