IRC log of BioRDF on 2007-06-25

Timestamps are in UTC.

15:01:17 [RRSAgent]
RRSAgent has joined #BioRDF
15:01:17 [RRSAgent]
logging to
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]
15:02:04 [Zakim]
15:02:05 [ericP]
Zakim, please dial ericP-office
15:02:05 [Zakim]
ok, ericP; the call is being made
15:02:06 [Zakim]
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]
15:05:03 [Zakim]
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]
15:11:52 [BillBug]
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]
15:12:54 [alanr]
15:13:29 [ericP]
q+ BillBug to discuss current LSID applications
15:13:32 [Zakim]
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]
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]
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]
15:17:05 [mscottm]
15:17:29 [ericP]
q+ to limit scope
15:17:43 [ericP]
ack alanr
15:17:47 [BillBug]
15:17:47 [ericP]
ack BillBug
15:17:48 [Zakim]
BillBug, you wanted to discuss current LSID applications and to
15:17:54 [ericP]
15:17:56 [alanr]
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]
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]
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]
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]
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]
15:29:23 [ericP]
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]
15:30:58 [alanr]
Action: ericp to add navigation to wiki pages
15:32:05 [ericP]
note header of , 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]
15:39:14 [alanr] mentions URIs?
15:39:19 [alanr]
can't see it
15:39:40 [ericP]
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]
15:46:46 [BillBug]
LSID Applications:
15:46:48 [BillBug]
* Tax Data WG -
15:46:50 [BillBug]
* just had an LSID Policy Workshop -
15:46:52 [BillBug]
* BioMOBY:
15:46:53 [BillBug]
* Mark Wilkinson - iCAPTURE Pjt - application of BioMOBY -
15:46:55 [BillBug]
* BioMOBY home -
15:46:56 [BillBug]
* iCAPTURE LSID client resolver -
15:46:58 [BillBug]
* iCAPTURE LSID metadata resolver -
15:46:59 [BillBug]
15:47:01 [BillBug]
* Carole Gobel -
15:47:02 [BillBug]
* Taverna & LSID - PPT by Carole -
15:47:04 [BillBug]
* Newcastle U. - Centre for Integrated Systems Biology of Ageing and Nutrition Data Portal
15:47:05 [BillBug]
* abstract -
15:47:07 [BillBug]
* home -
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]
15:49:36 [jar286]
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]
15:51:00 [mscottm]
Jonathan (?): I think that the requirements should come from the applications
15:51:08 [ericP]
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]
16:00:03 [alanr]
matthias - please send out ontology + query for review
16:00:30 [matthiassamwald]
16:01:32 [Zakim]
16:01:34 [Zakim]
16:01:35 [Zakim]
16:01:36 [Zakim]
16:01:38 [Zakim]
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]
16:02:52 [mscottm]
16:02:55 [Zakim]
16:02:57 [Zakim]
16:03:09 [Zakim]
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]
16:03:46 [matthiassamwald]
bye, marc.
16:23:18 [matthiassamwald]
matthiassamwald has left #BioRDF
17:02:36 [jar286]
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18:15:49 [Zakim]
Zakim has left #BioRDF
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