15:55:25 <RRSAgent> RRSAgent has joined #HCLS
15:55:25 <RRSAgent> logging to http://www.w3.org/2012/01/10-HCLS-irc
15:55:32 <michel> rrsagent, make logs public
15:55:57 <michel> Chair: michel
15:56:09 <michel> zakim, this is hcls
15:56:09 <Zakim> michel, I see SW_HCLS(COI)11:00AM in the schedule but not yet started.  Perhaps you mean "this will be hcls".
15:56:19 <michel> zakim, this will be hcls
15:56:19 <Zakim> ok, michel; I see SW_HCLS(COI)11:00AM scheduled to start in 4 minutes
15:56:23 <ericP> michel, i'll be there as soon as i get off the SPARQL call
15:56:37 <ericP> i think you can call in to start it
15:56:59 <ericP> (even before its scheduled start)
15:57:02 <michel> k
15:57:45 <Zakim> SW_HCLS(COI)11:00AM has now started
15:57:51 <Zakim> +??P31
15:57:57 <michel> zakim, ??P31 is michel
15:57:57 <Zakim> +michel; got it
15:58:40 <matthias_samwald> matthias_samwald has joined #hcls
16:00:49 <Zakim> +ericp
16:01:12 <Zakim> + +1.510.541.aaaa
16:02:08 <ericP> matthias_samwald, calling in?
16:03:02 <Zakim> +??P2
16:03:10 <ericP> Zakim, ??P2 is matthias_samwald 
16:03:40 <Zakim> +matthias_samwald; got it
16:06:09 <matthias_samwald> zakim, who is here?
16:06:09 <Zakim> On the phone I see michel, ericp, +1.510.541.aaaa, matthias_samwald
16:06:10 <Zakim> On IRC I see matthias_samwald, RRSAgent, Zakim, michel, MacTed, ericP
16:07:23 <mscottm2> mscottm2 has joined #hcls
16:08:20 <Zakim> + +31.62.427.aabb
16:08:55 <michel> zakim, +31.62.427.aabb is mscottm2
16:08:55 <Zakim> +mscottm2; got it
16:09:39 <mscottm2> Zakim, who is here?
16:09:39 <Zakim> On the phone I see michel, ericp, +1.510.541.aaaa, matthias_samwald, mscottm2
16:09:41 <Zakim> On IRC I see mscottm2, matthias_samwald, RRSAgent, Zakim, michel, MacTed, ericP
16:12:17 <michel> f2f meeting - potential   amia - end of march; ismb mid-july ; 
16:12:40 <michel>  ... joanne, michel, matthias can make it to amia
16:13:29 <michel>  ... cshals feb 22-24
16:16:12 <michel> mscottm2 - biordf - paper got accepted; w3c note in development; 
16:17:56 <michel>  ... interest in future work - helena & michael miller - new dataset - (add more details here)
16:18:34 <Zakim> - +1.510.541.aaaa
16:19:16 <michel>  ... how to produce and use expression array data; not quite there yet, have we fulfilled the requirements?
16:19:27 <Zakim> + +1.510.541.aacc
16:21:45 <Zakim> - +1.510.541.aacc
16:21:46 <michel> ericP Joanne and Jim were looking at LS-DAM
16:22:34 <matthias_samwald> zakim, who is here?
16:22:34 <Zakim> On the phone I see michel, ericp, matthias_samwald, mscottm2
16:22:35 <Zakim> On IRC I see mscottm2, matthias_samwald, RRSAgent, Zakim, michel, MacTed, ericP
16:24:28 <michel> matthias - were talking about linking ls-dam to tmo
16:24:59 <Zakim> + +1.510.541.aadd
16:25:09 <ericP> -> http://ncientarch.info/sandbox/LSDAM2_2_1/ LSDAM link
16:25:32 <michel> zakim, +1.510.541.aadd is charlie
16:25:32 <Zakim> +charlie; got it
16:26:15 <michel> charlie: bridg started as a UML model, and has now moved to a OWL representation
16:26:29 <michel>  ... board of directors recognize the importance of OWL 
16:27:11 <michel>  ... LS-DAM started 4 years ago, learn from bridge experience, started to work with content using OWL semantics, then reverse engineer to other formalisms
16:27:29 <michel>  ... reuse content from other ontologies
16:28:06 <michel>  ... valuable and viable content in BRIDG, LS-DAM; firm commitment to move to OWL; interop with other ontologies
16:28:41 <michel> ericP: 1. data?  2. should we adopt these models?
16:29:06 <michel> charlie 1. lots of BRIDG data; LS-DAM data. 
16:29:14 <michel>  ... including microarray data
16:29:46 <Zakim> -charlie
16:30:02 <mscottm2> charlie - we lost you again!
16:30:33 <mscottm2> just as you were discussing Jim's work with LSDAM
16:32:40 <Zakim> +charlie
16:34:42 <michel> charlie: Jim wrote software to semantically annotate data with LSDAM; 
16:34:54 <michel> ericp: the SKOS stuff (?details)
16:35:29 <mscottm2> [belated details that Michel requested above when I was talking about some of the ideas for projects discussed in BioRDF]
16:35:40 <mscottm2> from e-mail with Michael Miller: "* translating TCGA data into RDF (the kicker being the sample
16:35:40 <mscottm2> characteristics are in a different set of files than the MAGE-TAB)
16:37:11 <michel> charlie: LSDAM is pretty much from internal NCI ; BRIDG external oriented
16:37:54 <michel> scott: LODD article accepted by journal of web semantics; W3C note analog
16:38:39 <michel>  ... enthusiasm for creating RDF datasets
16:40:00 <michel>  ... SAGE bionetworks has interesting data, and similar values to HCLS. semantic access to data
16:40:26 <michel> ericP: sage folks are mining literature and homogenizing ways to get articles and supporting data; have they modeled the knowledge?
