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14:25:31 <ericP> q+ to ask about NIF license
14:26:51 <ericP> [slide 25: To Map or Not to Map]
14:30:16 <ericP> [slide 28: Concept-based search]
14:32:22 <ericP> [slide 32: NIFSTD:...]
14:34:30 <David_Shotton> Eric, your notes are v helpful.  Thanks!
14:36:29 <ericP> [slide 38: Neurolex]
14:36:42 <ericP> quite welcome David_Shotton 
14:38:14 <ericP> [slide 41: NIF in practice]
14:42:36 <David_Shotton> Excellent talk
14:42:53 <ericP> DavidB: have you published your best practices?
14:43:04 <ericP> Maryann: just about
14:43:13 <ericP> ... we're not sure if these things are really barriers
14:43:32 <ericP> ... discussions happen here (hcls), but not in neuroscience
14:43:56 <ericP> ... expect to push them out soon as "from our experience, here are five problems"
14:44:19 <ericP> DavidB: you have not included commercial sites
14:44:33 <ericP> Maryann: legacy from the Neuroscience gateway
14:44:50 <ericP> ... we're roughly adhering to this
14:45:05 <ericP> ... didn't want to flood the site with commercial products
14:45:14 <ericP> ... want to have ranking systems in place first
14:45:27 <ericP> ... we ask our users if they want to see commercial tools
14:45:50 <ericP> ... i believe NIF needs to both push community and be responsive
14:46:16 <ericP> johnB: what search results do you get from NIF vs. google
14:46:22 <ericP> ?
14:46:41 <ericP> Marryann: there is a lot of spurious stuff in NIFWEB
14:46:52 <ericP> ... in the early days, we needed to seed with some results
14:47:07 <ericP> ... we do stop crawls if we find fals results
14:47:45 <mscottm> ...focus more on educational sites but it's meant to be a broad spectrum.
14:48:25 <mscottm> Elgar: How much of a headache is the synchronization process? Do you have recommendations?
14:49:14 <mscottm> Maryann: One problem was deprecated OBI classes. Bill Bug made a set of proxy classes and update them. But we don't have a magic solution.
14:50:40 <David_Shotton> Signing off - many thanks.
14:50:47 <David_Shotton> David_Shotton has left #hcls
14:50:48 <jun> thanks Eric, for the notes
14:51:13 <Zakim> -??P10
14:51:14 <Zakim> -David
15:18:50 <Zakim> + +1.919.597.aabb
15:19:00 <Zakim> - +1.919.597.aabb
15:19:24 <Zakim> +John_Madden
15:20:21 <ericP> current slide set: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=view&target=biordf_f2f_2009.ppt
15:20:57 <ericP> ericP has changed the topic to: biordf task force update: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=view&target=biordf_f2f_2009.ppt
15:21:12 <johnM> johnM has joined #hcls
15:24:57 <ericP> johnM, i think your sound will be fine if you want to do the speaking while one of us clicks your slides
15:25:55 <ericP> you'll have to keep it as short as possible. we are, of course, behind schedule
15:25:58 <dbooth> dbooth has joined #hcls
15:26:20 <johnM> We can try that, sure.
15:28:09 <mscottm> Great! Thanks John.
15:29:03 <ericP> @@@2: At BioIT world, Susie referred to existing drugDBs
15:29:11 <ericP> ... do you have something like that for SNPs?
15:29:18 <ericP> Kei: not at present
15:30:25 <ericP> ericN: see also, Sean Moody, and mutedb (SP?)
15:31:43 <ericP> #topic LODD update: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=view&target=LODD.ppt
15:31:56 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=view&target=LODD.ppt LODD slides
15:32:05 <ericP> [slide: Published Data Sets]
15:34:05 <jun> jun has joined #hcls
15:38:37 <ericP> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=LODD.ppt
15:38:47 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=LODD.ppt LODD slides
15:40:11 <ericP> note: esw wiki has links for "...&do=get" as well as "...&do=view" . the latter does not work in links
15:40:45 <johnM> thx
15:41:15 <ericP> i've fixed the links in http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
15:41:39 <ericP> [slide 11: Conclusions]
15:42:24 <ericP> Anita: when the BBC publishes data, is that bits of text, numbers?
15:42:48 <ericP> Susie: we've been looking at semi-structured data represented in XML
15:43:38 <ericP> ericP: assume you've been focusing on data who's intended consumer is machines
15:43:47 <ericP> Anita: so what's the BBC data/
15:43:48 <ericP> ?
15:44:05 <ericP> Dave DeRoure: BBC data is typically cataloge info
15:44:16 <ericP> mscottm: is typically data from RDBs?
