<Fred> I'm hearing MIchel

<michel> 6132938657

scribenick BobP

Hi Fred!

<Fred> Hi Bob

Michel: Changes to agenda?

Scott: Looking across data, are we going to try to move SNPs into model?

Michel: Iker has some data too

<michel> http://phenomebrowser.net/

<michel> robert hoehndorf

<mscottm> Robert Hoehndorf - Phenomebrowser rat, mouse, human, yeast, few others, links genotypes to phenotypes

Fred(?): Try thrombolism

<Fred> thromboembolism

<michel> http://phenomebrowser.net/explore.php?val=OMIM_188050

Fred: I am consultant in clinical applications of genomics
... have Genomics Education Initiative
... Joanne asked me join in

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

<iker> my regrets but i must leave

Michel: Focus of paper is how to represent

Bosse: Generalizing from warfarin is a good example

Scott: Add in reference to warfarin's being problematical

Elgar: Predictive pgx, still working on
... have gone through Michel's papers
... papers on methods and algorithms
... can summarize at the bottom of google doc

Joanne: Conversion, talked to Tim
... Linked open biodata, have done one provenance enhancement parameter
... we did the warfarin data, have detailed notes about the conversion
... running through converted takes no time; but adding parameters and value add - using our brains

Scott: Part of problem is which vocabularies, which terms

Joanne: Manual process to create the right mapping

Michel: Using BioPortal?

Scott: Yes, this is the hard part about converting to RDF
... once chosen vocab, then which terms to use. Lots of variability

Michel: For TMO we had a spreadsheet of all terms to start
... then looked up terms in BioPortal to find the meanings that we wanted

<mscottm> Phenex Onto Pheno Diversity http://precedings.nature.com/documents/4068/version/1/files/npre20094068-1.pdf

Michel: we might have to do this for our work now
... Should we use TMO? on mailing list
... maybe entries in table move to spreadsheet

Elgar: -1 to spreadsheet

<mscottm> Another belated link related to the phenome browser: https://www.phenoscape.org/wiki/Main_Page

Michel: Pull terms into ontology, then create mapping
... Seq Ont, but do not want to import the whole thing
... we can create 'like' versions of terms

Scott: Trish told us about a way to refer to a term, w. some functionality in ?

Michel: Protege server, can query BioPortal

Scott: Option is BioPortal Reference plugin for protege
... slightly different from LODD and Term, use of proxy ontology or reference ontology
... like a spreadsheet, but put terms directly into ontology
... seeAlso for terms in other ontologies

Michel: We can play around w. web protege to help us make decision

Matthias: If we are using TMO, how should we go about it?
... add TMO directly in?

Michel: Yes

Scott: +1

Michel: Iker's Virtuoso is loaded
... are there other RDF datasets for KB?

Scott: Take all warfarin SNPs; start w. dbSNP, authoritative, stable approach
... name checker seems to be able to handle SNP nomenclature
... id warfarin SNPs, make URI or map
... future work: look for SNPs that would effect warfarin pathways
... there aren't that many warfarin SNPs

Bob: +1 here

<Joanne> regrests - have to go -- the CSHALS org call is now and I need to go.

<matthias_samwald> (i need to leave now as well, bye!)

<mscottm> http://www.snpedia.com/index.php/Warfarin

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