16:03:02 <RRSAgent> RRSAgent has joined #hcls
16:03:02 <RRSAgent> logging to http://www.w3.org/2010/01/07-hcls-irc
16:03:03 <Zakim> +??P48
16:04:17 <Zakim> +oliver
16:04:43 <mscottm> Zakim, ??P48 is Harold
16:04:45 <Zakim> +Harold; got it
16:04:52 <mscottm> Zakim, who is here?
16:04:52 <Zakim> On the phone I see Susie, +46.4.63.3.aaaa, Kei_Cheung, +1.650.319.aabb, ??P39, +1.507.319.aacc, Harold, oliver
16:04:59 <Zakim> On IRC I see RRSAgent, kei, curoli, matthias_samwald, Susie, bbalsa, mscottm, egonw, AlexPassant, Zakim, ericP
16:05:40 <mscottm> Zakim, +1.650.319.aabb is mscottm
16:05:40 <Zakim> +mscottm; got it
16:06:04 <Zakim> - +46.4.63.3.aaaa
16:06:18 <mscottm> Zakim, who is here?
16:06:18 <Zakim> On the phone I see Susie, Kei_Cheung, mscottm, ??P39, +1.507.319.aacc, Harold, oliver
16:06:25 <Zakim> On IRC I see RRSAgent, kei, curoli, matthias_samwald, Susie, bbalsa, mscottm, egonw, AlexPassant, Zakim, ericP
16:06:49 <Zakim> + +46.4.63.3.aadd
16:07:01 <mscottm> Zakim, +46.4.63.3.aadd is Bosse
16:07:04 <Zakim> +Bosse; got it
16:07:25 <mscottm> Zakim, pick a scribe
16:07:25 <Zakim> Not knowing who is chairing or who scribed recently, I propose oliver
16:07:41 <mscottm> Zakim, pick a scribe
16:07:41 <Zakim> Not knowing who is chairing or who scribed recently, I propose +1.507.319.aacc
16:07:47 <hsolbrig> hsolbrig has joined #HCLS
16:08:13 <mscottm> Zakim, +1.507.319.aacc is hsolbrig
16:08:13 <Zakim> +hsolbrig; got it
16:09:27 <hsolbrig> Update from Kei - doing microarry use case, working on RDF structure of representing microarry experiments
16:09:35 <ericP> Zakim, please dial ericP-office
16:09:35 <Zakim> ok, ericP; the call is being made
16:09:36 <Zakim> +EricP
16:10:46 <hsolbrig> In process of identifying relevent metadata and putting it into RDF structure.
16:11:21 <mscottm> http://wiki.knoesis.org/index.php/Provenir_Ontology
16:12:14 <hsolbrig> Looking at Provenir as generic ontology to repreresent gene data
16:12:19 <mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2
16:12:41 <mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/01-04_Conference_Call
16:13:16 <hsolbrig> Q: any idea of how to express gene lists?
16:13:57 <Zakim> +John_Madden
16:14:13 <hsolbrig> A: right now, doing it by hand. Mage Tab can export results of experiment, refs MGED ontology, but need to incorporate other types of ontologies.
16:14:46 <hsolbrig> Need to combine Mage Tab and other upper level ontologies, need meaningful relationships.
16:15:37 <ericP> hsolbrig: you [kei] should track bioportal
16:15:47 <mscottm> Harold: Please take a look at BioPortal, good resource
16:15:54 <ericP> ... they're creating resources to create and embed exactly that sort of map
16:16:01 <johnM> johnM has joined #hcls
16:17:56 <johnM> johnM has left #hcls
16:18:04 <johnM> johnM has joined #hcls
16:18:30 <johnM> yeah
16:18:35 <mscottm> tx
16:19:13 <mscottm> http://www.ncbi.nlm.nih.gov/pubmed/19208191
16:20:00 <hsolbrig> Scott: NCBO is submitting renewal right now.
16:20:01 <Zakim> + +1.781.839.aaee
16:20:40 <hsolbrig> Terminology update - John M.
