15:01:17 <RRSAgent> RRSAgent has joined #BioRDF
15:01:17 <RRSAgent> logging to http://www.w3.org/2007/06/25-BioRDF-irc
15:01:27 <ericP> Zakim, this will be BioRDF
15:01:27 <Zakim> ok, ericP, I see SW_HCLS(BioRDF)11:00AM already started
15:01:36 <Zakim> + +1.203.737.aaaa
15:01:37 <Zakim> +John_Barkley
15:02:04 <Zakim> +??P31
15:02:05 <ericP> Zakim, please dial ericP-office
15:02:05 <Zakim> ok, ericP; the call is being made
15:02:06 <Zakim> +EricP
15:02:43 <ericP> Zakim, 1.203.737.aaaa is Kei
15:02:43 <Zakim> sorry, ericP, I do not recognize a party named '1.203.737.aaaa'
15:02:48 <ericP> Zakim, +1.203.737.aaaa is Kei
15:02:48 <Zakim> +Kei; got it
15:03:07 <ericP> Zakim, who is here?
15:03:07 <Zakim> On the phone I see Don_Doherty, Scott_Marshall, susie, ??P27, Kerstin_Forsberg, John_Barkley, Kei, ??P31, EricP
15:03:09 <Zakim> On IRC I see RRSAgent, Zakim, BillBug, mscottm, matthiassamwald, eneumann, Don, MarcAlexandre_Bio, Susie, ericP
15:03:26 <ericP> Zakim, ??P27 is BillBug
15:03:26 <Zakim> +BillBug; got it
15:03:38 <ericP> Zakim, ??P31 is Kirsten
15:03:38 <Zakim> +Kirsten; got it
15:03:49 <ericP> Zakim, ??P31 is Kirsteen
15:03:49 <Zakim> I already had ??P31 as Kirsten, ericP
15:04:04 <ericP> Zakim, Kirsten is really Kirsteen
15:04:06 <Zakim> +Kirsteen; got it
15:04:57 <Zakim> +Eric_Neumann
15:05:03 <Zakim> +Jonathan_Rees
15:05:24 <ericP> Zakim, Kei is really Kei_and_Matthias
15:05:24 <Zakim> +Kei_and_Matthias; got it
15:05:39 <ericP> Zakim, Kei_and_Matthias holds Kei, Matthias
15:05:39 <Zakim> +Kei, Matthias; got it
15:05:46 <mscottm> Susie: focus of today's call URI work that we are proposing to do
15:05:49 <ericP> Zakim, Kei_and_Matthias holds Matthias
15:05:49 <Zakim> Matthias was already listed in Kei_and_Matthias, ericP
15:06:06 <alanr> alanr has joined #biordf
15:06:10 <ericP> Zakim, Kirsteen is really Kersten
15:06:10 <Zakim> +Kersten; got it
15:06:38 <ericP> Zakim, Jonathan_Rees is temporarily +Jonathan_and_Alan
15:06:38 <Zakim> ++Jonathan_and_Alan; got it
15:06:46 <alanr> where is ericn
15:06:53 <alanr> can someone ping him?
15:06:59 <ericP> Zakim, +Jonathan_and_Alan holds JonathanR, AlanR
15:06:59 <Zakim> +JonathanR, AlanR; got it
15:07:17 <ericP> Zakim, who is here?
15:07:17 <Zakim> On the phone I see Don_Doherty, Scott_Marshall, susie, BillBug, Kerstin_Forsberg, John_Barkley, Kei_and_Matthias, Kersten, EricP, Eric_Neumann, +Jonathan_and_Alan
15:07:20 <Zakim> +Jonathan_and_Alan has JonathanR, AlanR
15:07:21 <Zakim> Kei_and_Matthias has Kei, Matthias
15:07:22 <Zakim> On IRC I see alanr, RRSAgent, Zakim, BillBug, mscottm, matthiassamwald, eneumann, Don, MarcAlexandre_Bio, Susie, ericP
15:07:52 <mscottm> Susie: it would be nice to set a goal that we can reach by the end of the charter
15:09:11 <jar286> jar286 has joined #BioRDF
15:11:21 <eneumann> q+
15:11:52 <BillBug> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations
15:12:19 <mscottm> 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
15:12:23 <BillBug> URI Best Practices:
15:12:25 <BillBug>      http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices
15:12:54 <alanr> q+
15:13:29 <ericP> q+ BillBug to discuss current LSID applications
15:13:32 <Zakim> +Olivier_Bodenreider
15:14:34 <ericP> eneumann: suggest take top 3 or 4 items off the todo list
15:14:34 <eneumann> ack eneumann
15:14:43 <mscottm> EricN: what are things that can be achieved - let's take the top few items with time constraints in mind
15:15:11 <ericP> alanr: suggest drafting Mark Wilkinson as he has experience with LSID apps
15:15:25 <jar286> q+
15:15:37 <ericP> BillBug: taxonomic WG and an informatics program out of EBI are both using LSID
15:15:39 <alanr> uniprot is *not* using LSID
15:15:41 <mscottm> Bill: applications are using LSID's such as one out of EBI and the taxonomic WG
15:16:01 <jar286> the issue is LSID *in the semantic web*
15:16:29 <mscottm> Jonathan: tricky isn't LSID's as there were meant but their use in the semweb
15:16:30 <eneumann> however, I believe uniprot is using a form of URN's...
