15:00:38 <RRSAgent> RRSAgent has joined #hcls
15:00:38 <RRSAgent> logging to http://www.w3.org/2009/03/19-hcls-irc
15:00:44 <ericP> Zakim, please dial ericP-office
15:00:45 <Zakim> sorry, ericP, I don't know what conference this is
15:00:50 <ericP> Zakim, this is hcls
15:00:50 <Zakim> ok, ericP; that matches SW_HCLS()11:00AM
15:00:55 <ericP> Zakim, please dial ericP-office
15:00:55 <Zakim> ok, ericP; the call is being made
15:00:57 <Zakim> +EricP
15:01:41 <curoli> curoli has joined #hcls
15:03:01 <Zakim> + +1.949.481.aabb
15:03:05 <Zakim> + +1.617.724.aacc
15:03:14 <Zakim> + +1.860.255.aadd
15:03:40 <mscottm> Zakim, +1.949.481.aabb is TimClark
15:03:41 <Zakim> +TimClark; got it
15:03:52 <curoli> zakim, +1.860.255.aadd is oliver
15:03:52 <Zakim> +oliver; got it
15:04:04 <curoli> zakim, curoli is oliver
15:04:04 <Zakim> sorry, curoli, I do not recognize a party named 'curoli'
15:04:04 <mscottm> hi oliver
15:04:20 <Zakim> +??P0
15:04:22 <curoli> hi scott
15:04:49 <zhaoj> zhaoj has joined #hcls
15:04:55 <curoli> zakim, oliver is curoli
15:04:55 <Zakim> +curoli; got it
15:05:33 <Zakim> +Kei_Cheung
15:05:43 <kei> kei has joined #HCLS
15:06:53 <mscottm> Zakim, who is here?
15:06:53 <Zakim> On the phone I see +1.781.662.aaaa, Scott_Marshall, EricP, TimClark, +1.617.724.aacc, curoli, ??P0, Kei_Cheung
15:06:55 <Zakim> On IRC I see kei, jun, curoli, RRSAgent, Zakim, mscottm, Susie, egonw, Cloud, ericP
15:07:25 <ericP> meeting: HCLS
15:07:34 <curoli> zakim, i am oliver
15:07:34 <Zakim> sorry, curoli, I do not see a party named 'oliver'
15:07:43 <curoli> zakim, help
15:07:43 <Zakim> Please refer to http://www.w3.org/2001/12/zakim-irc-bot for more detailed help.
15:07:45 <Zakim> Some of the commands I know are:
15:07:46 <Zakim>  xxx is yyy       - establish yyy as the name of unknown party xxx
15:07:49 <ericP> chair: SusieS
15:07:50 <Zakim>                     if yyy is 'me' or 'I', your nick is substituted
15:07:53 <Zakim>  xxx may be yyy   - establish yyy as possibly the name of unknown party xxx
15:07:56 <ericP> topic: TF updates
15:07:57 <Zakim>  I am xxx         - establish your nick as the name of unknown party xxx
15:08:02 <Zakim>  xxx holds yyy [, zzz ...] - establish xxx as a group name and yyy, etc. as participants within that group
15:08:05 <Zakim>  xxx also holds yyy - add yyy to the list of participants in group xxx
15:08:10 <Zakim>  who's here?      - lists the participants on the phone
15:08:13 <Zakim>  who's muted?     - lists the participants who are muted
15:08:16 <Zakim>  mute xxx         - mutes party xxx (like pressing 61#)
15:08:18 <Zakim>  unmute xxx       - reverses the effect of "mute" and of 61#
15:08:20 <Zakim>  is xxx here?     - reports whether a party named like xxx is present
15:08:24 <Zakim>  list conferences - reports the active conferences
15:08:27 <Zakim>  this is xxx      - associates this channel with conference xxx
15:08:29 <Zakim>  excuse us        - disconnects from the irc channel
