14:56:32 <RRSAgent> RRSAgent has joined #hcls
14:56:32 <RRSAgent> logging to http://www.w3.org/2008/07/10-hcls-irc
14:56:37 <ericP> Zakim, this will be HCLS
14:56:37 <Zakim> ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 4 minutes
14:56:55 <Zakim> SW_HCLS()11:00AM has now started
14:57:02 <Zakim> + +1.301.975.aaaa
14:57:02 <ericP> Meeting: HCLS Telecon
14:57:26 <ericP> Chair: Susie 
14:57:57 <ericP> agenda+ Introductions
14:57:57 <ericP> agenda+ Marketing Update
14:57:57 <ericP> agenda+ Ideal Attributes of Projects
14:57:57 <ericP> agenda+ Representing Clinicaltrials.gov in RDF
14:57:57 <ericP> agenda+ Convert the Diseasome into RDF
14:57:59 <ericP> agenda+ HCLS KB Enhancements
14:58:02 <ericP> agenda+ AOB
14:58:03 <Zakim> + +1.781.662.aabb
14:58:09 <ericP> agenda?
14:58:23 <ericP> agenda- 1
14:58:26 <Zakim> +??P5
14:58:30 <ericP> agenda- 2
14:58:40 <ericP> Zakim, please dial ericP-office
14:58:40 <Zakim> ok, ericP; the call is being made
14:58:42 <Zakim> +EricP
14:58:51 <ericP> Zakim, please disconnect ericP-office
14:58:51 <Zakim> sorry, ericP, I do not see a party named 'ericP-office'
14:58:54 <ericP> Zakim, please disconnect ericP
14:58:54 <Zakim> EricP is being disconnected
14:58:56 <Zakim> -EricP
14:59:38 <Zakim> - +1.781.662.aabb
14:59:53 <ericP> Zakim, please dial ericP-office
14:59:53 <Zakim> ok, ericP; the call is being made
14:59:55 <Zakim> +EricP
15:00:04 <Zakim> + +1.781.662.aacc
15:00:16 <ericP> Zakim, aacc is Susie 
15:00:17 <Zakim> +Susie; got it
15:00:49 <ericP> Zakim, ??P5 Bhat
15:00:49 <Zakim> I don't understand '??P5 Bhat', ericP
15:00:53 <ericP> Zakim, ??P5 is Bhat
15:00:53 <Zakim> +Bhat; got it
15:01:27 <ericP> Zakim, who is here?
15:01:27 <Zakim> On the phone I see +1.301.975.aaaa, Bhat, EricP, Susie
15:01:28 <Zakim> On IRC I see RRSAgent, Susie, mscottm, Huajun, kanzure, Zakim, ericP
15:02:25 <matthiassamwald> matthiassamwald has joined #hcls
15:02:28 <Huajun> Why can't I see me on the phone?
15:02:37 <Huajun> I amfrom a iphone
15:02:45 <Zakim> +??P8
15:02:52 <ericP> Zakim, ??P5 is really Huajun
15:02:57 <Zakim> +Huajun; got it
15:02:57 <Donald_Doherty> Donald_Doherty has joined #HCLS
15:03:01 <matthiassamwald> zakim, ??p8 is matthiassamwald
15:03:01 <Zakim> +matthiassamwald; got it
15:03:47 <Zakim> +[Microsoft]
15:03:49 <Zakim> + +1.212.937.aadd
15:03:55 <Zakim> +Don_Doherty
15:04:03 <mscottm> having skype problems
15:04:13 <ericP> Zakim, +1.301.975.aaaa is Bhat
15:04:13 <Zakim> +Bhat; got it
15:04:24 <ericP> Zakim, +1.212.937.aadd Paul_H
15:04:24 <Zakim> I don't understand '+1.212.937.aadd Paul_H', ericP
15:04:28 <ericP> Zakim, +1.212.937.aadd is Paul_H
15:04:28 <Zakim> +Paul_H; got it
15:04:40 <Zakim> +Kei_Cheung
15:04:50 <ericP> Zakim, Micrsoft is temporarily Kristen
15:04:50 <Zakim> sorry, ericP, I do not recognize a party named 'Micrsoft'
15:04:55 <ericP> Zakim, who is here?
15:04:55 <Zakim> On the phone I see Bhat, Huajun, EricP, Susie, matthiassamwald, [Microsoft], Paul_H, Don_Doherty, Kei_Cheung
15:04:57 <Zakim> On IRC I see Donald_Doherty, matthiassamwald, RRSAgent, Susie, mscottm, Huajun, kanzure, Zakim, ericP
15:05:00 <ericP> Zakim, [Micrsoft] is temporarily Kristen
15:05:00 <Zakim> sorry, ericP, I do not recognize a party named '[Micrsoft]'
15:05:09 <ericP> Zakim, [Microsoft] is temporarily Kristen
15:05:11 <Zakim> +Kristen; got it
15:06:15 <ericP> agenda?
