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14:58:43 <michel> Meeting: W3C HCLS – General Meeting
14:58:48 <michel> Chair: Michel Dumontier
14:59:23 <mary> this is mary, for some reason i do not get the email from HCLS for this meeting. mary@knoesis.org
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15:01:36 <michel> zakim, who is making noise?
15:01:36 <Zakim> sorry, michel, I don't know what conference this is
15:01:42 <michel> zakim, this is hcls
15:01:42 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:01:43 <Zakim> +Bob_Powers
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15:03:45 <Zakim> + +1.937.768.aacc
15:04:26 <Zakim> + +46.7.08.13.aadd
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15:05:53 <Zakim> + +1.919.681.aaee
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15:08:16 <mscottm> Zakim, who is making noise?
15:08:27 <Zakim> mscottm, listening for 10 seconds I heard sound from the following: [GVoice] (95%), +1.613.293.aaaa (35%)
15:08:47 <michel> zakim, 1.613.293.aaaa is michel
15:08:47 <Zakim> sorry, michel, I do not recognize a party named '1.613.293.aaaa'
15:08:52 <michel> zakim, +1.613.293.aaaa is michel
15:08:53 <Zakim> +michel; got it
15:10:01 <bobP> Michel: Charting directions for the next year
15:10:52 <bobP> ... First, past HCLS meetings had introductions by email; send an email to the list w interests and task forces
15:11:22 <SimonLin> is there a list of the current task forces?
15:11:49 <michel> task forces: http://www.w3.org/wiki/HCLSIG
15:13:24 <bobP> Michel: ericP and Charlie Mead have been working on clinical interoperability
15:14:54 <bobP> Scott: What we could do to pick up when John Madden had to step down.
15:15:11 <bobP> ... Daniel and I are still interested in continuing
15:15:24 <michel> scribenick: bob powers
15:15:33 <bobP> :)
15:16:01 <bobP> ... Reports from task forces;
15:16:29 <bobP> Scott: Linked Life Data. Richard Boyce has been in final edit
15:16:50 <Zakim> + +1.937.775.aaff
15:16:56 <bobP> ... article tutorial style on different approaches to RDF and sparql for life science data
15:17:37 <bobP> ... also, an article came out last year of translating standards to practice
15:17:56 <bobP> ... navigating thru datasets using sparql on-the-fly
15:18:20 <bobP> ... we went to make a more tutorial style article; ongoing process, but has stalled out
15:18:49 <bobP> ... essentially: We are poised for the final re-structure and rewrite for target audience
15:19:08 <bobP> ... people who have microarray data and want to go to semweb
15:19:24 <bobP> ... also, we want to reinforce representations in RDF
15:19:42 <mary> mary has joined #hcls
15:19:56 <bobP> ... also, discussed moving forward w Data discovery platform for linked data
15:20:01 <Zakim> -[GVoice]
15:20:36 <bobP> ... Biohackathon 2011, there is interest in expression-RDF, interest in continuing on federated discovery
15:21:00 <bobP> ... this comes from two different groups, now consolidating
15:21:00 <Zakim> +[GVoice]
15:21:15 <bobP> ... most interesting is federating across cliinical data
15:21:40 <bobP> ... connecting up both life science and clinical, like radiology
15:22:06 <bobP> ... these all have practical applications, like Eureka(?) that I'm working on
15:22:18 <bobP> ... also DHR4CR from Kersten
15:22:31 <michel> s/DHR4CR/EHR4CR
15:22:43 <bobP> ... all related to FHIR that ericP and Charlie are working on
15:23:05 <bobP> ... can easily connect information for datamining in your clinic
15:23:30 <ericP> LLoyd is now able to represent most of HL7's RIM in OWL.
15:23:41 <bobP> ... semweb representation for patient info; Ex: my clinic has already used
15:23:42 <ericP> we're using that to define FHIR resources
15:23:56 <ericP> has the cool effect that anything in FHIR has a defined RDF representation
15:23:59 <bobP> ... potential path to the future for that group.
15:24:59 <bobP> ... couple of people are also interested in expression RDF;
15:25:32 <bobP> Michel: There was pretty cool work at the Biohackathon in Japan
15:25:58 <ericP> also can combine with OWL for SNOMED to discover equivalence between observations using a single pre-coordinated SNOMED term vs. the parameters in that term sprinkled throughout multiple observations and structural elements
15:25:58 <bobP> ... they used jBrowse to do sparql queries
15:26:24 <bobP> ... showed how to scan through the genome pretty fast
15:26:34 <ericP> this allows one to e.g. be (more) complete when querying for patient facets
15:26:58 <Zakim> -[GVoice]
15:27:06 <bobP> Scott: sparql to access(?)
15:27:19 <ericP> i'm now in a SMART Platforms meeting. hoping to unify SMART with TMO...
