19 Jul 2012

See also: IRC log


Erich, michel, +1.412.624.aaaa, matthias_samwald, +1.215.239.aabb, Tony


Michel: About revision of OMIM in RDF via Bio2RDF
... occasional revision is necessary due to changes
... so Michel picked OMIM for a revision because it seemed pretty out of date

<michel> omim entry - http://www.omim.org/entry/608547

Michel: plan to talk to Johns Hopkins University School of Medicine to offer RDF dump for their web page.

Scott: Possibly offer SPARQL endpoint that they could link to..?

Michel: Yes, this is a general question for data sources. Area of exploration.

<michel> omim api - http://www.omim.org/api

<michel> http://omim.org/help/api#1.4

Michel: API is *much* better and more complete than the data dump!
..Example: allelicVariantList isn't available in the downloadable data dump but is available via API (see Entry section of help URL above).
... update is in process, downloading now.

Scott: General question about SPARQL to SQL vs. SPARQL to set of APIs

Michel: Bio2RDF started out with an approach of dynamically calling e-Utils and converting on the fly.
... Since then, we've started downloading data wholesale and converting it to RDF.

Scott: Ever consider a procedural attachment to SPARQL query (ala SADI) and converting the results?

Michel: Yes, we've done things like that in SADI/SHARE but you can take a performance hit.

Scott: Where specifically do you take the performance hit?

Michel: If you have a large scan of 10,000 rows, it could translate to 10,000 API calls.
... For example, OMIM can translate into 10 entries per request.
... If there are no questions, we'll move on to Richard's work.


<michel> rich discussing FDA PGx biomarkers

<boycer> http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/FDA-pharmacogenetic-info-mapping/

Richard: http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/FDA-pharmacogenetic-info-mapping/FDAPharmgxTable.csv is the manually edited version of the table extracted from the link that Scott posted above.
... fda-active-moiety-string-name-rxnorm-mapping.csv was made using the NCBO Annotator

<boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/directory/FDAPharmgxTable

<boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/page/FDAPharmgxTable/1

<boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/resource/structuredProductLabelMetadata/9b32f5a4-d0f7-486b-b699-8dc9202b6869

<boycer> Regardless of HLA-B*5701 status, permanently discontinue TRIZIVIR if hypersensitivity cannot be ruled out. (5.1) Following a hypersensitivity reaction to abacavir,

Scott: What kind of server? (it's a little slow, a few seconds to respond)

Richard: Using D2R server. Have resorted to dumping RDF and loading into Virtuoso for speed (see e-mail for link to Virtuoso server).

<boycer> http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/

<boycer> Known Issues (July 2012)

<michel> topic - pharmgkb genotype phenotype association

<michel> https://docs.google.com/spreadsheet/ccc?key=0Aoy0zfdRviKsdGFJR0ZwQWs4TE9ZUVhuSGpFSWFOQXc

<michel> will be working to i) do mappings and ii) normalize phenotypes

<bobf> apologies - I need to drop off

<boycer> http://www.cdc.gov/genomics/gtesting/EGAPP/recommend/

<michel> https://github.com/alisoncallahan/bio2rdf-lucene-searcher

<michel> http://sindicetech.com/

<michel> Chair: michel

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.136 (CVS log)
$Date: 2012/07/19 16:15:53 $

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Default Present: Erich, michel, +1.412.624.aaaa, matthias_samwald, +1.215.239.aabb, Tony
Present: Erich michel +1.412.624.aaaa matthias_samwald +1.215.239.aabb Tony

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Got date from IRC log name: 19 Jul 2012
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People with action items: 

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<dbooth> Topic: Review of Amy's report

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