15:06:23 <sivaram> sivaram has joined #HCLS
15:07:11 <Susie> Zakim, pick a scribe
15:07:11 <Zakim> Not knowing who is chairing or who scribed recently, I propose matthiassamwald
15:07:15 <Zakim> +Sivaram
15:07:46 <kei> kei has joined #HCLS
15:08:22 <matthiassamwald> susie: we will start a "scribe-list" for the teleconferences.
15:09:12 <matthiassamwald> susie: lets start with introductions from participants.
15:10:54 <ericP> kanzure is Bryan Bishop
15:11:50 <matthiassamwald> [introductions from don doherty, eric P, huajun chen, kei cheung, matthias samwald]
15:12:58 <matthiassamwald> [introduction from sivaran Arabandi (cleveland clinic)]
15:13:01 <mscottm> sorry - going to try reboot to solve "Problem with recording device" in Skype 
15:13:32 <ericP> http://lists.w3.org/Archives/Public/public-semweb-lifesci/2008Jul/0015 says that Bryan Bishop is a semweb hacker, currently working with data from the Allen Institute
15:13:40 <matthiassamwald> [introduction from kristen ??? (microscoft)]
15:14:08 <matthiassamwald> [introduction from bryan bishop]
15:14:08 <ericP> Zakim, take up agendum 4
15:14:08 <Zakim> agendum 4. "Marketing Update" taken up [from ericP]
15:14:56 <matthiassamwald> susie: we need to think about how to "market" the things we as a group are doing.
15:15:40 <matthiassamwald> susie: chimezie, scott and I had a discussion with a contact at W3C, the W3C will help us in "marekting", e.g., media outreach
15:15:42 <Susie> http://esw.w3.org/topic/HCLSIG
15:16:28 <matthiassamwald> susie: at the moment we are compiling lists of for the most important venues that we should be at.
15:17:00 <matthiassamwald> susie: see http://esw.w3.org/topic/HCLSIG under the header 'marketing'
15:17:16 <matthiassamwald> susie: this will help us target papers etc.
15:17:20 <mscottm> mscottm has joined #hcls
15:17:25 <Susie> http://esw.w3.org/topic/HCLSIG/Conferences
15:17:29 <matthiassamwald> susie: at the moment the list is biased towards my interests
15:17:43 <Susie> http://esw.w3.org/topic/HCLSIG/Media
15:18:25 <matthiassamwald> susie: it is important that we do not only focus on journals, papers etc., but also on other media such as radio, the blogging community etc.
15:18:35 <cgi-irc> cgi-irc has joined #hcls
15:18:43 <matthiassamwald> susie: i put up a list of around 15 journals that might be of interest to us.
15:18:49 <Zakim> +??P17
15:19:08 <mscottm> Zakim,  +??P17 is mscottm
15:19:08 <Zakim> sorry, mscottm, I do not recognize a party named '+??P17'
15:19:21 <ericP> matthiassamwald: when we have identified the channels, how do we generate the content?
15:19:21 <mscottm> Zakim, +??P17 is mscottm
15:19:21 <Zakim> sorry, mscottm, I do not recognize a party named '+??P17'
15:19:43 <ericP> ... we had challenges generating a colaborative paper in the last edition of this IG
15:19:43 <mscottm> Zakim, "+??P17" is mscottm
15:19:43 <Zakim> sorry, mscottm, I do not recognize a party named '"+??P17"'
15:20:00 <ericP> q+ eric to mention consensus process
15:20:04 <matthiassamwald> matthias: but how do we create the content we disemminate? we need a streamlined process for collaborating.
15:20:19 <ericP> Zakim, ??P17 is mscottm 
15:20:19 <Zakim> +mscottm; got it
15:20:38 <matthiassamwald> susie: people that work on a specific project should have the lead about writing something about their projects
15:20:59 <matthiassamwald> susie: other participants only do 'polishing' 
15:21:28 <kei> q+
15:21:33 <mscottm> thanks eric
15:21:57 <ericP> q- eric
15:22:03 <ericP> ack kei 
15:22:08 <matthiassamwald> kei: what about recruitment of personal (e.g. post docs)?
15:22:34 <ericP> q+ to endorse putting a message after the g+
15:22:46 <matthiassamwald> susie: we should try to get 'key people' in the community on board of the HCLS IG.
15:24:06 <matthiassamwald> susie: posting notifications about open positions to the mailing list is OK.
