17:03:56 <RRSAgent> RRSAgent has joined #hcls2
17:03:56 <RRSAgent> logging to http://www.w3.org/2010/11/11-hcls2-irc
17:04:08 <michel> zakim, this is tmo
17:04:15 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
17:04:29 <matthias_samwald> zakim, who is on the phone?
17:04:33 <Zakim> On the phone I see Bob_Powers, +1.518.276.aaaa, ??P24, +200000aabb, Bo_Anderson, +1.302.598.aacc
17:04:36 <Bob> Bob has joined #hcls2
17:04:44 <Zakim> +??P9
17:04:50 <michel> zakim ?PP9 is michel
17:04:58 <matthias_samwald> zakim, ??P24 is matthias_samwald
17:04:58 <Zakim> +matthias_samwald; got it
17:05:43 <Zakim> + +1.781.431.aadd
17:06:05 <michel> +1.781.431.aadd is epichler
17:06:29 <michel> zakim, 1.781.431.aadd is epichler
17:06:29 <Zakim> sorry, michel, I do not recognize a party named '1.781.431.aadd'
17:07:12 <michel> zakim, +1.781.431.aadd is epichler
17:07:12 <Zakim> +epichler; got it
17:08:14 <matthias_samwald> zakim, help
17:08:14 <Zakim> Please refer to http://www.w3.org/2001/12/zakim-irc-bot for more detailed help.
17:08:16 <Zakim> Some of the commands I know are:
17:08:17 <Zakim>  xxx is yyy       - establish yyy as the name of unknown party xxx
17:08:20 <Zakim>                     if yyy is 'me' or 'I', your nick is substituted
17:08:23 <Zakim>  xxx may be yyy   - establish yyy as possibly the name of unknown party xxx
17:08:26 <Zakim>  I am xxx         - establish your nick as the name of unknown party xxx
17:08:28 <Zakim>  xxx holds yyy [, zzz ...] - establish xxx as a group name and yyy, etc. as participants within that group
17:08:31 <Zakim>  xxx also holds yyy - add yyy to the list of participants in group xxx
17:08:33 <Zakim>  who's here?      - lists the participants on the phone
17:08:37 <Zakim>  who's muted?     - lists the participants who are muted
17:08:39 <Zakim>  mute xxx         - mutes party xxx (like pressing 61#)
17:08:41 <Zakim>  unmute xxx       - reverses the effect of "mute" and of 61#
17:08:43 <Zakim>  is xxx here?     - reports whether a party named like xxx is present
17:08:45 <Zakim>  list conferences - reports the active conferences
17:08:46 <Zakim>  this is xxx      - associates this channel with conference xxx
17:08:48 <Zakim>  excuse us        - disconnects from the irc channel
17:08:49 <Zakim> I last learned something new on $Date: 2010/03/15 18:49:04 $
17:09:04 <epichler> thanks matthias!
17:09:31 <matthias_samwald> you can do the same for RRSagent, which is actually more helpful for the minutes
17:09:44 <matthias_samwald> (i think)
17:10:13 <michel> rrsagent, help
17:11:18 <Jim> Jim has joined #HCLS2
17:11:32 <michel> wiki page: http://esw.w3.org/HCLSIG/PharmaOntology/Paper
17:12:26 <whetzel> a discussion on the HCLS & TMO structure and activities. 	Michel 	Confirmed 
17:13:24 <Bob> Michel: 1) will add paragraph on weekly calls etc
17:14:23 <Bob> Michel: Paper should indicate that the KB is an important component, plus patient records
17:14:36 <whetzel> agree
17:15:11 <Bob> Trish: Ontology is just a framework for something more interesting
17:15:48 <Bob> Michel: Bridge patient records over the LODD
17:17:18 <Bob> ... would like to see the paper more about the entire effort
17:17:20 <Zakim> + +20416aaee
17:18:01 <Bob> Joanne: We talk about research to clinic and back again, but the research component isn't really addressed
17:18:22 <Bob> ... 15) talk about it from a research perspective
17:20:17 <Bob> Michel: 2) Ref. ontologies try to cover comprehensively; but we are much more applied
17:20:34 <Bob> ... text should describe our evaluation
17:20:54 <Bob> ... need to contrast our effort vs. efforts of the reference ontologies
17:23:22 <mscottm> mscottm has joined #hcls2
17:23:51 <Bob> Joanne: 3) 5) and 10) are covered by PeterT and PeterK
17:24:37 <Bob> Michel: 4) Eric has come up w. framework for unit testing
17:24:54 <mscottm> ericP has come up - ericP's bot is now alerted ;)
17:25:25 <Bob> ... convert to Indivo XML, converted then to RDF in a quad format
17:26:42 <Bob> ... final piece for unit testing, will translate to RDF, describe your sparql
17:27:01 <Bob> ... system needs to be described
17:27:12 <Bob> Scott: It's a really cool system
17:27:29 <Bob> Yes.
17:31:51 <Bob> Joanne: Scott for number 4)
17:32:21 <Joanne> Authors- add scott
17:33:10 <Bob> Michel: 5) detailing consistency; came from reviewer comments
17:33:12 <Jim> Scott, what is your affiliation?