15:16:34 <jar286> q+
15:16:36 <matthiassamwald> Projects are only 'using LSIDs' if they actually resolve to anything useful. If they do not, they are just arbitrary strings.
15:16:51 <alanr> +1
15:17:05 <mscottm> 1+
15:17:29 <ericP> q+ to limit scope
15:17:38 <BillBug> I agree with Susie.  Bringing up the LSID topic again, may just get us lost in the HTTP vs. LSID debate again.
15:17:43 <ericP> ack alanr 
15:17:47 <BillBug> q+
15:17:47 <ericP> ack BillBug 
15:17:48 <Zakim> BillBug, you wanted to discuss current LSID applications and to 
15:17:54 <ericP> oops!
15:17:56 <alanr> oxymoron
15:18:02 <ericP> q+ BillBug 
15:18:08 <mscottm> Susie: maybe we should focus on what we want to do if the consensus is to use web architecture
15:18:12 <alanr> lsids/best practices
15:19:25 <alanr> solicit wikinson + goble for requirements
15:19:48 <ericP> ack jar
15:19:54 <ericP> q-
15:20:01 <alanr> we won
15:20:09 <mscottm> :)
15:20:18 <jar286> lsid supporters have not wanted to talk to us
15:20:43 <ericP> ack BillBug 
15:21:08 <ericP> q+ to suggest forgetting LSIDs until we have a strong sense we need them
15:21:43 <matthiassamwald> (I agree)
15:21:52 <mscottm> q+
15:21:58 <ericP> ack me
15:21:58 <Zakim> ericP, you wanted to suggest forgetting LSIDs until we have a strong sense we need them
15:22:40 <mscottm> All agreed: we move on from LSID's and consult people not present in email
15:22:41 <ericP> ACTION: alanr and Susie to contact useful LSID users and get them on board with what we do
15:23:07 <ericP> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations
15:25:27 <mscottm> Taverna uses versioning
15:26:05 <mscottm> Alan: ontology that describes the contract with regard to versioning
15:26:41 <eneumann> Alan, can you draft a minimum core list of "URI contract" items for any HCLS URI?
15:26:46 <matthiassamwald> Is versioning actually an issue of URIs? I see it more as an issue of ontologies, and out of scope for this discussion.
15:27:00 <BillBug> q+
15:27:02 <mscottm> Jonathan: all of the problems have solutions but we lack a structure for the current set of solutions
15:28:42 <jar286> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/RequirementsTalk
15:29:23 <ericP> q?
15:29:27 <ericP> ack mscottm 
15:29:36 <mscottm> ACTION: Scott review Requirements URL (in IRC)
15:29:51 <ericP> q+ to propose template header that limits scope of documents to read
15:30:21 <jar286> http://wiki.neurocommons.org/CommonNaming
15:30:58 <alanr> Action: ericp to add navigation to wiki pages
15:32:05 <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
15:32:20 <ericP> plus it has those cooool numers
15:33:15 <mscottm> Susie: push local caching to second tier priority?
15:34:12 <alanr> cooool numbers?
15:35:04 <BillBug> q+ - granularity of versioning
15:35:49 <mscottm> Susie: what is the status of the versioning topic?
15:36:50 <mscottm> somebody will take something to do with version up as an action item (still)?
15:37:47 <mscottm> Jonathan: wondering about the plan to contact stakeholders
15:38:51 <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.
15:39:14 <mscottm> +1
15:39:14 <alanr> http://www.w3.org/2001/sw/hcls/charter mentions URIs?
15:39:19 <alanr> can't see it
15:39:40 <ericP> q?
15:40:42 <mscottm> 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.
15:41:32 <mscottm> EricN: one of the first questions is "What happens if I put the URI in the browser?"
15:42:17 <MarcAlexandre_Bio> it should return the corresponding RDF document
15:42:18 <mscottm> EricN: I will ping some of these people and try to involve them in the process.
15:44:40 <alanr> should return the corresponding RDF document only if the URI denotes an RDF document.
15:45:21 <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
15:45:41 <eneumann> alan, see Guidelines and Best Practices for Resource Identification:
15:46:03 <alanr> actually, I suggest MarcAlexandre reads said. I have.
