HCLSIG/PharmaOntology/Meetings/2009-10-01 Conference Call

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Conference Details

  • Date of Call: Thursday October 1 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

  • Identify subset of use case to implement - all
  • Ontology enhancements & considerations - Colin
  • Jun's application demo - all
  • F2F meeting - Susie

Minutes

in attendance: colin, susie, chris, julia, joanne, elgar, bosse, trish, michel

Susie: http://esw.w3.org/topic/HCLSIG/PharmaOntology/Actions

susie: Chris - were you able to assign data sources to the patient use case?

chris: have gathered them off-wiki, but can we finalize use case first?

susie: wonderful if you could wikify; focus on data sources that are publicly available and easy to access

chris: will aim for next meeting

susie: deadline for paper end of month

susie: haven't yet performed my action

susie: Michel - assigning tmo terms to use cases?

michel: did the research use case

michel http://esw.w3.org/topic/HCLSIG/PharmaOntology/UseCases

michel: will do physician use case shortly

bosse: i had imagined it involving a hypothesis

susie: we're trying to home in on the aspects of the use case we're trying to implement

susie: we're very much game for further information

susie: not sure how to write down the use case without doing it stepwise

susie: Trish,Joanne - were you able to assign other ontologies to use cases?

joanne: not yet.

trish: how did the use cases divide up? I have a question about #6 in the patient scenario. what are the standard coding criteria about?

chris: need to consult guidelines for diagnosing for example Alzheimer's, eg DSM V

joanne: could we use icd?

chris: for making a diagnosis you need the dsm criteria

joanne: are we sticking to alzheimer's?

susie: we need to demonstrate utility of ontology with a specific disease

susie: we can also use clinicaltrials.gov

joanne: where do you want the ontology terms added?

susie: follow what michel has done on the research scenario

susie:_i'm_ planning to include uris and sparql endpoints

susie: can we be more specific?

colin: yes

elgar: i have specified sources in the spreadsheet

elgar: possibility of users using other candidates for ontology terms

susie: how far can we get with the obo foundry?

joanne: i use http://www.ebi.ac.uk/ontology-lookup

trish: obo foundry might be a bit limiting

trish: umls has some really old terminologies

colin: i've tried to use obo foundry first, then nci thesaurus, then my head

elgar: i need current version of owl ontology

Joanne http://terminizer.org/terminizerFrontEnd/Terminizer.jsp

Joanne I find the terminizer to be useful

Joanne (as well as the ebi ontology lookup)

susie: FOLLOWUPS FOR NEXT WEEK - susie to assign data sources to research use case; chris to assign data sources to physician use case; michel to add tmo terms to physician use case; trish and joanne to add other ontology terms to both use cases; bosse to refine use cases

chris: what use cases are we working on?

susie: the two use cases at the v bottom of wiki page - the physician use case and researcher use case - are the ones we're working on

susie: by next week's call we MUST decide what part of the use case and what data sources to use

susie: Now, the ontology...

colin: have been migrating annotations to iao and adding curation statuses

colin: also matthias samwald has sent useful and cogent observations

elgar: i have more xrefs and sources ready to go. how do we share ontology?

elgar: i have created a snapshot the following url:

ElgarPichler http://esw.w3.org/topic/HCLSIG/PharmaOntology/Ontology#preview

colin: i have created a project on google code:

colin http://code.google.com/p/translationalmedicineontology/

Joanne this is the correct bioportal ontology lookup http://bioportal.bioontology.org/

susie: any other updates?

colin: have found richard scheuermann's amia paper and am using defs from there

colin http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

trish: the search i good for individual terms and for text such as the use case, the annotator is useful, but more so the prototype tool called the ontology recommender: http://obs.bioontology.org/oba/Recommender.html

susie: for our use case we'll need an application. did the people who did see jun's application think it had legs?

chris: thought it was vg

joanne: too much information, and too many technical terms for the lay person

susie: at moment we're constrained to using material that is publicly available. we could maybe state that the preferred source for something is X but the open source we will actually use is Y

chris: would it be ok to approach data providers and ask for samples?

susie: we're hoping to change the world and maybe we could demonstrate utility of approach

joanne: is hl7 open?

colin: volunteer to find out ip status of hl7

susie: there was a question on the w3 mailing list about reuse. some data sources are slightly funny about reuse

chris: do we have someone on the legal side?

susie: w3c has legal support

susie: summary in terms of jun's application is that it has promise but needs work for our use case

susie: 2 h call next week

susie: Trish - could you submit the paper?

trish: not in google docs?

susie: yes. not in google docs

susie: I will circulate it

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