17:33:39 <Joanne> Michel suggests, all agree keep 1st and last and rest will be alphabetical
17:34:36 <mscottm> I had trouble hearing Michel just now too
17:35:26 <Bob> Michel: 6) BigOWLIM
17:36:14 <Bob> Matthias: Checked consistency of TMO + LODD
17:36:55 <Bob> ... can try to execute sparql queries, but need to check datasets
17:37:09 <Joanne> Scott's afiliation (scott, please correct) Leiden University Medical Center and the University of Amsterdam.
17:38:19 <Bob> Michel: 7) overview figure, next couple of days
17:38:38 <Bob> ... 8) figure for Fig.1, Chime's got it done
17:38:45 <mscottm> I have double affil.. LUMC and University of Amsterdam
17:38:56 <Joanne> thanks Scott!
17:39:05 <michel> http://esw.w3.org/HCLSIG/PharmaOntology/Diagrams
17:39:16 <mscottm> If it gets too crowded, just use the LUMC. :)
17:39:40 <Zakim> - +1.302.598.aacc
17:39:52 <mscottm> Zakim, who is here
17:39:52 <Zakim> mscottm, you need to end that query with '?'
17:39:55 <mscottm> Zakim, who is here?
17:39:55 <Zakim> On the phone I see Bob_Powers, +1.518.276.aaaa, matthias_samwald, +200000aabb, Bo_Anderson, ??P9, epichler, +20416aaee
17:39:57 <Zakim> On IRC I see mscottm, Jim, Bob, RRSAgent, epichler, Zakim, Joanne, michel, whetzel, matthias_samwald, ericP
17:40:25 <Bob> Michel: Fig. 1 will be overview, then a query diagram
17:40:47 <Bob> Michel: 9) mapping to CPR: EricP and Chime have to do this
17:47:09 <ericP> Zakim, please dial ericP-office
17:47:09 <Zakim> ok, ericP; the call is being made
17:47:11 <Zakim> +EricP
17:48:56 <Bob> Eric: Documenting what the queries, here's how the mapping works, etc
17:49:29 <Bob> ... talked about Indivo XML, Michel also suggested testing framework
17:50:24 <Bob> Eric: Bragging points: If you have a sense of test coverage from user community
17:50:53 <Bob> ... then you can get messages saying which queries failed and can get quick feedback
17:51:06 <Bob> ... don't have to gang up all the testing at the end
17:51:27 <Bob> Scott: Xtreme programming for ontological development
17:51:39 <Bob> XPOD!!
17:52:13 <Bob> Eric: Every sparql implementation has this functionality
17:52:35 <Bob> Michel: Update KB w. patient data?
17:53:03 <Bob> ... see if it fits at the last minute
17:53:46 <Bob> Michel: Query that spans more or all datasets
17:55:23 <Bob> Michel: 14) related work is now broader than before: snomed, nci thesaurus
17:55:57 <Bob> Jim McCusker: Send your suggestions re related work
17:56:57 <Bob> Michel: 15) Research use case
17:57:18 <Bob> Joanne: 13) and 15) are two different aspects of just about the same thing
17:57:57 <Bob> Joanne: a) Enabling eScience on a much larger scale
17:58:32 <Bob> ... b) focussed on pharma might miss the message of having a translational medicine ontology
17:59:11 <Bob> ... users of different roles; Message should be clear that different users can view w diff lenses
17:59:50 <Bob> ... a) If we could say something important re eScience
18:00:14 <Bob> Scott: NL trying to get Science Center established
18:00:39 <Bob> ... eSci sometimes start talking re big data
18:02:23 <Bob> ... TMO talks about something in the gene list that might be useful
18:05:33 <Bob> Scott: I will give it a go.  This is important.
18:06:18 <ericP> my model for a high-throuput analysis lab is Fred Hutchinson Cancer Research
18:07:07 <ericP> they were the folks who convinced me that they weren't good users of SemWeb stuff
18:07:08 <Bob> Chat on the document itself!  Go to the 'Share' button and add your email.
18:07:32 <Bob> https://docs0.google.com/document/d/1sh0lttGpqXZuQL-WxTSqj5ZjMRFeYUciHhkHfqRSrTk/edit?hl=en&authkey=CK7D5YYO&pli=1#
18:07:34 <Joanne> https://docs.google.com/document/d/1sh0lttGpqXZuQL-WxTSqj5ZjMRFeYUciHhkHfqRSrTk/edit?authkey=CK7D5YYO&hl=en#
18:07:56 <Zakim> -epichler
18:07:57 <Zakim> -matthias_samwald
18:08:00 <Zakim> -Bo_Anderson
18:08:02 <Zakim> -??P9
18:08:11 <michel> scribenick bobP
18:08:21 <michel> rrsagent, draft minutes
18:08:21 <RRSAgent> I have made the request to generate http://www.w3.org/2010/11/11-hcls2-minutes.html michel
18:08:21 <Zakim> - +200000aabb
18:08:27 <michel> rrsagent, make log world-visible
18:45:03 <Zakim> - +1.518.276.aaaa
18:46:51 <matthias_samwald> matthias_samwald has left #hcls2
19:09:06 <Zakim> -Bob_Powers
19:13:42 <Zakim> -EricP
19:13:43 <Zakim> - +20416aaee
19:13:43 <Zakim> SW_HCLS(TMO)11:00AM has ended
19:13:45 <Zakim> Attendees were Bob_Powers, +1.518.276.aaaa, +200000aabb, Bo_Anderson, +1.302.598.aacc, matthias_samwald, epichler, +20416aaee, EricP
20:39:57 <Zakim> Zakim has left #hcls2