See also: IRC log
<mscottm> Zakim keeps hanging up on me
Michel: CSHALS submission, plus...
<matthias_samwald> IMIA Medinfo
Matthias: Deadlines are coming
up. CHALS today, IMIA Dec 10
... we should be at both conferences
... think about integration of resources that we have
... cshals, we can use what we have now; re-use resources from summit next year
... slightly different audiences: AMIA translational, CSHALS more people from pharma
<mscottm> Zakim is telling me that 4257 is not a valid passcode.. ?
Joanne: CSHALS focussed on pharma, but well aware of semweb tech
Matthias: CSHALS relatively short submission
<mscottm> Wow, thanks Zakim for letting me in! with passcode 4257 even.
<mscottm> echo echo
Michel: Happy to do CSHALS
... SWAT4LS was last week in Paris
Michel: Should list resources and dates accessed
Michel: add more than the OWL KB?
Matthias: KB, only referring to the OWL ontology; but includes other data: Michel's data++
Michel: OWL profile?
Michel: Can reason, dump
inferences to OWLim for query
... or set up website too, or just a file for query
Matthias: Just a file for
... parts of Bio2RDF + Richard's data, but no real interface
Michel: PharmGKB, dbSNP, OMIM
Scott: What is the biological use
... we have snps, structured product labels
Matthais; Show how to integrate different datasets, then demo how OWL reasoning can connect to clinical guidlines
Michel: Brainstorm, w product label for codeine(?)
<michel> that's rich ;)
Michel: statement applied to pregnant women
Rich: Interesting part was that sem model could capture PGx (view)
Matthias: Could use owl for
automated reasoning and for matching pts to clinical
... RDF model for capturing slightly more (subtle rules)
... would be hard to capture everything in clincial rule sets
... OWL inferencing would add here
Michel: Matthias' point is very
... RDF can express opaque relationships
... we can cherry pick RDF parts, then construct much more powerful ontological inference
Matthias: 3-4 coherent, not too complex in presentation
Scott: Another idea: We are
bringing in structured product labels; should we address
... sparql resource for AE reporting systems
... we could use this resource in our scenario
Matthias: but time constrant
Scott: Can use AE pdf w sparql endpoint
<BobF> As full disclosure, the developer of ADEpedia is located directly across the hall from my office :-)
BobF(?): There has not yet been rigorous validation of the quality
scribe: (someone else) addressed
... to bring it in, there has to be a connection between PGx and AE
<BobF> (Rich Boyce is speaking)
Rich: Something to think about in
the big picture, very nice to address AE outcomes
... 3rd resource is SIDER, slightly different process
Michel: SWAT4LS I wrote a parser for SIDER
Rich: SIDER has 900 drugs, not
... dbPedia value is the cloud platform
... Jian Yu(?)
<BobF> Qian Zhu - another colleague of mine
<BobF> ADEpedia: Guoqian Jiang
(discussion that BobF is geographically close to ADEpedia :)
Matthias: ADEpedia, RDF does not
contain much other than drug -> side effect
... not not much info on (context, provenance)
... still under development(?)
Rich(?): Part of the proposal is to include this provenance
scribe: item for further
discussion, to develop metadata standard for structured
... manually annotated AE + structured label: these are claims about the drug
... should be tied to evidence
... to be more concrete, should be SBML
Michel: We had a group on
SciDisc, out of which come other ongoing groups
... not too difficult to assemble from these semweb assets
ericP: Anybody else w curated stuff?
Rich: FDA has indexing
initiative; there is some validation
... ericP: have done homework on this.
Michel: Trying to link PGx
aspects; when talk about drugs we get AE, drug-drug. All
... AE, mining structure product label are key endpoints
... for PGx: Do we have what we *can* have?
... PGx has a lot of assertions, needs curation(?)
... excited about pulling out facts w provenance from lots of different sources
... connect to other resources; what is the process to curate the lit?
Matthias: People can go overboard w complex ontologies; 10=headache :)
BobF: One of things to be
careful: Separate knowledge from interpretation!
... PGx line greys easily; genotype-phenotype, PGx has habit of tying to intermediate metabolites
... but these are arbitrary, historical in nature but w/o good semantic meaning
... for assertions, consider how much of PGx to include in this project
Joanne: +1 on observations
... worth re-stating this.
... for medical conference
Matthias: Address intermediate metabolite info problems
BobF: Talking re data, resources,
queries outside of PGx; but (ex) intermediate metabolite
connections between genes may lead us to bad inferences
... primary data sources like pubs, we can have provenance; but then there are lab-to-lab differences
... see this periodically; careful of this trap.
Thanks to Matthias for taking the lead!
This is scribe.perl Revision: 1.137 of Date: 2012/09/20 20:19:01 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: bobP Inferring Scribes: bobP WARNING: No "Topic:" lines found. WARNING: No "Present: ... " found! Possibly Present: ADEpedia BobF Bob_Powers GVoice IPcaller Joanne Joanne_Luciano MacTed Matthias Michel P37 P38 Rich Scott Tony aaaa achille_zappa bobP boycer ericP https matthias_samwald mscottm You can indicate people for the Present list like this: <dbooth> Present: dbooth jonathan mary <dbooth> Present+ amy Got date from IRC log name: 05 Dec 2012 Guessing minutes URL: http://www.w3.org/2012/12/05-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]