16:20:51 <hsolbrig> Terminology is back on line, calls moved to Monday at noon.
16:21:06 <hsolbrig> Still on hcls2
16:22:04 <hsolbrig> Main project was working w/ Scott on putting SNOMED in IEDA (sp?)
16:22:31 <hsolbrig> Now easier to specify mapping rules between SKOS representation of SNOMED and other ontologies.  Includes an OWL reasoner.
16:23:55 <hsolbrig> who is speaking?
16:24:01 <mscottm> ericP
16:24:09 <mscottm> Eric Prud'hommeaux
16:25:03 <hsolbrig> ericP: COI update - putting together proposal to caBIG to work w/ HCLS
16:26:04 <ericP> hsolbrig: does the caBIG proposal have a document name?
16:26:22 <ericP> mscottm: no name. working on an ARA grant
16:26:43 <ericP> hsolbrig: are you working with boseallen or @@1?
16:26:52 <ericP> ... i.e. how can i track this?
16:26:54 <hsolbrig> Booz Allen or SAIC
16:27:09 <ericP> s/boseallen/Booz Allen/
16:27:12 <hsolbrig> Susie: LODD update
16:27:21 <ericP> s/@@1/Booz Allen/
16:27:54 <hsolbrig> Susie: looking at licensing issues.  Will always contact data providers going forward..
16:28:21 <jerven> jerven has joined #hcls
16:28:24 <hsolbrig> ... get permission to convert into RDF first.  Will be extra cautious and will also ask existing sources.
16:29:01 <hsolbrig> ... In terms of LODD  Working with translational medicine ontology group, have alzheimers and fake patient data.
16:29:22 <hsolbrig> ... Working CEMBL - chem db from EBI.
16:29:58 <hsolbrig> ... Outreach - Matthias working on paper on traditional Chinese medicine
16:30:32 <hsolbrig> kei: What is approach to converting different data and formats to RDF?
16:30:42 <hsolbrig> ... bottom up, syntactic?
16:31:12 <hsolbrig> Susie:  so far bottom up, but becoming increasingly interested in semantic mapping using consistent terminology.
16:31:45 <hsolbrig> ... drugs have been a challenge, work done on consistent naming through NIH and RxNORM, but no drug ontology available.
16:32:12 <hsolbrig> Susie: Translational Medicine Ontology update
16:32:39 <hsolbrig> ... Submitted paper to JBI issue on translational ontologies
16:33:35 <hsolbrig> ... A huge amount of work went into it.  Created draft TM ontology but still working
16:34:38 <hsolbrig> .... worked on a physician centric use case, in dx and rx area.
16:35:19 <hsolbrig> .... include insurance, dx, patient, pharmgkb and other data sources. Mapped to RDF, put in triple store.
16:36:16 <hsolbrig> ... Going forward - work on UI.  Idea is one integrated body of data and many specific UI's (physician, researcher, etc.)
16:37:13 <hsolbrig> ... TM Ontology - terms already in other domain ontologies.  
16:38:20 <hsolbrig> mscottm: Scientific Discource
16:38:38 <hsolbrig> ... next task is use cases for structured rhetorical document.
16:39:02 <hsolbrig> ... how do you represent discourse in scientific articles?
16:39:25 <hsolbrig> ... looking at SWAN, SALT and ABCDE (Elsevier)
16:40:11 <hsolbrig> ... ongoing work with MyExperiment.  Looking at CETO (sp?)
16:41:48 <hsolbrig> s/Discource/Discourse/
16:42:15 <hsolbrig> mscottm: CSHALS
16:42:27 <hsolbrig> ... giving tutorial on HCLS at CSHALS conference Feb 24.
16:42:57 <hsolbrig> ... Lief and Eric will give general intro in morning.  Afternoon will be HCLS tutorial
16:43:35 <hsolbrig> ... Ask folks to think about what sort of material they'd like to contribute.  Mark calendar as well.