15:24:14 <ericP> ack ericP 
15:24:14 <Zakim> ericP, you wanted to endorse putting a message after the g+
15:24:51 <ericP> s/g+/q+/
15:25:02 <ericP> Zakim, take up next agendum
15:25:02 <Zakim> agendum 3. "Introductions" taken up [from ericP]
15:25:10 <ericP> Zakim, close agendum 3
15:25:10 <Zakim> agendum 3, Introductions, closed
15:25:11 <Zakim> I see 5 items remaining on the agenda; the next one is
15:25:12 <Zakim> 5. Ideal Attributes of Projects [from ericP]
15:25:12 <ericP> Zakim, take up next agendum
15:25:12 <Zakim> agendum 5. "Ideal Attributes of Projects" taken up [from ericP]
15:25:47 <matthiassamwald> susie: projects need to have at least some scientific focus.
15:26:48 <matthiassamwald> susie: HCLS IG task forces will have separate calls
15:27:00 <matthiassamwald> susie: and dedicated coordinators.
15:28:19 <matthiassamwald> susie: we would prefer projects that link to other activities, making it possible to have a common "mission"
15:29:40 <matthiassamwald> scott: we would like to have a applied approach in HCLS
15:30:04 <ericP> +1 to framing as scientific question as early as possible
15:30:35 <matthiassamwald> scott: projects should aim at answering specific questions
15:30:48 <kei> q+ can a task force span multiple projects
15:30:55 <matthiassamwald> kei: can a task force span multiple projects?
15:31:25 <matthiassamwald> susie: generally, i expect that there is one project per task force. the BIORDF task could contain several tasks, though.
15:32:28 <ericP> Zakim, take up next agendum
15:32:28 <Zakim> agendum 6. "Representing Clinicaltrials.gov in RDF" taken up [from ericP]
15:32:47 <matthiassamwald> susie: ok, let's discuss some ideas for projects.
15:33:44 <kanzure> Hello.
15:34:23 <matthiassamwald> susie: Representing Clinicaltrials.gov --- users might want to be able to do more expressive queries.
15:34:41 <kanzure> Rapid brainstorm of potential semantic web projects?
15:34:55 <matthiassamwald> susie: but integrating it with other datasets would also be interesting.
15:35:18 <matthiassamwald> susie: Lilly has a website called http://www.lillytrials.com/
15:35:41 <matthiassamwald> susie: at the moment, most of the information is inside PDF documents.
15:36:24 <matthiassamwald> susie: NIH orange book is another dataset in this domain
15:36:57 <ericP> q+ to ask if we can get our hands on the backend data for Clinicaltrials.gov
15:36:58 <matthiassamwald> susie: or drugbank
15:37:16 <matthiassamwald> susie: this connects to the work of COI
15:37:56 <matthiassamwald> susie: we should first do a survey on relevant datasets.
15:38:44 <ericP> ack me
15:38:44 <Zakim> ericP, you wanted to ask if we can get our hands on the backend data for Clinicaltrials.gov
15:40:14 <ericP> ack me
15:40:46 <kei> q+
15:42:03 <ericP> Zakim, take up next agendum
15:42:03 <Zakim> I see a speaker queue remaining and respectfully decline to close this agendum, ericP
15:42:09 <ericP> ack kei 
15:42:10 <ericP> Zakim, take up next agendum
15:42:10 <Zakim> agendum 7. "Convert the Diseasome into RDF" taken up [from ericP]
15:43:05 <Susie> http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/
15:44:02 <ericP> note that links are not apparent in the style for the above resource, but they are there
15:44:13 <matthiassamwald> susie: there needs to be a specific scientific question when we start such collaborations.
15:44:50 <matthiassamwald> susie: there is something called "connectivity map" that looks at gene expression profiles of drug responses
15:46:03 <matthiassamwald> scott: it would be interesting to query the association between different diseases via common proteins and pathways.
15:46:22 <chimezie> chimezie has joined #hcls
15:46:55 <matthiassamwald> scott: there could be some synergy with other projects, e.g. projects that link proteins to diseases via textmining
15:47:01 <Zakim> -Bhat
15:48:19 <ericP> i'm eager to work on this
15:49:08 <Donald_Doherty> I'd like to help.
15:49:25 <ericP> ack me
15:49:47 <matthiassamwald> kirsten: i know that some data sets exist about breast cancer, for example. 
15:49:58 <mscottm> Alz, HD, PD: it's a 'marriage of convenience' :)
15:50:06 <Zakim> +Chimezie_Ogbuji
15:50:28 <matthiassamwald> eric: it is a question of whether we want to branch out or not.
15:50:59 <matthiassamwald> kirsten: but can we at this point still decide what domains we want to deal with?
15:51:51 <ericP> Zakim, take up next agendum
15:51:51 <Zakim> agendum 8. "HCLS KB Enhancements" taken up [from ericP]
15:52:16 <mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/KB
15:53:52 <matthiassamwald> scott: it would be good to demonstrate that we can distribute our knowledge sources over several locations.