15:08:31 <Zakim> I last learned something new on $Date: 2009/03/19 18:29:44 $
15:08:40 <ericP> timClack: Scientific Discourse: doing 3 IG notes
15:08:56 <ericP> ... Paolo and Alex working on them
15:09:04 <ericP> ... on schedule for having something in early may
15:10:08 <ericP> scribenick: ericP 
15:10:46 <ericP> timClark: looking at swan, sioc, myExperiment, we are missing the ontology piece 
15:11:07 <ericP> ... is a big piece to attack, so starting with the provenance
15:11:40 <ericP> ... starting with Sudeshna's microarray and lilly's @@1 ontology
15:11:45 <johnM> johnM has joined #hcls
15:11:47 <ericP> ... awaiting approval from lilly
15:11:50 <jun> zakim, ??P0 is jun
15:11:50 <Zakim> +jun; got it
15:12:46 <ericP> carl: what's the scope of scientific discourse
15:12:50 <KevinDoyle> KevinDoyle has joined #HCLS
15:12:59 <ericP> timClark: google "swan sioc"
15:13:07 <ericP> ... not a general view
15:13:18 <ericP> ... using pre-existing ontologies in the area
15:13:32 <ericP> ... integrating them - bottom-up approach
15:14:00 <ericP> ... working with specific goals in use cases
15:14:08 <Zakim> + +1.617.710.aaee
15:14:24 <ericP> ... you (carl) have a scientific discourse portal. we'd like to integrate your ontology
15:15:01 <ericP> carl: goes back to toni kasik's appeal for scholarly discourse networks
15:15:13 <ericP> ... i guess your's is geared to concrete apps
15:15:26 <curoli> zakim, curoli is really oliver
15:15:26 <Zakim> +oliver; got it
15:15:46 <ericP> ... toki's use case was connecting researchers with publishers
15:16:12 <ericP> timClark: sioc relates statements to inviduals
15:16:28 <ericP> ... in swan, there is a citation ontology
15:17:18 <ericP> ... many folks interested in e.g. disambiguating authors
15:17:26 <ericP> carl: will read up and contribute
15:17:49 <ericP> timClark: we'll read your [carl's] paper
15:18:08 <ericP> susie: will scientific discourse have a break-out at the f2f?
15:18:32 <ericP> timClark: there's a meeting on linked biomedical web ontologies the day before
15:18:48 <ericP> ... can't do too much prep
15:19:29 <Susie> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
15:20:40 <ericP> ... with dave derue, karen skinner, marian, i can come up with work material
15:20:51 <mscottm> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
15:21:03 <matthias_samwald> matthias_samwald has joined #hcls
15:22:12 <Zakim> +??P8
15:22:23 <matthias_samwald> Zakim, ??P8 is matthias_samwald
15:22:23 <Zakim> +matthias_samwald; got it
15:22:30 <matthias_samwald> sorry for being late.
15:22:38 <ericP> ACTION: timClark to write break-out plans on http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
15:24:30 <ericP> topic: f2f
15:25:10 <ericP> susie: f2f is backed on to timClark's meeting, a URI workshop, and BIO-IT
15:25:39 <ericP> ... feel free to drag along other folks who might be interested/interesting
15:26:11 <mscottm> yes.
