<mscottm> I am muted

<mscottm> Zakim was behind..

<mscottm> latency

scott: idea is to get dbsnp into linked data form for proof of concept and to validate models
... iker has run into problems because of the large size of data (250GB disk)
... took a subset - 30M SNPs - what are the criteria?
... genes related to warfarin; dbSNP queries in SQL to retrieve snp information related to those genes
... waiting on ericP/other to setup SWObjects
... need to choose RDF rendering to translate SQL
... let's look at the scenarios
... spoke with Bob and Joanne, to brainstorm about article and how to spin it
... title change to "On the application of pharmacogenomic knowledge in the personalized medicine setting"
... personalized medicne, snps, linked data
... pseudo patients with snp data using the scenarios we create
... use tmo + linked data, but not much detail - refer to prior publications
... information needs of a clinical patient pipeline
... applying biomarkers in a clinical setting

Joanne: try to target this paper to Future Medicne's pharmacogenomics journal http://www.futuremedicine.com/loi/pgs

aims and scope: Pharmacogenomics (ISSN 1462-2416) is a peer-reviewed journal presenting reviews and reports by the researchers and decision-makers closely involved in this rapidly developing area. Key objectives are to provide the community with an essential resource for keeping abreast of the latest developments in all areas of this exciting field. Pharmacog

Pharmacogenomics focuses on those aspects that have the most direct relevance to the pharmaceutical industry and wider clinical community, including:

The emergence of new pharmacogenomic initiatives and their impact on R&D and regulatory strategies

Emerging technologies for accessing and exploiting genomic information

Reviews of genotyping and clinical data in particular therapeutic areas

Development of novel diagnostic products and strategies

matthias: don't think we need to convince this audience of the benefit of pharmacogenomics

scott: integrated pipeline; exists?

fred: physicians receive incentive to make use of EHR

<epichler> michel: paper needs to address how SW technologies facilitates access to pharmacogenomics data, how to make this part of future approach

scott: difference between stated aims of hospitals and those in practice
... good for us to show that it's not as hard as it seems
... bottom up is good

matthias_samwald: focus on potential, capabilities - but should also talk about technical aspects, but not too much detail

michel: think our sell is with semantic web

scott: the use cases are important

matthias_samwald: use cases are quite detailed - we need to focus on some aspects

<Joanne> to michel, say more re: sell w/ sem web. I think i agree (Scott, Bob and I discussed this at length).

<Joanne> Note: I'm stepping away for a moment to get some food (just out my door). brb

matthias_samwald: what can we do with our knowledge model to sensibly represent data
... leave use cases for the moment and focus on the development

michel: so let's discuss the ontology - material entity vs informational entity

matthias_samwald: IAO - gives 'about' property to link 'information content entities' with physical objects;
... genotypes; alleles; part hood is fine, but use owl individuals instead of classes

michel: for material entities - the idea is that when we make a measurement on some sample, we are making a measurement of a collection of material objects (dna and their parts)

fred: bridge the gap with the audience and also explain what you are doing

joanne: make sure what you do is most relevant

fred: use of genomics in the clinic is developing and there is a lot of confusion; if you want to write a paper for physicians; not everything has been verified or is clinically valid; what data has reached clinical significance and is clinically useable

scott: if you look at genes related to warfarin in the LOD cloud; dbsnp is too far from this use case

fred: a large percentage of the conclusions in the literature is wrong or insufficient supported
... clinicians will operate on the clinical guidelines

matthias_samwald: need competency questions

<mscottm> want to suggest having two extra telcons in the next week 1/2 hour long

matthias_samwald: when creating the knowledge model, i pondered how to query alleles from snp data. etc

<ericP> weak, i forgot this meeting

<ericP> anything i should try to join for?

<mscottm> I'll fill you in - in a minute.

<ericP> ok

<mscottm> shall we talk?

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