HCLSIG/PharmaOntology/Meetings/2009-10-08 Conference Call

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Conference Details

  • Date of Call: Thursday October 8 2009
  • Time of Call: 11:00am - 1pm ET
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 42572 ("HCLS2").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
  • Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel
  • Duration: 2h
  • Convener: Susie

Agenda

  • Identify subset of use case to implement - all
  • Ontology enhancements & considerations - Colin
  • User Interface - all
  • F2F meeting - Susie

Minutes

Attendees: Chris, Colin, Michel, Matthias, Elgar, Bosse, Joanne, Lee, Trish, Allen

Apologies: Christi

<jluciano> colin: update on ontology:

<jluciano> finishing task of migrating annotations to new form (rather than rdfs comments) and using IAO

<jluciano> up on google code

<jluciano> Elgar also has write access, everyone has read access

<jluciano> access will be granted if others want to make changes, no problem!!

<jluciano> issues - people have said comes form NCI Thesaurus without giving ID, request ID included in future?

<jluciano> Colin suggests using issue tracker

<Susie> Joanne: Been looking at the patient use case

<Susie> Joanne: Been adding the URL to the use case

<jluciano> Action Item: colin will take IDs from Use Case Wiki and transfer them to ontology

<jluciano> onology almost done, need to attach to use case and add IDs

<jluciano> Elgar: notes small mistake in uploaded current ontology - will throuh an error. Wait an hour or so for an updated version.

<jluciano> Elgar and Colin will meet offline before next meeting

<jluciano> Today we decide which use case, Susie asks Colin if he has preferences before he leaves. Colin leaves it to those closer to TM application

<jluciano> Michel - aks to add to be added as developer

<jluciano> Michel - will be using SVN

<jluciano> Joanne (silently) agrees

<jluciano> Michel asks Elgar to have colin comit current version to SVN

<jluciano> Michel will be part of calls, Joanne too, if schedule permits

<jluciano> Trish joins call

<jluciano> Susie asks Trish status of abstract submssion to AMIA - Yes, submitted and T will send updates to group (some edits in beginning).

<jluciano> Susie - suggests working through use cases and highlight what data we would be able to access and to consider how translational the steps are, then based on what we discover, we decide which.

<jluciano> goal to make paper strongest - but not intended to cover everything in futurte

<Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology/UseCases

<jluciano> Susie: the data spand should be broad (clinical, discovery)

<jluciano> going through use cases:

<jluciano> bbsksa - wasn't able to complete the scenario as he would like to see it

<jluciano> issue with data sources (?)

<jluciano> susie suggests that he contribute as we go throgh, he agreed

<jluciano> starting with Patient Scenario:

<jluciano> Some bits not tied to data,

<jluciano> Chris: there are some real world places that are held by clinicial

<jluciano> and not in data

<jluciano> Joanne: makes it more real

<jluciano> Susie: realistic important, ask if physician will enter

<jluciano> Chris: yes

<jluciano> some discussion / the discussion went into specifics (emergency room) as an example

<jluciano> Chris - physician or clinican or P assistant - (not always physician) ---> working on usecase

<jluciano> Susie making edits on Wiki directly

<jluciano> Chris had updated to include "differential diagnosis"

<jluciano> Joanne had added the links to DB - yes there was term (and ID) for differential diag.

<jluciano> Chris says there is all the differential - a list of differential daignosis and then selects one as the working diagnosis

<jluciano> bbasla: how does this ad value?

<jluciano> Chris: one wil need to know with persoanlized medicine - will medications treat it,

<jluciano> ontology fliters and provides data for answers

<jluciano> Chris: will help to not harm in particular in presonalized medicines

<jluciano> Joanne asked about data sources - Chris said they are tin the "more details on the data sources" attached to the wiki:

<jluciano> NICE - UK National Institute for Clinical Excellence - clinic progocols and which drugs avail through UK health sources

<bbalsa> Nice as a data source, what is the license?

<bbalsa> ICD is used for coding.

<jluciano> This is an interesting source for psyc stuff.... will check for AD

<jluciano> http://psyweb.com/Drughtm/DrughtmAdv/jsp/pickAD.jsp

<bbalsa> Is AD a suitable disease? So far the scenario is generic. If data sources is easier to find for other disease, it's possible to change.

<bbalsa> Susie: Shall we aply this on existing guidelines or shall we demonstrate an alternative scenario?

<jluciano> For (future) reference: Lee Hood, Institute for Systems Biology on Systems Medicine:

<jluciano> http://www.google.com/url?sa=t&source=web&ct=res&cd=2&url=http%3A%2F%2Fwww.itl.nist.gov%2FHealth...

<jluciano> (should be in the use cases)

<jluciano> P4 medicine

<jluciano> Susie - and others dicuss that it would be useful to have a data source Which SNPs are implicated in which drug???

<jluciano> Michel - took PharmGKB and looked with respect to Depression

<jluciano> extracted which alleles (genetic markers) linked to drug outcomes

<jluciano> next step - then can ask if any of these varinants involved

<michel> pharmgkb data - http://ontology.dumontierlab.com/pharmacogenomics-pgkb

<michel> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19240125

<michel> http://dumontierlab.com/pdf/2008_BIB_pharmacogenomics.pdf

<michel> depression - http://ontology.dumontierlab.com/pharmacogenomics-depression

<matthias_samwald> (i have to leave the call now, bye!)

<michel> toxicity: we have also rdfized i) comparative toxicogenomics database, and are processing ToxNet resources

<bbalsa> Side effect information, any known sources? Chris will investigate some sources he has used.

<bbalsa> Susie: Potential interesting scenarios around diagnosis and drug selection. Will require a EHR that we then have to make up.

<bbalsa> Susie: Merge physician and trial scenario.

<bbalsa> Need both patient and research scenarios. SNP:s important. Michel's work core.

<michel> http://www.pharmgkb.org/do/serve?objId=PA443319&objCls=Disease#tabview=tab2

<michel> look into whether alzheimer's has sufficient information to link variants to drug outcomes

<michel> otherwise depression a straightforward choice

<michel> we could however, use both. alzheimer's sets the first stage, depression points to what added curation will provide

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