16:40:53 <michel> scott: not sure... perhaps not further than anybody else
16:41:42 <michel>  ... but they have valuable datasets from participants/clients including snp and patient data. SAGE APIs available. If we could expose that as RDF / SPARQL, could integrate with other datasets
16:43:18 <michel> terminology; annotation of image data ; from xml to owl; student from daniel rubin. john madden started looking at that data. how to inject pathology terminology to the image annotation. radiologist + pathologist findings together
16:43:47 <ericP> scribenick: ericP
16:44:09 <michel> michel: oral presentation to AMIA summit for translational bioinformatics
16:44:15 <michel>  ... future medicine review accepted
16:44:38 <ericP> michel: pub date for the future medicine review?
16:44:42 <ericP> mscottm2: 12 Jan
16:45:20 <ericP> michel: please send me a copy of the final manuscript and i'll write an HCLS blog article
16:45:26 <ericP> mscottm2: you already have it
16:45:51 <ericP> michel: working on an ICBO (int conference on Bio ontologies)
16:46:04 <ericP> ... matthias_samwald is in charge of article
16:46:18 <ericP> ... extending with pharma terms 
16:46:43 <ericP> matthias_samwald: extending the OWL TMO ontology to capture pharmacogenomic categorizations
16:47:13 <ericP> ... using OWL reasoning on matching patient classes to provide automated decision support
16:47:36 <ericP> ... the paper will experiment with two or three OWL representation to see which is most practical
16:47:54 <ericP> ... i started drafting the ontology in an ontology editor
16:48:01 <ericP> ... paper due at end of month
16:48:03 <michel> matthias:  use owl reasoning to match individual patients to molecularly defined subgroups for clinical decision support
16:48:49 <ericP> ... also have a prototype of a larger paper including transforming pharmacogenomic data into RDF, using SPARQL, OWL for reasoning, etc.
16:48:57 <ericP> ... expect to be done in ~ 3 months
16:49:17 <ericP> michel: we should formalize our relationships with BRIDG and LS/DAM
16:49:53 <ericP> topic: use cases
16:50:23 <ericP> michel: need to finalize "enhancing drug product labels" use case
16:50:44 <ericP> ACTION: michel to contact promoters of enhancing drug product labels use case
16:51:18 <ericP> michel: matthias_samwald is pushing on the clinical decision support use case
16:51:26 <matthias_samwald> http://www.w3.org/wiki/HCLSIG/CDS
16:51:27 <ericP> ... i see five sub-use cases
16:52:13 <ericP> matthias_samwald: within TMO, we're taking on the 1st use case: extending TMO to cover pharmacogenomics for personalized and stratified medicine
16:52:27 <ericP> ... also working on the 2nd (using OWL)
16:52:47 <ericP> michel: lots of work to be done on the business case for the OWL sub-use case
16:52:53 <ericP> ... we need some external partners
16:53:04 <ericP> ... you clearly have interest from the medical center
16:53:22 <ericP> ... can we get support from cleveland clinic and other folks working with OWL?
16:54:04 <ericP> matthias_samwald: Russ Altman interested in OWL representation for pharmacogenomics (from pharmaco DB perspective)
16:54:31 <ericP> ACTION: matthias_samwald to invite Russ Altman (SP?) to participate in TMO
16:54:44 <ericP> michel: i'll be in Stanford in Feb
16:55:06 <ericP> ... we should pre-empt my arrival with a discussion with him
16:55:20 <ericP> matthias_samwald: should hash out on the mailing list
16:56:33 <ericP> ... with michel's progress on pharmgk kb, we can have useful material soon
16:56:39 <ericP> ... re: other use cases:
16:56:53 <ericP> ... .. medical SPARQL -- using SPARQL to answer medical questions
16:57:36 <matthias_samwald> OpenCDS
16:57:39 <ericP> ... .. allignment between [TMO] ontologies and HL7's Open CDS 
16:58:20 <ericP> ... this would be the natural next step in bringing our CDS work forward and aligning with other orgs
16:58:45 <matthias_samwald> http://opencds.org/
17:00:51 <mscottm2> http://researchremix.wordpress.com/2012/01/07/rwa-data/
17:00:59 <ericP> mscottm2: any familiar with Research Works Act?
17:07:22 <Zakim> -michel
17:07:23 <Zakim> -mscottm2
17:07:24 <Zakim> -matthias_samwald
17:07:25 <Zakim> -charlie
17:07:33 <michel> rrsagent, draft minutes
17:07:33 <RRSAgent> I have made the request to generate http://www.w3.org/2012/01/10-HCLS-minutes.html michel
17:07:40 <michel> rrsagent, make log world-visible
17:09:08 <Zakim> -ericp
17:09:09 <Zakim> SW_HCLS(COI)11:00AM has ended
17:09:11 <Zakim> Attendees were michel, ericp, +1.510.541.aaaa, matthias_samwald, mscottm2, +1.510.541.aacc, charlie
18:34:51 <Zakim> Zakim has left #HCLS