lena: initial aim was to query various sbml models together
... a few sbml models are modeling the same thing
... map kinase pathway as a use case
... biopax representation available
... loaded into workbench
... query to capture all the reactants, products
... when products are reactants, we should see a network
... tried to match on labels, but incomplete
... no URIs specified, difficult to parse

<Lena> https://www.google.com/fusiontables/DataSource?snapid=S595021IJTA

above -> graph of interconnected molecules

scribe: problem largely lies in the complexes

mike: are there no references in the SBML files?

let's look at the biomodel file

<Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000019

<Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000033

<Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000399

<Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000151

<Lena> michel loaded pathwaycommons into an endpoint

<Lena> good way for do disambiguation

pathwaycommons endpoint - http://bio2rdf.semanticscience.org:8010/fct/

<Lena> wikipathways used bridgedb for solving the identifiers problem

<Lena> openphans - query expander

<andrawaag> http://www.wikipathways.org/index.php/Pathway:WP17

<andrawaag> http://www.bridgedb.org/

<Lena> EGFR

REACT_9417.3

<Lena> http://www.bridgedb.org/wiki/BridgeWebservice

search on the pathwaycommons endpoint - http://bio2rdf.semanticscience.org:8010/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%3EREACT%209417%3C%2Ftext%3E%3Cview%20type%3D%22text-d%22%20limit%3D%2220%22%20offset%

http://goo.gl/kGzGx

the pathway - http://bio2rdf.semanticscience.org:8010/describe/?url=http%3A%2F%2Fcbio.mskcc.org%2Fcpath%23CPATH-485564

pathway step - http://bio2rdf.semanticscience.org:8010/describe/?url=http%3A%2F%2Fcbio.mskcc.org%2Fcpath%23CPATH-LOCAL-7272826

<Lena> https://deri.webex.com/deri/e.php?AT=WMI&EventID=218837347&PW=86b2bf0305181b021e185503&RT=MTgjMjE%3D

pathway commons sources - http://www.pathwaycommons.org/pc/dbSources.do

<Lena> next steps: assemble queries from pathwaycommons sparql endpoint

<Lena> try to integrate with wikipathways sparql endpoint

<Lena> todo for michel: proper URIs

<Lena> challenge: can we disambiguate physical entities in sbml to disambuate the entities

<Lena> can we use it for finding an equivalent using some fancy string match

<andrawaag> Pathway commons on biopax_level3 : http://awabi.cbio.mskcc.org/cpath2-demo/

michel.dumontier@gmail.com

<Lena> todo for lena: talk with biomodels curators and flesh out a strategy for validating our predictions

<Lena> r/prediction/invalidated annotation

todo for michel: load pathwaycommons, biomodels and wikipathways biopax into one endpoint, each in their own graph

todo for michel: generate bio2rdf uris, generate identifiers.org uris

This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

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<dbooth> Meeting: Weekly Baking Club Meeting


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Got date from IRC log name: 25 Jul 2012
Guessing minutes URL: http://www.w3.org/2012/07/25-hcls-minutes.html
People with action items: 

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<dbooth> Topic: Review of Amy's report