15:04:48 <RRSAgent> RRSAgent has joined #hcls
15:04:48 <RRSAgent> logging to http://www.w3.org/2012/07/25-hcls-irc
15:05:03 <michel> michel has joined #hcls
15:05:06 <Zakim> Zakim has joined #hcls
15:05:30 <Lena> zakim, who is here
15:05:33 <Zakim> Lena, you need to end that query with '?'
15:05:38 <Lena> zakim, who is here?
15:05:39 <Zakim> sorry, Lena, I don't know what conference this is
15:05:46 <Zakim> On IRC I see michel, RRSAgent, Lena, michael, achille_zappa, andrawaag, MacTed, ericP
15:05:47 <Lena> zakim, this is SysBio
15:05:53 <Zakim> sorry, Lena, I do not see a conference named 'SysBio' in progress or scheduled at this time
15:05:59 <ericP> Zakim, this is hcls
15:06:03 <Zakim> ok, ericP; that matches SW_HCLS(LODD)11:00AM
15:06:56 <Zakim> +michel
15:09:59 <Zakim> +??P27
15:10:03 <ericP> Zakim, ??P27 is me
15:10:03 <Zakim> +ericP; got it
15:10:11 <ericP> Zakim, who is here?
15:10:11 <Zakim> On the phone I see +31.43.388.aaaa, ??P16, +1.206.732.aabb, michel, ericP
15:10:13 <Zakim> On IRC I see michel, RRSAgent, Lena, michael, achille_zappa, andrawaag, MacTed, ericP
15:11:14 <michel> lena: initial aim was to query various sbml models together
15:11:26 <michel> ... a few sbml models are modeling the same thing
15:11:32 <michel> ... map kinase pathway as a use case
15:12:02 <michel> ... biopax representation available
15:12:07 <michel> ... loaded into workbench
15:12:46 <michel> ... query to capture all the reactants, products
15:13:08 <michel> ... when products are reactants, we should see a network
15:13:29 <michel> ... tried to match on labels, but incomplete
15:14:08 <michel> ... no URIs specified, difficult to parse
15:14:46 <Zakim> -ericP
15:15:03 <Lena> https://www.google.com/fusiontables/DataSource?snapid=S595021IJTA
15:15:56 <michel> above -> graph of interconnected molecules
15:16:06 <michel> ... problem largely lies in the complexes
15:19:03 <michel> mike: are there no references in the SBML files?
15:19:12 <michel> let's look at the biomodel file
15:19:15 <Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000019
15:19:45 <Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000033
15:19:58 <Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000399
15:20:09 <Lena> http://www.ebi.ac.uk/biomodels-main/BIOMD0000000151
15:24:04 <Lena> michel loaded pathwaycommons into an endpoint
15:24:21 <Lena> good way for do disambiguation
15:25:02 <michel> pathwaycommons endpoint - http://bio2rdf.semanticscience.org:8010/fct/
15:25:43 <Lena> wikipathways used bridgedb for solving the identifiers problem
15:25:49 <Lena> openphans - query expander
15:26:35 <andrawaag> http://www.wikipathways.org/index.php/Pathway:WP17
15:27:19 <andrawaag> http://www.bridgedb.org/
15:27:47 <Lena> EGFR
15:27:49 <michel> REACT_9417.3
15:30:51 <Lena> http://www.bridgedb.org/wiki/BridgeWebservice
15:33:25 <michel> 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%
15:34:21 <michel> http://goo.gl/kGzGx
15:35:46 <michel> the pathway - http://bio2rdf.semanticscience.org:8010/describe/?url=http%3A%2F%2Fcbio.mskcc.org%2Fcpath%23CPATH-485564
15:37:27 <michel> pathway step - http://bio2rdf.semanticscience.org:8010/describe/?url=http%3A%2F%2Fcbio.mskcc.org%2Fcpath%23CPATH-LOCAL-7272826
15:38:38 <Lena> https://deri.webex.com/deri/e.php?AT=WMI&EventID=218837347&PW=86b2bf0305181b021e185503&RT=MTgjMjE%3D
15:41:18 <michel> pathway commons sources - http://www.pathwaycommons.org/pc/dbSources.do
15:43:48 <Lena> next steps: assemble queries from pathwaycommons sparql endpoint
15:44:03 <Lena> try to integrate with wikipathways sparql endpoint
15:44:45 <Lena> todo for michel: proper URIs
15:45:19 <Lena> challenge: can we disambiguate physical entities in sbml to disambuate the entities
15:46:44 <Lena> can we use it for finding an equivalent using some fancy string match
15:48:53 <andrawaag> Pathway commons on biopax_level3 : http://awabi.cbio.mskcc.org/cpath2-demo/
15:49:39 <michel> michel.dumontier@gmail.com
15:52:28 <Lena> todo for lena: talk with biomodels curators and flesh out a strategy for validating our predictions
15:54:15 <Lena> r/prediction/invalidated annotation
15:54:55 <michel> todo for michel: load pathwaycommons, biomodels and wikipathways biopax into one endpoint, each in their own graph
15:55:19 <michel> todo for michel: generate bio2rdf uris, generate identifiers.org uris
15:55:58 <Zakim> - +1.206.732.aabb
15:55:59 <Zakim> - +31.43.388.aaaa
15:55:59 <Zakim> -??P16
15:56:00 <Zakim> -michel
15:56:00 <Zakim> SW_HCLS(LODD)11:00AM has ended
15:56:01 <Zakim> Attendees were +31.43.388.aaaa, +1.206.732.aabb, michel, ericP
15:56:01 <michael> michael has left #hcls
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16:08:30 <Lena> RRSAgent, please draft the minutes
16:08:30 <RRSAgent> I have made the request to generate http://www.w3.org/2012/07/25-hcls-minutes.html Lena
16:08:43 <Lena> RRSAgent, please make the logs world-visible
16:08:43 <RRSAgent> I'm logging. I don't understand 'please make the logs world-visible', Lena.  Try /msg RRSAgent help
16:09:32 <Lena> RRSAgent, set logs world-visible
17:12:08 <Zakim> Zakim has left #hcls