15:26:37 <ericP> topic: BioRDF task update
15:26:46 <ericP> ... focusing on BMC informatics paper
15:26:59 <ericP> ... is basically an update from the C-SHALS meeting
15:27:35 <ericP> ... adrian paske is a co-organizer of this issue, they've extended the deadline to 3 weeks from now
15:27:41 <ericP> ... need to move on this
15:28:08 <ericP> ... will discuss break-out goals with the task force
15:29:15 <ericP> ... working on Query Federation and ATAG
15:29:37 <ericP> ... will look at aida toolkit ( mscottm )
15:29:56 <ericP> ... interface is one of the goals of biordfd
15:31:22 <ericP> ACTION: kei to sketch break-out ideas in http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
15:32:37 <ericP> timClark: JohM will be at f2f. wants to do a co-break-out
15:32:54 <ericP> ... if everyone meets with everyone, it's not a break-out
15:34:22 <cdenney> cdenney has joined #HCLS
15:34:34 <ericP> topic: coi update
15:34:45 <ericP> ericP: focused up AMIA submisison and finishing demo
15:34:57 <ericP> ACTION: ericP to talk to coi about break-outs at COI
15:35:07 <ericP> topic: lodd update
15:35:16 <ericP> Susie: we got a paper accepted
15:36:07 <ericP> ... (at WWW)
15:36:09 <ericP> ... looks like either william sanchez or oktai will present at WWW
15:36:29 <ericP> ... just met one accomplished. tidying up
15:36:46 <ericP> mscottm: does that include managing URI synonyms?
15:37:05 <ericP> Susie: yes (for identifiers). field names as well
15:37:25 <ericP> ... fields sometimes at different or inconsistent levels of aggregation
15:37:35 <ericP> ... adding links which we were tentative about
15:37:47 <ericP> ... working on rules to automate adding linkages in the future
15:37:50 <ericP> ... so:
15:37:55 <ericP> ... .. cleaning up existing data
15:38:37 <ericP> ... .. considering new data sets (e.g. chemical structure -- concensus around gross structure)
15:39:00 <egonw> gross structure?
15:39:01 <Zakim> +??P15
15:39:23 <mscottm> Zakim, mute ??P15
15:39:23 <Zakim> ??P15 should now be muted
15:39:30 <johnM> johnM has joined #hcls
15:39:44 <ericP> ... .. been using naive @@2s
15:40:05 <ericP> ... many of the LOD folks are interested in pharma ontology
15:40:24 <johnM> Yes sorry, mute me if necessary. I can actually talk from here if called on.
15:40:31 <ericP> ... see connections to scientific discourse as we
15:41:12 <ericP> carl: is the prob with synonyms for chemical entity better in the non-healthcare chem industry?
15:41:16 <mscottm> johnM - can you give a Terminology update? If not, I can. 
15:41:25 <ericP> ... or is chem industry better able to standardize?
15:41:41 <ericP> susie: different strings used for the same chemical
15:41:43 <egonw> carl: no, unless you use something like InChI
15:42:06 <ericP> ... many names, but not exactly the same thing
15:42:09 <johnM> Scott could you do it? I can chime in briefly about OWLIM.
15:42:23 <ericP> ... e.g. active ingredients vs. buffers vs...
15:42:41 <ericP> ... for chem structure, IInCHIs work
15:42:56 <egonw> for organic structures, yes
15:43:01 <egonw> like most drugs
15:43:31 <ericP> mscottm: InCHIs can produce mutilple names for the same structure, depending on traversal
15:44:25 <ericP> Susie: yes, and can be very long, but still fairly effective
15:44:25 <mscottm> johnM - sure, I'll do it.
15:44:36 <ericP> topic: pharma ontology update
15:44:54 <ericP> Susie: id'd steps, dates and actors
15:45:12 <ericP> ... want to work out ontology for translational medicine
15:45:39 <ericP> ... covering drugs to patients, genomics to medicine
15:46:11 <ericP> ... started by defining questions which players (pharmas, payers, medical orgs) want to ask
15:46:47 <ericP> ... will then pick 2-3 translational medicine use cases
15:47:06 <ericP> ... then build an ontology for one use case, then an app tests it
15:47:23 <ericP> ... expecting to drive better ontology development
15:48:15 <ericP> ACTION: Susie to check f2f logisitcs for Pharma Onotology Task Force
15:48:45 <ericP> Carl: can contribute a radio@@3 ontology
15:49:10 <ericP> mscottm: looking at side-effect similarity?
15:49:31 <ericP> Susie: not yet. but side-effects are likely to be captured in the high-level template
15:50:05 <johnM> can you unumute me?