16:44:12 <hsolbrig> ... Mark calendar for April 19 and 20 or 22 and 23 for FTF at BioIT World
16:44:31 <ericP> s/Lief/Lee Feigenbaum/
16:44:39 <hsolbrig> ... Will be in MIT in Boston
16:45:00 <hsolbrig> ... Fall meeting will be in Europe
16:45:33 <hsolbrig> ... want to create integrative impression at CSHALS, so need material ahead of time to coordinate.
16:46:28 <hsolbrig> Susie: Tutorials are 2 hours in the afternoon  Not a lot of time.
16:48:52 <ericP> ericP: how valuable would trackability be?
16:49:08 <ericP> hsolbrig: there are a bunch of RFPs for the caBIG community
16:49:27 <ericP> ... if we can reference this caBIG submission, we can reference it in ours
16:50:14 <ericP> s/there are/Mayo Clinic has/
16:50:33 <ericP> hsolbrig: our focus in caBIG is ontology services
16:50:46 <ericP> ... we're submitting allignment tools and wikis
16:52:05 <mscottm> ..LexCVS - controlled vocabulary services from Mayo, working closely with NCBO
16:52:30 <ericP> hsolbrig, can you make it to Tue 11am EDT COI calls?
16:53:05 <hsolbrig> eric, yes.
16:53:23 <mscottm> http://healthit.hhs.gov/portal/server.pt?open=512&objID=1436&mode=2
16:53:29 <mscottm> = SHARP
16:53:39 <hsolbrig> johnM: submitted to SHARP grants, ARRA grant turn around was short.
16:55:06 <hsolbrig> ... Duke decided that turn around time was too short, so they changed focus from collaboration to existing work.
16:55:36 <mscottm> johnM: DHCI call this morning decided to change focus away from external participation (not enough time for alignment).
16:56:34 <hsolbrig> ... had hoped to include HCLS, but didn't work.  Lesson: ARRA has short turn around.  Need on-file biosketches and a couple of pages about possible participation, funding, etc.
16:57:42 <hsolbrig> ... suggests a site as a repository of ideas, etc
16:57:50 <hsolbrig> kei: formats are changing this year.
16:58:11 <hsolbrig> johnM: just need starter material, not final format.
16:59:42 <hsolbrig> ... need a collection of small (eg $25k range) projects that can be combined into a larger package.
17:00:21 <hsolbrig> johnM: will help set one up with ericP.
17:01:06 <Zakim> -Susie
17:01:12 <hsolbrig> mscottm: Best way to include W3C is to write them in as a full partner vs. just eric.  They need visibility.
17:01:15 <Zakim> - +1.781.839.aaee
17:01:39 <bbalsa> Need to leave for the TMO cal, bye.
17:01:56 <Zakim> -Bosse
17:02:02 <Zakim> -oliver
17:02:23 <hsolbrig> next call in one month.
17:02:23 <Zakim> -Harold
17:02:40 <ericP> RRSAgent, please draft minutes
17:02:40 <RRSAgent> I have made the request to generate http://www.w3.org/2010/01/07-hcls-minutes.html ericP
17:02:42 <Zakim> -Kei_Cheung
17:02:47 <hsolbrig> I'm still here!
17:02:53 <ericP> RRSAgent, please make log world-visible
17:03:00 <Zakim> -??P39
17:07:23 <ericP> hsolbrig: we want to index expertise and interest and resources
17:15:56 <mscottm> Zakim, who is here?
17:15:56 <Zakim> On the phone I see mscottm, hsolbrig, EricP, John_Madden
17:15:57 <Zakim> On IRC I see johnM, RRSAgent, curoli, bbalsa, mscottm, egonw, AlexPassant, Zakim, ericP
17:16:44 <Zakim> -hsolbrig
17:16:45 <mscottm> bye
17:16:45 <Zakim> -EricP
17:16:46 <Zakim> -John_Madden
17:17:19 <Zakim> -mscottm
17:17:22 <Zakim> SW_HCLS()11:00AM has ended
17:17:23 <Zakim> Attendees were Susie, +46.4.63.3.aaaa, Kei_Cheung, oliver, Harold, mscottm, Bosse, hsolbrig, EricP, John_Madden, +1.781.839.aaee