HCLSIG/PharmaOntology/Meetings/2009-10-15 Conference Call

From W3C Wiki

Conference Details

  • Date of Call: Thursday October 15 2009
  • Time of Call: 12:00pm - 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: 1h
  • Convener: Susie

Agenda

  • Ontology (namespace) - Colin
  • Use case - Chris
  • Data sources - Anja
  • User interface - Susie
  • Paper - Susie
  • AOB

Minutes

In attendance: Lynn, Christi, Matthias, Jim McGurk, Michel, Joanne, Elgar, Susie, Colin, Chris, Trish, Jun, Bosse

susie: what progress on ontology?

colin: telecon between colin, elgar, michel & joanne

colin: minutes: http://docs.google.com/Doc?id=dc9qc59t_17f244jtdv&btr=EmailImport

elgar: minutes from Mon 10/12 meeting on TMO: http://esw.w3.org/topic/HCLSIG/PharmaOntology/Meetings

colin: protege 4, SVN on google code project, external terms in tmo-external.owl, whereas tmo.owl is just TMO terms

colin: comments about unplaced items were solicited

colin: try to get more xrefs to other ontologies

colin: ontological coercion -> use terms that are in thesauri like mesh, but place them in such a way that we can reason about them

susie: things broken were fixed?

colin: yes

susie: w3c namespace will be available on monday by eric

susie: what else to be done?

colin: definitions for undefined terms

elgar: data, datasets, influence on final version of tmo?

colin: undefined terms need to be concretized in terms of what they mean based on the data that we plan to annotated with them

colin: biomarker has several definitions... which is the most appropriate depends on the data

colin: disambiguation

susie: we need to talk about data sources

susie: michel and I have come up with list

susie: pharmagkb (personalization), drugbank (drugs), sider (side effects), clinicaltrials.gov (clinical trials), diseasome (disease--gene correlations), medicare (what drugs are available on particular plans)

susie: also diagnostic information and electronic health record information

susie: Linked Data available for first 5.

susie: Anja Jentzsch is RDFifying the medicare set

susie: statements like is_available_on(aricept, medicare) - available by end of week

susie: ehr - assume this exists - open system called indivo developed at Harvard - schemata publicly available and used by google & microsoft

susie: asked them for fake patients but they weren't forthcomingso we will make up our own

bosse: was there personal health information in the COI task?

susie: ours focuses on AD; theirs on diabetes

susie: will contact them

susie: only 5 patients needed

joanne: Peter Tonellato at the Library for Personalized Medicine (http://lpm.hms.harvard.edu/), part of the Center for Biomedical Informatics @ Harvard creates fake patients, "avatars" - I can look into this

susie: we do need cognitive information, genetic information e.g. ApoE, SNPs implicated in recent Nat. Genet. paper posted on wiki

chris: what about toxicity/efficacy?

chris: and SNPs?

susie: JnJ and ?Illan jointly own a drug and trials of this have shown differing effects for people with ApoE

susie: also important to make up ADME data, variant version of cytochrome P450

susie: another option - Lilly developed DMet chip with key genes

susie: I'll make up data and pass to joanne and ping coi people

joanne: inquire about suggestions Peter may have about generating fake patient data

susie: chris has pointed me to data sources with diagnostic information, also academic papers

susie: we could run unstructured text through bioportal

susie: and then triplify that

susie: and make sure we're using those terms in the fake patient data

michel: key Alz / drug / variant / outcome papers:

michel: http://www.pharmgkb.org/do/serve?objId=569429393&objCls=RelationshipReport#publications

michel: http://www.pharmgkb.org/do/serve?objId=569436230&objCls=RelationshipReport#publications

michel: http://www.pharmgkb.org/do/serve?objId=569434972&objCls=RelationshipReport#publications

michel: http://www.pharmgkb.org/do/serve?objId=569429027&objCls=RelationshipReport#publications

chris: what about real medical sources?

susie: much harder than in bioinformatics; we need to be credible rather than working with really really difficult real sources

susie: PharmaSurveyor (a company) run text-mining on top of semantic web data looking for drug-drug interactions

susie: and michel has kindly volunteered to stick data in a triplestore

susie: and then map to ontology

michel: the lodd triplestore : http://bio2rdf.semanticscience.org:8017/sparql/?default-graph-uri=&should-sponge=&query=select+distinct+%3FConcept+where+{[]+a+%3FConcept}&format=text/html&debug=on&timeout=

susie: and then run application from that

michel: pharmgkb - http://bio2rdf.semanticscience.org:8016/sparql/

susie: Trish - do you have time to run data sources through Bioportal by say Tuesday?

susie: also by then Anja's medicare data should beready

trish: sure

susie: any questions?

susie: and now, the interface

susie: option (1) pubby

susie: option (2) Anja's top questions interface

susie: option (3) Jun's AD application

jun: doable but really difficult by end of month

susie: option (4) bosse's experience of OntoText interface on LarKC

bosse: not in time for paper

joanne: also will be travelling last 2 weeks in October.

susie: ok so Anja could provide top questions, or we could use Pubby as extension unlikely

joanne: need not be polished

susie: need to think about what the interface would look like

susie: jun - could you work with us on look of interface?

jun: sure!

jun: available till thursday

bosse, elgar, michel: all interested

susie: let's schedule for lodd slot 1100 edt weds

susie: october 21st

susie: last item is paper itself susie: google doc available - colin what's the position?

colin: written aspects of the introduction, the aim, scope, general outline

colin: ontology, design methology, mappings

colin: moved lots of chris's stuff to new context section

colin: data sources & their descriptions

susie: chris and susie will work on conclusion

susie: when do we ask for an extension?

joanne: no harm in asking upfront

susie: we're getting there