15:54:09 <ericP> q+ to say that COI is sort of leaning on SPASQL
15:54:44 <matthiassamwald> scott: the queries at the moment require a lot of specialised knowledge
15:56:02 <matthiassamwald> scott: one idea to aid in querying is to offer support based on terms in the knowledge base (google-style lookup)
15:56:41 <kei> I have to sign off ...
15:57:10 <chimezie> bye Kei
15:59:40 <matthiassamwald> scott: we are not limited to neuroscientific data, but it also makes sense to build upon what we already have (which is centered on neuroscience)
16:00:19 <matthiassamwald> SUGGESTION: let's start discussion threads about all these issues on the mailing list.
16:00:39 <ericP> q?
16:01:05 <cgi-irc> I'm happy to follow up offline on the breast cancer data
16:01:11 <cgi-irc> This is Kristin
16:01:16 <mscottm> ok, great.
16:01:22 <chimezie> Zakim, who is on the phone?
16:01:22 <Zakim> On the phone I see Huajun, EricP, Susie, matthiassamwald, Kristen, Paul_H, Don_Doherty, Kei_Cheung, Sivaram, mscottm, Chimezie_Ogbuji
16:01:52 <matthiassamwald> s/Kristen/Kristin/
16:02:16 <ericP> next call: 24July
16:02:51 <ericP> Zakim, please draft minutes
16:02:51 <Zakim> I don't understand 'please draft minutes', ericP
16:02:54 <Zakim> -Paul_H
16:02:56 <Zakim> -Sivaram
16:02:56 <Zakim> -Chimezie_Ogbuji
16:02:58 <Zakim> -Don_Doherty
16:02:59 <Zakim> -Kristen
16:03:01 <Zakim> -Susie
16:03:06 <Zakim> -Huajun
16:03:23 <matthiassamwald> @eric, could you please tell RRSagent to create the minutes?
16:03:35 <ericP> Zakim, please draft minutes
16:03:35 <Zakim> I don't understand 'please draft minutes', ericP
16:03:48 <ericP> RRSAgent, please draft minutes
16:03:48 <RRSAgent> I have made the request to generate http://www.w3.org/2008/07/10-hcls-minutes.html ericP
16:03:57 <ericP> RRSAgent, please make log world-visible
16:04:15 <matthiassamwald> thanks.
16:04:28 <Zakim> -matthiassamwald
16:22:51 <kanzure> Is the meeting over?
16:23:09 <mscottm> yes
16:23:25 <mscottm> it was about an hour long
16:40:35 <kanzure> Oh well. That's what I get for pulling all-nighters and crashing at the last minute ;-)
16:41:52 <kanzure> Has the group ever considered model/object/scaffold serialization into code instead of just datasets with unreferenced metadata (like table structure difficulties, which could be avoided just by transferring the code in the first place) ?
16:42:13 <Zakim> -EricP
16:42:20 <Zakim> -mscottm
16:42:47 <ericP> kanzure, i believe not, though i may have missed your method
16:43:09 <ericP> i have to run off now, but can poll back here later to see what you write
16:43:20 <mscottm> same here
16:43:50 <kanzure> http://yaml.org/ or even http://pyyaml.org/ for instance.
16:43:55 <mscottm> actually - feel free to send e-mail - I don't have irc set up on a server yet, just using from a laptop client.
16:44:09 <kanzure> hm, but I mentioned it in my intro email but left it kind of vague
16:44:20 <kanzure> anyway, the basic idea is that we *know* people are doing programming
16:44:25 <kanzure> and this is why there exists implementations
16:44:29 <kanzure> that code that they are making is what is important
16:44:44 <kanzure> and then we just need pipes/streams for the data and a way to describe it (which we have as RDF)
16:45:21 <kanzure> if you've ever found a new database and said "crap, now how am I going to integrate this" you'll see why object/model serialization would be nice :)
16:45:47 <kanzure> since it can be deserialized and immediately executed on the system in whatever framework you're implementing (dependent on compatability/dependencies, but debian has solved this in '92 and others even earlier IIRC)
16:47:20 <Zakim> disconnecting the lone participant, Kei_Cheung, in SW_HCLS()11:00AM
16:47:23 <Zakim> SW_HCLS()11:00AM has ended
16:47:25 <Zakim> Attendees were +1.781.662.aabb, EricP, +1.781.662.aacc, Susie, Huajun, matthiassamwald, Don_Doherty, Bhat, Paul_H, Kei_Cheung, Kristen, Sivaram, mscottm, Chimezie_Ogbuji
16:47:42 <kanzure> I'll have to look into attending the meetings.