15:46:13 <MarcAlexandre_Bio> true, if you ask the html page, you should receive the html page
15:46:30 <matthiassamwald> q+
15:46:46 <BillBug> LSID Applications:
15:46:48 <BillBug>    * Tax Data WG - http://www.tdwg.org/
15:46:50 <BillBug>       * just had an LSID Policy Workshop - http://www.tdwg.org/homepage-news-item/article/lsid-policy-workshop/
15:46:52 <BillBug>    * BioMOBY:
15:46:53 <BillBug>       * Mark Wilkinson - iCAPTURE Pjt - application of BioMOBY - http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml
15:46:55 <BillBug>       * BioMOBY home - http://www.biomoby.org/
15:46:56 <BillBug>       * iCAPTURE LSID client resolver - http://bioinfo.icapture.ubc.ca/ekawas/data/LSID_resolver.html
15:46:58 <BillBug>       * iCAPTURE LSID metadata resolver - http://mobycentral.icapture.ubc.ca:8090/authority/lsid/ResolveLSID?lsid=urn:lsid:biomoby.org:objectclass:DNASequence
15:46:59 <BillBug>    * EBI
15:47:01 <BillBug>    	  * Carole Gobel - http://www.cs.man.ac.uk/~carole/
15:47:02 <BillBug>    	  * Taverna & LSID - PPT by Carole - http://twiki.mygrid.org.uk/twiki/pub/Mygrid/PresentationStore/GGFTavernaOMII.ppt
15:47:04 <BillBug>    * Newcastle U. - Centre for Integrated Systems Biology of Ageing and Nutrition Data Portal
15:47:05 <BillBug>    	  * abstract - http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016
15:47:07 <BillBug>    	  * home - http://www.cisban.ac.uk/index.html
15:47:09 <BillBug>    	  
15:47:39 <mscottm> Susie: maybe a F2F would help to move things along, shall we try to organize something in July
15:47:55 <BillBug> Sorry - I must be off.  I'll get back to Jonathan re: the PURL use in the Banff demo.
15:48:03 <Zakim> -BillBug
15:49:36 <jar286> q+
15:50:34 <mscottm> Matthias: I think that we should base our discussion on concrete examples (such as comparing what was done in Banff to LSID's)
15:50:53 <ericP> ack me
15:50:53 <Zakim> ericP, you wanted to propose template header that limits scope of documents to read
15:50:58 <ericP> q=
15:51:00 <mscottm> Jonathan (?): I think that the requirements should come from the applications
15:51:08 <ericP> queue=
15:53:56 <alanr> matthias is getting flack :(
15:54:16 <alanr> I will do some figures for poster
15:54:48 <mscottm> Matthias (about BioOntologies poster): if you have (better) ideas about a visualization, please send them.
15:55:10 <alanr> maybe we can draft JAR for common naming for poster
15:56:00 <mscottm> Susie: Let's talk more about the poster at next week's call.
15:56:16 <alanr> do we know the date of the demo yet?
15:57:27 <mscottm> EricN: considering additional touches to demo such as the ability to move images around
15:57:54 <eneumann> no dates yet, but we should here by beginning of July
15:58:25 <mscottm> Don: we're setting up a demo machine here
15:59:02 <mscottm> Alan: still arranging the new server at Wright Univ via email
15:59:30 <Zakim> -Kerstin_Forsberg
16:00:03 <alanr> matthias - please send out ontology + query for review
16:00:30 <matthiassamwald> http://neuroscientific.net/res/kidb_to_obo/kidb070131.turtle
16:01:32 <Zakim> -Eric_Neumann
16:01:34 <Zakim> -John_Barkley
16:01:35 <Zakim> -susie
16:01:36 <Zakim> -Don_Doherty
16:01:38 <Zakim> -EricP
16:02:10 <mscottm> Matthias: Datasources - incorporating KI sources, can link ligands with receptors from NeuronDB, can link to pubmed articles
16:02:38 <Zakim> - +Jonathan_and_Alan
16:02:51 <Zakim> -Kei_and_Matthias
16:02:52 <mscottm> bye
16:02:55 <Zakim> -Olivier_Bodenreider
16:02:57 <Zakim> -Kersten
16:03:09 <Zakim> -Scott_Marshall
16:03:10 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:03:11 <Zakim> Attendees were Don_Doherty, Scott_Marshall, susie, Kerstin_Forsberg, John_Barkley, EricP, BillBug, Eric_Neumann, Kei, Matthias, Kersten, JonathanR, AlanR, Olivier_Bodenreider
16:03:40 <MarcAlexandre_Bio> Bye
16:03:46 <matthiassamwald> bye, marc.
16:23:18 <matthiassamwald> matthiassamwald has left #BioRDF
17:02:36 <jar286> jar286 has joined #BioRDF
18:15:49 <Zakim> Zakim has left #BioRDF
18:57:46 <jar286> jar286 has joined #BioRDF