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15:04:13 <mscottm> https://docs.google.com/document/d/1VrBWM133Pxxqe5jbjgg2IPiwv5JaHo98DDJdqOT1yh0/edit
15:04:47 <mscottm> http://www.w3.org/2012/05/07-HCLS-minutes.html
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15:11:46 <mscottm> http://www.w3.org/2012/05/07-HCLS-minutes.html
15:11:51 <mscottm> https://docs.google.com/document/d/1VrBWM133Pxxqe5jbjgg2IPiwv5JaHo98DDJdqOT1yh0/edit
15:14:05 <mscottm> Erich: How about HMDB? - the big metabolite database
15:15:38 <michael> mass spec data: http://www.peptideatlas.org/ (although there isn't much experimental context)
15:16:13 <boycer> Discussion: directions and data sets of interest...
15:16:40 <boycer> Joanne - what is the end product? Would it be interesting to look at patient stratification for personalized medicine?
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15:17:16 <boycer> Scott - rather than specific product - meta requirements for such a product...
15:17:31 <joannne_luciano> What if we created a Minimum Information Standard for a EHR/PHR
15:17:40 <joannne_luciano> (if it doesn't already exist)
15:17:47 <boycer> Scott - example with discussion of EHR - doing an example would lay the groundwork for patient stratification
15:17:48 <egonw_> sorry, cannot join today...
15:18:09 <boycer> Scott: "patient stratification implies an EHR"
15:19:19 <boycer> Michael Miller (Insightful): involved in pre-term birth study...intended to make data public, along with EHR and nextgen sequencing data....
15:19:23 <mscottm> Scott: Lot's of interest in data description for the purposes of federation: Kalpana Krishnaswami (Metaome), Paul Rigor, Richard Boyce, Biohackathon participants, etc. + interest in specific datasets (see above). 
15:19:54 <boycer> Biomarkers can pop out without the use of EHR
15:20:41 <joannne_luciano> it's from last year, but this paper is coming to mind...  http://www.selventa.com/attachments/publications/early-patient-stratification-is-critical-to-enable-effective-and-personalised-drug-discovery-and-development.pdf
15:21:06 <mscottm> Richard: looking at data such as microarray for biomarkers (without EHR) looks like where it's at, but you can only get so far with it.
15:21:20 <mscottm> Richard: Quality and provenance are very important
15:23:03 <boycer> Scott: how to combine these things...if some of the named datasets are going to be used by members of the task force, then we should take that dataset along ....
15:23:35 <boycer> Scott: gives us a better chance of engaging stakeholders needs...
15:24:29 <boycer> Scott: a problem relevant to clinic and Pharmgx -- how can you assemble the various models (refs to ontologies) in a patient record so as to cover the fundamental needs of a clinic (i.e., genetic clinic)
15:25:28 <boycer> Scott: geneology file might be linked to hospital system - how to declare privacy requirements
15:26:27 <boycer> Scott: if talking about mutations, biomarkers, SNPS, etc...and have an unambiguous way to refer to them, 
15:27:09 <mscottm> my line was dropped - calling in again
15:27:10 <boycer> Scott: if you can integrate into HL7 what you would have, is a system that could be integrated into hospital system 
15:28:55 <boycer> Scott: Eric and Michael's work on HL7 might be relevant for providing traction w/ hospitals
15:31:15 <boycer> Scott: what allot of clinical departments are missing, a way to carry information on genetic markers, geneology, w/ clinical data from one machine to another
15:32:11 <boycer> Scott: clinical genetics - currently cannot look through patient or family history in an sharable, reusable, cross-platform way
15:32:23 <boycer> Scott: silos of clinical genetics data
15:32:56 <boycer> Scott: If I can get XML of that data, transform to RDF, now have a substrate for an exchange language for future platforms.
15:37:20 <mscottm> Richard: I know that personalized medicine requires information from several spaces, including molecular data, drugs, and other BioRDF areas of work.
15:37:50 <mscottm> Richard: Isn't TCGA centered on sequencing the tumors? and the clinical data is in their clinic
15:38:35 <mscottm> Michael: Yes - I'm looking at some right now. :)
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15:40:19 <joannne_luciano> is there a link for that dataset?
15:40:39 <mscottm> Michael: Yes, the personal "people" data is all private but there's sequence data, mRNA, and many types of related data that aren't protected.
15:42:07 <mscottm> Richard: The LODD cloud represents a network of chemical identity.