15:44:46 <ericP> Kei: data doesn't automatically generate knowledge. requires lots of human processing
15:45:18 <ericP> Susie: i think linked data does work better for some granularities of data than others
15:45:28 <ericP> ... e.g. linking Berlin is better than linking the number 2
15:45:49 <ericP> ... don't want to use it for publishing whole abstracts
15:46:22 <ericP> Anita: can use representations of scientific data sets. you don't mean as produceed by experiments?
15:48:05 <ericP> ... we have this issue at Elsevier. We can impose some structure on our documents and project it into RDF. but what uses cases does it support?
15:48:21 <ericP> Becky: what's your coverage of diseases?
15:48:35 <ericP> Susie: every drug that folks are developing drugs for
15:48:49 <ericP> ... per clinicaltrials.gov
15:49:01 <ericP> Olivier: from 2001 on
15:50:23 <ericP> Bosse: there is a lot of text info in LODD...
15:50:36 <dbooth> Re whether text qualifies as data, it's a qualitative judgement call.
15:50:39 <ericP> Joanne: how difficult was it to linke these datasets?
15:50:53 <ericP> susie: they sometimes talk about slightly different things
15:51:14 <ericP> ... e.g. active compound vs. the whole thing (with buffers)
15:51:28 <ericP> Joanne: of your target, how much coverage did you get?
15:51:47 <ericP> Susie: hard to quantify
15:52:05 <ericP> ... data providers would be best folks to establish the linked data
15:52:19 <ericP> Joanne: for follow-up, what makes a good quality link?
15:53:29 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=Presentation_20090430_PharmaOntology_v02.pdf Pharma Ontology slides
15:54:06 <Karen> Karen has joined #hcls
15:54:56 <ericP> [slide 2: Pharma Ontology]
15:59:05 <ericP> [slide 4: Goals & Deliverables]
16:01:40 <ericP> [slide 7: Existing Resources]
16:05:03 <ericP> [slide 11: Summary]
16:09:31 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=TERMPresentation.ppt Terminology Task Force slides
16:10:05 <ericP> ericP has changed the topic to: Terminology Task Force update: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=TERMPresentation.ppt
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16:14:03 <ericP> [slide 3: Medical terminologies today]
16:14:03 <Joanne> where are the slides?
16:14:09 <Zakim> + +1.317.277.aacc
16:14:58 <Joanne> ignore question (i see the link now). thanks
16:18:11 <ericP> [slide 6: Taskforce repository]
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16:22:31 <ericP> [slide 8: (screenshot)]
16:24:23 <dbooth> I'm amused that the value of SKOS was seen as its *lack* of formal semantics.
16:24:45 <anitawaard> why amused? is that not the point of skos?
16:25:09 <ericP> it's ironic in the SW context 'cause we're always arguing to add semantics to stuff
16:25:37 <ericP> what we rarely say, but really mean, is "lable stuff with the *appropriate* semantics"
16:25:41 <anitawaard> I thought he point of skos was to allow the 'broader-narrower than' relationships - because people (if not machines) really like them?
16:25:55 <anitawaard> good enough semantics, kid of like good-enough parenting...
16:26:13 <anitawaard> kid -> kind
16:26:23 <ericP> [slide 11: Immediate next steps]
16:27:32 <ericP> note the proliferation of the "Raw Data Now" mime
16:27:42 <dbooth> y, it's not quite the *lack* of semantics that bring value, but the presence of semantics that are not overly constraining.
16:28:04 <anitawaard> or overly incomprehensible...
16:28:09 <dbooth> y
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16:28:35 <ericP> yeah, rdfs:seeAlso is used quite a lot because it has almost no interpreation beyond, get this, "see also"
16:28:48 <anitawaard> wonderful
16:29:06 <ericP> otoh, when ever you try to use rdfs:seeAlso, you have no idea if it was coded for the scenario in which you intend to use it
16:29:18 <anitawaard> we are successfully dumblng down the standards to our level
16:29:28 <anitawaard> :D
16:29:29 <dbooth> :)
16:30:34 <ericP> [slide 13: Social Challenges]
16:31:03 <anitawaard> our systems are too smart for us... 
16:31:15 <anitawaard> we have to learn what they want us to do at some point in the future - 
16:31:18 <anitawaard> but not today...
16:31:26 <anitawaard> :P
16:32:01 <anitawaard> I like the last bullet - RDF connects us to our documents...
16:32:55 <ericP> dbooth: did you mean URNs?
16:33:02 <ericP> ericP: URIs is the superset
16:33:10 <dbooth> URI is the general term.  URNs and URLs are a subset of URIs.
