25 Jun 2007

See also: IRC log


Don_Doherty, Scott_Marshall, susie, Kerstin_Forsberg, John_Barkley, EricP, BillBug, Eric_Neumann, Kei, Matthias, Kersten, JonathanR, AlanR, Olivier_Bodenreider
Susie Stevens
mscottm, ericP


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> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/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> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices

<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


<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 http://www.w3.org/2007/06/25-BioRDF-irc]

<ericP> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/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> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/RequirementsTalk

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

<jar286> http://wiki.neurocommons.org/CommonNaming

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

<ericP> note header of 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.


<alanr> 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 - http://www.tdwg.org/

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

<BillBug> * BioMOBY:

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

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

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

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

<BillBug> * EBI

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

<BillBug> * Taverna & LSID - PPT by Carole - http://twiki.mygrid.org.uk/twiki/pub/Mygrid/PresentationStore/GGFTavernaOMII.ppt

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

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

<BillBug> * home - 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> 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


<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 http://www.w3.org/2007/06/25-BioRDF-irc]
[NEW] ACTION: ericp to add navigation to wiki pages [recorded in http://www.w3.org/2007/06/25-BioRDF-irc]
[NEW] ACTION: Scott review Requirements URL (in IRC) [recorded in http://www.w3.org/2007/06/25-BioRDF-irc]
[End of minutes]

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$Date: 2007/06/26 15:59:18 $