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