16:33:48 <ericP> anitawaard, dbooth, it would be interesting to look at existing uses of rdfs:seeAlso and with an eye towards factoring common uses of it which would benefit from more explicit terms
16:33:58 <Zakim> -John_Madden
16:34:19 <ericP> johnM, tx a zillion!
16:35:09 <anitawaard> is "rdfs:/eeAlso" = rdf-a?
16:35:20 <johnM> David, sorry you are quite right. (I never can keep that straight!!!)
16:35:25 <anitawaard> or am i missing something (quite likely)
16:36:17 <dbooth> ericP, Pat Hayes a few months ago threatened/offered/proposed to write a new version of RDF, which would "fix" various omissions/mistakes, such as the lack of a way to name a graph (duh!) and other things.
16:36:44 <dbooth> If he goes forward, maybe he'd be open to putting something more in.
16:37:45 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=COI-Overview-HCLS2009.ppt COI Task Force update slides
16:38:01 <ericP> ericP has changed the topic to: COI Task Force update: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=COI-Overview-HCLS2009.ppt
16:39:12 <ericP> [slide 5: Use Case Step-Through]
16:44:18 <ericP> -> http://www.w3.org/2009/Talks/0225-cshals-ep/ pictorial click-through of the COI query transformation
16:45:11 <ericP> slides 1-10,23-27
16:46:44 <ericP> [http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=COI-Overview-HCLS2009.ppt slide 11: Medication]
16:47:01 <ericP> [slide 12: Criteria in SPARQL]
16:48:46 <ericP> [slide 15: Drug Ontology by Stanford]
16:49:57 <Zakim> +??P3
16:51:13 <ericP> [slide 27]
16:51:19 <ericP> [slide 28]
16:52:49 <ericP> [slide 31]
16:52:55 <ericP> [slide 32]
16:53:01 <jun> jun has joined #hcls
16:54:05 <ericP> ericN: would like to discuss drug ontologies
16:54:37 <Zakim> +??P4
16:54:55 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=Sci+Discourse+Status.ppt Scientific Discourse Task Force update
16:55:13 <ericP> ericP has changed the topic to: Scientific Discourse Task Force update: http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F?action=AttachFile&do=get&target=Sci+Discourse+Status.ppt
16:56:05 <mscottm> Zakim, ??P4 is marco
16:56:05 <Zakim> +marco; got it
16:56:07 <ericP> [slide 4: Anser]
16:56:19 <ericP> salut, marco
16:57:22 <ericP> [slide 5: (chart)]
16:58:13 <ericP> [slide 5: (diagram)]
16:58:22 <Joanne> Joanne has joined #hcls
16:58:29 <jun> jun has joined #hcls
16:58:53 <ericP> [slide 8]
16:59:26 <ericP> [slide 9: Scientific knowledge ecosystem]
16:59:35 <jun> thanks. got it:)
17:01:34 <ericP> [slide 11: Scientific Discourse Task Status April 20 2009]
17:02:10 <anita> anita has joined #hcls
17:08:08 <ChristiDenney> my apologies. i have been called into a meeting and i will not be able to attend the pharma ontology breakout.
17:08:59 <ericP> ChristiDenney, i'll relay to susie
17:09:32 <ericP> CarlT: intested in connecting brain behavoir with imaging
17:10:19 <anita> PortalDoors
17:10:35 <ericP> ... an overall scheme called PortalDoors addresses most of what's been brought up here
17:10:39 <ChristiDenney> thank you eric!  :-)
17:10:54 <Zakim> - +1.317.277.aacc
17:11:22 <Zakim> -marco
17:13:24 <Zakim> -??P3
17:19:55 <junzhao_> junzhao_ has joined #hcls
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17:28:43 <Zakim> - +1.713.745.aaaa
17:32:46 <david_newman> david_newman has joined #HCLS
17:34:42 <david_newman> Hi.  Is there something clever I am suppose to do if I want to join a particular breakout group from the afternoon session?  i.e. the scientific discourse one.  The wiki suggest there is just one general line
17:37:56 <Zakim> + +0196266aadd
17:47:47 <mscottm> breakouts begin at 14:05
17:48:25 <mscottm> you need to join hcls for biordf, hcls1 for Pharma Ontology, hcls2 for Sci Discourse
17:48:55 <david_newman> thanks.
17:50:28 <mscottm> I suppose that you supply the analogous codes to Zakim.. Checking.
17:51:00 <david_newman> so it would be 42572 for sci discourse then?