15:27:20 <mscottm> SPARQL to access tracks in Genome Browser
15:27:27 <ericP> (Indivo already unified with SMART)
15:27:31 <bobP> Michel: Worked with a simple ontology to query a resource that already exists
15:27:32 <mscottm> EURECA project http://eurecaproject.eu/
15:27:35 <ericP> (so that job is done)
15:27:37 <Zakim> +[GVoice]
15:27:59 <mscottm> Ratnesh mentioned http://www.linked2safety-project.eu
15:28:07 <bobP> ... we have genomic info, not just microarray data; plus all of the other typical data
15:28:21 <bobP> ... need to show how to get from a certain kind of data and integrate
15:29:06 <bobP> Scott: Excited about the genome browser; have been talking about for years
15:29:13 <michel> http://2012.biohackathon.org
15:29:21 <Zakim> + +1.518.276.aagg
15:29:24 <bobP> Michel: link to wiki has details
15:30:02 <mscottm> SPARQL-enabled Genome Browser - Yes!
15:30:46 <mscottm> http://www.ehr4cr.eu/
15:30:54 <bobP> Michel: Biohackathon contribution from Angiana(?)
15:31:02 <mscottm> http://www.hl7.org/implement/standards/fhir/introduction.htm
15:31:19 <bobP> ... other major issue is adoption for URIs
15:32:01 <bobP> ... all of this has to be consolidated, canonical URIs
15:32:04 <mscottm> identifiers.org
15:32:24 <bobP> ... tried to map to canonical URIs; would like to push this out in HCLS
15:32:31 <mscottm> s/Angiana/Andrea
15:32:35 <bobP> ... to normalize namespaces and URI patterns
15:32:41 <bobP> :)
15:32:46 <mscottm> Andrea Splendiani
15:33:26 <bobP> Michel: Scientific Discouse no longer to continue(?)
15:33:53 <bobP> Scott: I was always interested in having a sparql interface to a discussion forum
15:34:14 <bobP> ... Alzheimer's Forum is an example
15:35:26 <bobP> Joanne and Michel discussing Sci Discourse
15:35:46 <mary> Would you please send the link for different project at HCLS
15:35:57 <bobP> Joanne: Drug label enhancement came out of this
15:36:12 <bobP> ... had served its purpose
15:36:26 <mscottm> mary - does this help? http://www.w3.org/wiki/HCLSIG
15:38:33 <mary> thanks
15:39:09 <bobP> Joanne: Mining treatment outcomes on hold
15:39:45 <bobP> Michel: Would go under clinical decision support when starts again
15:40:13 <bobP> Michel: Systems Biology for Drug Discovery
15:40:48 <bobP> ... working with a variety of biopax data; using G fusion tables
15:41:14 <bobP> ... protein complex evolution, to map out metabolics
15:42:06 <bobP> Scott: wrote an email about this
15:42:42 <bobP> ... can use G refine to clean data; export to RDF etc
15:43:12 <bobP> Michel: Pathways Commons now has sqarql endpoint!
15:43:22 <bobP> ... using Fuzeki(?)
15:43:40 <bobP> ... using identiifiers.org
15:43:48 <bobP> ... identifiers.org
15:44:30 <bobP> ... Xfefs for proteins in interactions; they intend to make this a strong recommendation for data producers
15:45:02 <bobP> ... we can all use identifiers.org URIs
15:45:51 <bobP> ... there is a whole discussion around this; Uniprot would try to go to source first, then go to identifiers.org (have this correct?)
15:46:04 <bobP> ... HCLS: what should data providers do?
15:46:26 <bobP> ... happy to discuss this in a linked life data call
15:46:39 <mary> Did she make federated query from gene to pathway? or from gene to biological process? and does she use biopax?
15:46:40 <bobP> Joanne; Also invite them to call and put in note
15:47:24 <bobP> Michel: Long discussion w Uniprot. They are moving toward significantly less restrictive licensing
15:47:51 <bobP> ... we are in position to provide guidance on how to deal with licenses, when going to LOD
15:48:16 <bobP> ... show people how to do this; Should be on the table for Linked Life Data
15:48:30 <bobP> Joanne: Just came back from Wolfram conference
15:48:54 <bobP> ... some people were not convinced about sharing data; Surprising
15:49:08 <bobP> ... So Linked Life Data has a huge mandate right now
15:49:23 <bobP> ... take over the slot for Discourse?
15:49:55 <bobP> Michel: Scott has to do more multi-tasking? :)
15:50:20 <bobP> Scott: Can still work some of this into the emerging practice note
15:51:02 <bobP> ... some people just don't get why to use a URI that is not from the authoritative issuer
15:51:17 <bobP> ... hard to get over this cultural old fashioned way
15:51:24 <bobP> ... we need to change this.
