HCLSIG/PharmaOntology/Meetings/2011-05-12 Conference Call/Minutes

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Minutes for the HCLS Translational Medicine conference call for May 12, 2011

Michel:

... HCLS summary; to promote and develop the use of semweb

... HCLS charter, new one is developing

... Translational Medicine: link info, close the gap between treatment, clinical research, etc

... also identify gaps in knowledge

... paper: how to represent pgx; symptoms, signs, treatments, genetic and physiol backgrounds

... ultimately toward a predictive context

... Three new people will join us

... Dr. Fred Whipple

Fred: Specialist in SNP-based diagnostics, prognostics; breast cancer etc

... director of Genomics Initiative to educate clincians

... education gets them to understand SNPs, risk association, risk tools

... PhD Tufts; Harvard Med; Cal State; then business!

Joanne: Joanne and Fred go way back.

... to Wang Labs, in the 1970s

Michel : Dr. Robert Freimuth ... BIO: My doctoral work was in the field of pharmacogenomics (wet lab work). I have since migrated through the fields of bioinformatics and medical informatics. I have been very active in the National Cancer Institute's Cancer Biomedical Informatics Grid program, where I lead the Information Representation Working Group and its development of the Life Sciences Domain Analysis Model (LS DAM). I am also the Director of the Vocabulary Knowledge Center (VKC), which provides education and support for the NCI semantic infrastructure. Finally, I am co-lead of the Ontology Network Resource (PHONT) for the Pharmacogenomics Research Network (PGRN).

BobF : Junior investigator, working thru bioinf at Mayo

... NCI caBIG program; have worked on data standards; leading inf-representation WB

... Second project is PGx research network; recently funded to bring standardization

... interested in progress in this group

Michel: Coincides well with our work; timely

BobF: Have known pharmGKB group; have established collab w them


... help them to incorporate mappings; rolling towards semweb, expose in RDF

... application point for this work

... aware of HCLS; convergences with my projects; number of people have such experience

Iker: Support personalized med by using sem tech

... aim to relate patient data w available info;

... demo http://85.48.202.13:8080/oncologico.jsp

... http://www.oncologico.org/02oncologico.htm

Michel: is there predictive work also?

Iker: Prototype does not predict; will be working on pgx; we are close to the market

Michel: What about the demo that uses the TMKB

Joanne: TMO / TMKB Journal of Biomedical Semantics Link: http://www.jbiomedsem.com/content/2/S2/S1/abstract Publ Date May 17, 2011 (ready on line and in PDF)

iker: http://85.48.202.13:8080/AD/index.html

... Alzheimer knowledge sharing platform

... "How many patients experienced side effects while taking Donepezil?"

... http://85.48.202.13:8080/AD/physicians.jsp

Joanne: Queries look different when they're live!

Iker: Goal is to enroll as many patients as possible

... aim to develop a platform like this one for breast cancer

Michel: take a look at http://www.patientslikeme.com/

... want to define a gathering point for patients, physicians and researchers

Joanne: Patient's names anonymized?

... Here's the link to the SMART Health App Challenge: http://www.smartplatforms.org/challenge/

Iker: Yes

Michel: Paper https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#

... Figure https://docs.google.com/drawings/d/1OaqlmiTbIAkgHM6kCV-4xbRddHJiN1YZkCWdNHvwiGI/edit?hl=en&authkey=CIT4rcwM

... represent pgx for warfarin

... need to define patient-centered use cases

... warfarin-sensitive, -insensitive

... tabular form for dosing decision

... convert the table to RDF; then query

epichler: who has access to the papers that describe the prediction algorithms and could share those with me? - thanks

Bob: Paper from Chest: http://www.ncbi.nlm.nih.gov/pubmed/18574265

matthias: the paper compares the efficacy of a simple table that makes dosage recommendations for specific combinations of alleles with a more sophisticated algorithm.

matthias: we need to (at least) be able to represent combinations of alleles.

BobF discussing how a *1 allele defintion can change

BobF haplotypes p.164 S H1, H2 vs H7, H8, H9

BobF: Allele nomenclature can become out of date, one must map thru time

BobF: This is like a superclass

... but *not* a nice clean hierarchy

... subclass can be from multiple superclasses.

Joanne: Can we get an example to chew on off-line?

Scott: This is an important modelling issue: nesting of SNPs and dependence between them

Michel: We need to focus on paper; add comment w goog doc