17:51:20 <mscottm> yes
17:51:24 <david_newman> great
17:52:31 <Zakim> - +0196266aadd
17:52:47 <JoanneLuciano> JoanneLuciano has joined #hcls
18:03:31 <ericP> Zakim, who is here?
18:03:31 <Zakim> On the phone I see MIT-Star
18:03:32 <Zakim> On IRC I see JoanneLuciano, david_newman, marco, Stefano, Karen, RRSAgent, Zakim, mscottm, HelenaDeus, jonas, Cloud, ericP
18:06:23 <Zakim> + +2
18:07:14 <ericP> hello, who just joined the phone bridge?
18:07:30 <ericP> julia: you've implemented something that is a lot like the semantic web
18:07:43 <ericP> ... why not just use semweb technology?
18:07:55 <peterA> peterA has joined #HCLS
18:08:06 <marco> marco just joined by phone (skype)
18:08:13 <ericP> carl: rules on declaring a URI is up to the registry
18:08:14 <david_newman> ericP: I have joined on the hcls2 phone branch
18:08:38 <ericP> Zakim, +2 is Marco
18:08:38 <Zakim> +Marco; got it
18:09:03 <ericP> david_newman, on hcls1 or 2?
18:09:16 <david_newman> david_newman is +0196266aadd on hcls2
18:09:22 <ericP> tx
18:12:51 <mscottm> we're just now splitting into different rooms for breakouts
18:13:27 <Zakim> -Marco
18:13:57 <Zakim> +??P1
18:14:39 <Zakim> -??P1
18:19:06 <Zakim> +??P1
18:24:23 <junzhao> junzhao has joined #hcls
18:34:38 <Zakim> + +49.421.218.6.aaff
18:41:29 <HelenaDeus> HelenaDeus has joined #hcls
18:42:14 <HelenaDeus> sorry, i lost the connection. which number shoudl I call for the Bio2RDF breakout?
18:44:49 <junzhao> you should just dial the general number on the wiki page
18:44:59 <junzhao> it is used for biordf breakout at the moment. scott is talking
18:45:08 <Zakim> +??P9
18:45:35 <HelenaDeus> cool, thanks :)
18:45:56 <junzhao> you are welcome:)
19:02:29 <Zakim> - +49.421.218.6.aaff
19:29:17 <Zakim> -??P1
19:45:19 <HelenaDeus> is there a url for the slides being presented in each of the breakout sessions?
19:46:28 <mscottm> Ouch. Francois just started but I'm afraid that we don't have a copy to upload - I'll ask his colleague.
19:47:02 <HelenaDeus> yeah... i can hear him speak but nothing to look at :)
19:48:05 <mscottm> I talked to Marc-Alexandre. He says that it is on slide share and he will send it to me.
19:48:36 <mscottm> He is showing the Bio2RDF could map of 2,3 billion triples in 2009
19:50:03 <mscottm> Voila! http://www.slideshare.net/fbelleau/bio2rdf-w3c-hcls2009
19:50:27 <mscottm> He is on "Why do it?"
19:50:44 <HelenaDeus> aha! Thank you so much 
19:51:29 <mscottm> Zakim, who is on the phone?
19:51:29 <Zakim> On the phone I see MIT-Star, ??P9
19:51:45 <mscottm> Zakim, ??P9 is HelenaDeus
19:51:45 <Zakim> +HelenaDeus; got it
20:30:08 <Zakim> +??P3
20:41:05 <david_newman> david_newman has joined #HCLS
20:42:24 <Zakim> -HelenaDeus
20:42:54 <mscottm> Zakim, who is on the phone
20:42:54 <Zakim> I don't understand 'who is on the phone', mscottm
20:42:59 <mscottm> Zakim, who is on the phone?
20:42:59 <Zakim> On the phone I see MIT-Star, ??P3
20:43:15 <mscottm> Zakim, ??P3 is david_newman
20:43:15 <Zakim> +david_newman; got it
21:10:01 <anitawaard> anitawaard has joined #hcls
21:18:37 <Zakim> -david_newman
21:21:25 <Zakim> -MIT-Star
21:21:26 <Zakim> SW_HCLS(F2F)9:00AM has ended
21:21:27 <Zakim> Attendees were MIT-Star, David, +1.713.745.aaaa, +1.919.597.aabb, John_Madden, +1.317.277.aacc, marco, +0196266aadd, +49.421.218.6.aaff, HelenaDeus, david_newman
21:24:24 <ericP> RRSAgent, please draft minutes
21:24:24 <RRSAgent> I have made the request to generate http://www.w3.org/2009/04/30-hcls-minutes.html ericP
21:24:31 <ericP> RRSAgent, please make log world-visible