15:52:02 <bobP> Michel: After Biohackathon, I'm confident that we can do this job
15:52:21 <bobP> Joanne: Q about Emerging practice doc
15:52:43 <bobP> Scott: Clocking down to a few weeks
15:53:17 <bobP> Michel: Matthias couldn't come for PGx task force
15:53:35 <bobP> ... dealing w sources of data of genetic variation
15:53:57 <bobP> ... strategy to dbSNP to RDF to endpoint
15:54:26 <bobP> ... Matthias and I and other have been working on snp-to-haplotype, looks good
15:55:06 <bobP> ... genetic variation for pharmacogenomic sensitivity; all being done in Clinical Decision Support
15:55:33 <bobP> ... safetycode.org can provide decision support
15:56:13 <bobP> ... check back in the archives for Matthias' websites
15:56:39 <bobP> ... Richard Boyce has been working on structured product labels
15:56:54 <mary> for the project was involved in itegration data from NCBI, OMIM,... I did this work in last summer at NIH. who is working in this project? 
15:57:04 <bobP> ... rxNorm, curating evidence and linking to clincial studies
15:57:34 <bobP> ... need to regularize the knowledge representation, to help support personal health lens(?)
15:58:30 <bobP> Mary: HCLS summer school
15:58:45 <michel> http://www.w3.org/wiki/HCLSHackathon2012
15:58:48 <bobP> ... we went through SADI and other tools
15:59:16 <bobP> ... it was very good.
15:59:39 <mscottm> http://swat4ls.blogspot.nl/2012/09/swat4ls-2012-keynotes.html
15:59:51 <bobP> Scott: I have asked ericP to organized swat4ls in Paris
16:00:39 <michel> http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/
16:01:05 <bobP> Michel: We will be hosting in Montreal next year; three conferences back-to-back
16:01:29 <bobP> ... all in first week of July 2013; hoping to organize a hackathon in Montreal
16:02:21 <bobP> Michel: Principle issues, update the wiki to show all the work
16:02:21 <mscottm> I asked Eric if he would help with the SWAT4LS hackathon along with Toshiaki Katayama in Paris in November. Parallel hackathon and tutorial for 2 days (wed, thu) followed by plenary session on friday.
16:03:21 <bobP> Mary: I already integrated OMIM etc at NIH
16:03:43 <bobP> Michel: BioRDF has about 50 datasets being managed
16:04:21 <bobP> ... BIo2RDF release in mid-Sept(?)
16:04:38 <mscottm> +1 on archiving/sharing RDF conversion scripts for reference
16:05:53 <mscottm> http://www.w3.org/blog/hcls/
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16:06:44 <mscottm> Thanks to Bob for scribing!!
16:06:55 <Zakim> - +1.715.389.aabb
16:06:57 <Zakim> - +1.919.681.aaee
16:06:58 <Zakim> - +1.518.276.aagg
16:07:00 <Zakim> - +1.937.775.aaff
16:07:00 <Zakim> -mscottm
16:07:01 <Zakim> -michel
16:07:01 <Zakim> -Bob_Powers
16:07:02 <Zakim> - +1.937.768.aacc
16:07:02 <Zakim> - +46.7.08.13.aadd
16:07:12 <michel>  rrsagent, draft minutes
16:07:12 <RRSAgent> I have made the request to generate http://www.w3.org/2012/09/11-hcls-minutes.html michel
16:07:21 <michel> rrsagent, make log world-visible
16:12:03 <Zakim> disconnecting the lone participant, [GVoice], in SW_HCLS()11:00AM
16:12:04 <Zakim> SW_HCLS()11:00AM has ended
16:12:04 <Zakim> Attendees were [GVoice], mscottm, +1.715.389.aabb, Bob_Powers, +1.937.768.aacc, +46.7.08.13.aadd, +1.919.681.aaee, michel, +1.937.775.aaff, +1.518.276.aagg
17:02:14 <egonw> egonw has joined #HCLS
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17:17:03 <dbooth> zakim, who is here?
17:17:03 <Zakim> apparently SW_HCLS()11:00AM has ended, dbooth
17:17:04 <Zakim> On IRC I see dbooth, egonw, Ashutosh, Sal, achille, RRSAgent, Zakim, MacTed, ericP
17:17:47 <dbooth> s/scribenick: bob powers/scribenick: bobP/
17:17:52 <dbooth> rrsagent, draft minutes
17:17:52 <RRSAgent> I have made the request to generate http://www.w3.org/2012/09/11-hcls-minutes.html dbooth
17:18:18 <dbooth> Scribe: Bob Powers
17:21:25 <dbooth> i/Reports from task forces/Reports from task forces
17:22:00 <dbooth> i/this is mary, for some reason/Introductions, Charting directions for the next year
17:22:06 <dbooth> rrsagent, draft minutes
17:22:06 <RRSAgent> I have made the request to generate http://www.w3.org/2012/09/11-hcls-minutes.html dbooth
17:23:07 <dbooth> s/Introductions, Charting/Topic: Introductions, Charting/
17:24:05 <dbooth> s/<inserted> Reports from task forces/<inserted> Topic: Reports from task forces/
17:24:10 <dbooth> rrsagent, draft minutes
17:24:10 <RRSAgent> I have made the request to generate http://www.w3.org/2012/09/11-hcls-minutes.html dbooth
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