15:50:24 <Zakim> - +1.617.724.aacc
15:50:24 <mscottm> Zakim, unmute ??P15
15:50:25 <Zakim> ??P15 should no longer be muted
15:50:50 <ericP> topic: terminology task force
15:51:03 <ericP> johnM: haven't done much on the sesame server this week
15:51:37 <ericP> ... our main produce is a server which serves skos versions of SNOMED, LOINC, and @@@4
15:51:50 <ericP> ... current snomed representation has no inferencing
15:52:18 <ericP> ... trying to do another interface with rdfs closures
15:52:27 <ericP> ... working out tech details with aida
15:52:54 <ericP> ... means that mappings to other ontologies can be done with a few additional triples
15:53:16 <ericP> ... strugging with owlim to work with sesame2
15:53:39 <ericP> ... next goal is to federate with the repositories in berlin and vienna
15:54:01 <ericP> ... expect that we have triples that other groups want to share and expect others have triples that we want
15:54:19 <ericP> ... Simon Schenk has a federation add-in for sesame
15:54:28 <ericP> ... can be used across any sparql endpoint
15:55:30 <ericP> mscottm: kolstas and matthias_samwald got aida to talk to the vienna deri database
15:55:42 <ericP> ... re-coded some to talk to virtuoso
15:56:24 <ericP> ... allows you to take a term from a terminology and look for a similar name in the deri installation
15:56:44 <ericP> ... to find e.g. GO term for dendrites
15:57:43 <matthias_samwald> s/vienna/galway/
15:57:52 <matthias_samwald> it is located in ireland.
15:59:31 <ericP> ACTIONL: johnM to update http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F with break-out ideas/goals
15:59:35 <ericP> topic: AMIA
15:59:53 <mscottm> re: ireland - Oops! eegads.
15:59:57 <ericP> susie: fokls from text mining, ontology, NCI
16:00:14 <ericP> ... tim clark did an update on scidis
16:00:31 <ericP> ... nigam shah did an update on bio ontologies
16:00:43 <ericP> ... did a talk on pharma ont
16:00:53 <ericP> ... room was fool -- maybe 100 folkks
16:00:56 <Zakim> - +1.781.662.aaaa
16:00:57 <Zakim> -Kei_Cheung
16:01:20 <Zakim> -matthias_samwald
16:01:23 <ericP> RRSAgent, please draft minutes
16:01:23 <RRSAgent> I have made the request to generate http://www.w3.org/2009/03/19-hcls-minutes.html ericP
16:01:28 <Zakim> -jun
16:01:30 <ericP> RRSAgent, please make log world-visible
16:01:54 <Zakim> -EricP
16:02:01 <Zakim> -oliver
16:03:18 <mscottm> marshall@science.uva.nl
16:03:28 <Zakim> - +1.617.710.aaee
16:03:32 <KevinDoyle> KevinDoyle has left #HCLS
16:06:13 <mscottm> Zakim, who is here?
16:06:13 <Zakim> On the phone I see Scott_Marshall, TimClark, ??P15
16:06:14 <Zakim> On IRC I see johnM, cdenney, matthias_samwald, curoli, RRSAgent, Zakim, mscottm, egonw, Cloud, ericP
16:07:00 <johnM> zakim, ??P15 is johnM
16:07:01 <Zakim> +johnM; got it
16:11:01 <mscottm> ctaswell@telegenetics.net
16:11:23 <matthias_samwald> matthias_samwald has left #hcls
16:13:37 <johnM> I gotta go -- talk tomorrow!!!!
16:14:13 <Zakim> -johnM
16:23:00 <Zakim> -Scott_Marshall
16:23:01 <Zakim> SW_HCLS()11:00AM has ended
16:23:03 <Zakim> Attendees were +1.781.662.aaaa, Scott_Marshall, EricP, +1.617.724.aacc, TimClark, Kei_Cheung, jun, +1.617.710.aaee, oliver, matthias_samwald, johnM
18:27:43 <Zakim> Zakim has left #hcls