W3C HCLS – Pharmacogenomics

17 May 2012

See also: IRC log




<HarryH> +1.412.623.aabb would be me - Harry Hochheiser, University of Pittsburgh

<michel> Erich - building a big kb, selecting certain datasets - interested in pharmgkb, etc

<michel> Harry - biomedical informatics - interested in how to present clinically useful information

Kalpana: We (Metaome) have a product http://www.distilbio.com/ , gave a webinar for M. Scott Marshall to BioRDF/LODD a month or so ago. We are interested in providing some features interesting in the clinical setting, for clinical decision support, etc.

<michel> matthias: PGx in clinical setting - medical doctors & patients with IP tools to make sense of it

Kalpana is an Invited Expert to HCLS.

<michel> mscottm: applying PGx in the clinical setting; CDS and generic information retrieval; link in gene variants into pathology, radiology, etc

<michel> ericP: W3C staff contact for HCLS; initially on life sciences now more on health care

Michel: interested in PGx in the clinical setting, also from Bio2RDF perspective, furthering pharmacogenomics for drug development

<michel> pharmgkb: http://www.pharmgkb.org/downloads.jsp

I should mention that Joanne sent her regrets (conflict with meeting).

Michel: Some RDFization was done by Joanne Luciano and Jim McCusker, and I did some RDFization focused on (OWL) modeling.
... A couple datasets of interest: 1) side effects not on the label (off-label side effects)
... 2) Drug-drug interactions
... We are especially interested in side effects that can be related to a genetic variation

<michel> github for bio2rdf scripts: https://github.com/bio2rdf/bio2rdf-scripts

<michel> pharmgkb: https://github.com/bio2rdf/bio2rdf-scripts/blob/master/pharmgkb/pharmgkb.php

variants and clinical annotations - need license to access, can't redistribute.

<michel> pharmgkb sparql endpoint: http://bio2rdf.semanticscience.org:8006/sparql/

<michel> pharmgkb sparql endpoint : http://bio2rdf.semanticscience.org:8006/fct/


<egombocz> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=text&sid=35

<michel> warfarin as text search with drug-drug-interaction type : http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=set_class&iri=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Adrug-drug-interaction&lang=&datatype=uri&sid=28

Michel: <demo> Start with http://bio2rdf.semanticscience.org:8006/fct/ , enter warfarin
... Go to bottom of page, click on Type
... Click on drug-drug-interaction (top of list)

<michel> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=set_view&sid=41&type=list-count&limit=20&offset=0

Michel: Go to bottom of page, right side: click on Referencing Attributes
... Click on event in attribute list

<egombocz> http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fumls%3AC0013404&sid=41

<michel> http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?cmd=open_property&iri=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Achemical&lang=&datatype=uri&sid=41

<michel> facet permalink: http://bio2rdf.semanticscience.org:8006/fct/facet.vsp?qxml=%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%20%3F%3E%3Cquery%20inference%3D%22%22%20same-as%3D%22%22%20view3%3D%22%22%20s-term%3D%22%22%20c-term%3D%22%22%3E%3Ctext%3Ewarfarin%3C%2Ftext%3E%3Cclass%20iri%3D%22http%3A%2F%2Fbio2rdf.org%2Fpharmgkb_vocabulary%3Adrug-drug-intera

Select "choking sensation".

<michel> warfarin - variant drug annotation - http://goo.gl/66M2g

Michel notes that he needs to load labels for PubChem Ids so that we don't see id numbers for the list of Entities

<matthias_samwald> Could we have a link again?

<michel> warfarin-linked clinical phenotype annotation - http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3A769146159&sid=50

<matthias_samwald> yes

<michel> warfarin entry: http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3APA451906&sid=50

<michel> warfarin-linked clinical annotation :http://bio2rdf.semanticscience.org:8006/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fpharmgkb%3A655384758&sid=50

<michel> http://goo.gl/tTORx

<matthias_samwald> need to leave -- bye!

Michel proposes to write a script to select clinically relevant validated SNPs and query the NCBI service and convert a selection of the XML records for inclusion in the KB

<michel> i'll convert only some fields - we can talk about exactly which ones when we get there

<HarryH> Thanks! This is fascinating.

<michel> sparql javascript - http://www.thefigtrees.net/lee/sw/sparql.js

<michel> http://www.thefigtrees.net/lee/blog/2006/04/sparql_calendar_demo_a_sparql.html

Michel mentioned screen sharing with a Google Hangout earlier in the call. Something to think about for next demo.

Michel: PharmGKB has restructured their web pages to present clinically relevant information *first*.

<scribe> scribenick: mscottm

Summary of Action Items

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Possibly Present: CCXML CLOUD Daniel Daniel_Rubin DecisionXG Eval HarryH INC_ MacTed Math_IG MelliA Michel P28 P38 SW_HCLS SW_RDFa SYMM_TTWG S_GLDWG Styl_XSL-FO- TF TMO Team_ Team_Comm UW_WebTVIG VB_VBWG WAI_ERTWG WF_TF XML_PMWG XML_QueryWG XSLT aaaa aabb aadd achille_z active egombocz egonw ericP harryhochheiser kalpana matthias matthias_samwald mscottm onix pharmgkb scribenick
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        <dbooth> Present+ amy

Got date from IRC log name: 17 May 2012
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