See also: IRC log
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%
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/ Guessing input format: RRSAgent_Text_Format (score 1.00) No ScribeNick specified. Guessing ScribeNick: michel Inferring Scribes: michel WARNING: No "Topic:" lines found. Default Present: +31.43.388.aaaa, +1.206.732.aabb, michel, ericP Present: +31.43.388.aaaa +1.206.732.aabb michel ericP WARNING: No meeting title found! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth 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: WARNING: No "Topic: ..." lines found! Resulting HTML may have an empty (invalid) <ol>...</ol>. Explanation: "Topic: ..." lines are used to indicate the start of new discussion topics or agenda items, such as: <dbooth> Topic: Review of Amy's report[End of scribe.perl diagnostic output]