- 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
mobile: +1.617.599.3509
(eric@w3.org)
Feel free to forward this message to any list for any purpose other than
email address distribution.
Received on Tuesday, 26 June 2007 16:07:00 UTC