15:42:41 <mscottm> ..you can map the identities to the strings that are used to represent a drug. 
15:43:33 <mscottm> ..Then quality of the network of chemical identity and its provenance become important.
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15:44:50 <boycer> Michel: the network of chemical identity is of interest 
15:45:00 <mscottm> G+ post about chem identity (from Egon): https://plus.google.com/u/0/103703750118158205464/posts/Ld2cwfJM8Kd
15:45:14 <boycer> Michel: to his lab -- did some work in TMO 
15:45:32 <boycer> Michel: incorrect reference to semantic types a major problem
15:45:55 <boycer> Michel: example, gene product vs gene identifier
15:46:08 <boycer> Michel: source data contains semantic nonsense
15:46:27 <boycer> Michel: does this get propogated from the source to the linked data 
15:46:51 <boycer> Michel: what responsibility does the linked data group have in identifying the limitations of the source?
15:47:09 <boycer> Michel: initial work with TMO 
15:47:50 <mscottm> I'm still here (that was pc2)
15:52:21 <boycer> Rich: what work can this group do to contribute to improving quality of data?
15:52:43 <boycer> Rich: what elements are source issues, linked data developer issues, and user issues?
15:52:51 <mscottm> Richard: Talked about the difficulty of provenance for drug interaction - different sources of selection, DrugBank 1 vs. 2 vs. 3
15:53:09 <boycer> Michel: we need to clarify the relationship of linked data curators and the source data sets
15:53:34 <boycer> Michel: where does the responsibility lie when there are known problems with the source data
15:55:19 <boycer> Michel: provenance of relevance to linked data: where did the data come from, how did you get from the source to the linked data resource
15:55:42 <boycer> Rich: also, how to share what has been done by the linked data curator -- community developed 
15:55:43 <mscottm> Michel: In Bio2RDF, we created a github repository for the scripts 
15:55:48 <egombocz> excellent meeting today! - apologies, but I need to sign out due to another upcoming meeting
15:55:59 <mscottm> tx Erich!
15:56:21 <boycer> Michel: part of our mandate - make it possibly to branch linked data sets
15:56:27 <joannne_luciano> i recommend looking at the conversion tools developed at RPI -- csv2rdf4lod for example
15:56:40 <joannne_luciano> also datafaqs that i mentioned earlier
15:57:28 <boycer> Scott: also a need in the clinic - how to relate DICOM represented scan to metadata 
15:57:39 <joannne_luciano> and the recent work coming out of the provenance working group 
15:57:45 <michel> in our experience, it is never the case that you simply take data and naively convert it in order to generate high quality (e.g. well represented) data
15:58:22 <michel> it takes substantial parsing to generate structured data
15:58:39 <joannne_luciano> agree michel - that's not what is being suggested/proposed.  it;s to convert and add the appropriate metadata to make quality linked data, not junk rdf
15:59:15 <boycer> Scott:  Daniel Rubin working on links between EHR, DICOM, and genomic data 
15:59:56 <boycer> Scott: basic work - standard way of representing metadata in a DICOM file....proprietary issues
16:01:29 <boycer> Michael: the framework for running an analysis would be desired
16:01:36 <boycer> (what kind of analysis?)
16:02:14 <boycer> Michael: making use of linked data that is available during analysis, how do you represent the analysis for a particular expression data?
16:03:29 <boycer> e.g, what does it mean to tak RDF , run an analysis, and incorporate the end results....
16:03:49 <boycer> Michael: can you do that within the context of RDF
16:03:58 <boycer> (need to go in  1 minute)
16:04:10 <michel> HyQue does just this: http://www.slideshare.net/micheldumontier/hyque-evaluating-scientific-hypotheses-using-semantic-web-technologies
16:05:33 <boycer> See slide 29
16:05:33 <mscottm> Michel: on slide 29, you can see how results are linked together with the source
16:06:30 <mscottm> Michel: SADI implements the policies of making use of RDF to produce RDF
16:07:08 <mscottm> Thanks to everyone for the valuable input!
16:07:34 <mscottm> RRSAgent, please draft minutes
16:07:34 <RRSAgent> I have made the request to generate http://www.w3.org/2012/05/14-HCLS-minutes.html mscottm
16:07:51 <mscottm> RRSAgent, please make minutes world visible
16:07:51 <RRSAgent> I'm logging. I don't understand 'please make minutes world visible', mscottm.  Try /msg RRSAgent help
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