HCLSIG BioRDF Subgroup/Meetings/2006-09-25 Conference Call
Conference Details
- Date of Call: Monday September 25, 2006
- Time of Call: 11:00am Eastern Time
- Dial-In #: +1.617.761.6200 (Cambridge, MA)
- Participant Access Code: 246733 ("BIORDF")
- IRC Channel: irc.w3.org port 6665 channel #BioRDF (see W3C IRC page for details, or see Web IRC)
- Duration: ~1 hour
- Convener: Susie Stephens
- Scribe: Marja-Riitta Koivunen (Zakim instructions)
Attendees: Oliver Bodenreider, Alan Ruttenberg, Kei Cheung, Susie Stephens, Jonathan Rees, Vipal Kashyap, John Barkley, Marja Koivunen, Joanne Luciano, Daniel Rubin, Don Doherty, and Scott Marshall.
Regrets: Ora Lassila, Kerstin Forsberg, Carole Goble and Matthias Samwald.
Agenda
- We'll collect URI statements for the F2F
- Kei Cheung will give a demo of AlzPharm. To view the demo go to https://conference.oracle.com and then enter the ID 56605701.
- Vipal Kashyap will give an overview of BIONT, highlight possible intersection points between BioRDF and BIONT for the F2F meeting, and describe BIONT use cases
1 Collection of URI statements
- collection of URI statements will be done by e-mail (Action item: Susie)
2 Kei Cheung demo
- Kei Cheung demo of AlzPharm combines Brainpharm drug data and SWAN RDF data (subset from AlzPharm)into Oracle RDF data model and creates queries to that data
- Slides are available at BioRDF wiki
Run demo
- goto AlzPharm
- query drug: Donepezil
- Result page has a list of articles related to the drug with description, journal, title and some other semantic information
- Last column has PubMed article information e.g. http://www.ncbi.nlm.nih.gov/entrez/query.fcgiCMD=search&DB=pubmed&term=12469988 and corresponding discussions on the Alzforum
- Explore a sample article with a lot of Alzforum discussions with title: Long-term donepezil treatment in 565 patients with Alzheimer's disease (AD2000): randomised double-blind trial (http://www.alzforum.org/pap/annotation.asp?pmid=15220031).
3 Vipal Kashyap overview of BIONT
- the actual ontology is discussed outside this call
- BIONT use cases
- aim is to do use case modelling in style of UML
- we concentrate more on what's the value of the technologies than the details of the technologies
- use case main page(id problems have been solved in these cases)
case 1: correlation between SNPs and genes
http://esw.w3.org/topic/HCLSIGUseCases/BiomedicalDataIntegrationaction=AttachFile&do=get&target=UseCase1.doc
- today just keyword search but here aim is for better semantic matching between concepts in different data sources using different ontologies
case 2:
http://esw.w3.org/topic/HCLSIGUseCases/BiomedicalDataIntegrationaction=AttachFile&do=get&target=UseCase2.doc
- again, SW can be helpful in semantic matching steps
case 3:
http://esw.w3.org/topic/HCLSIGUseCases/BiomedicalDataIntegration?action=AttachFile&do=get&target=UseCase3.doc
- checking if pathway information explains the correlations
- flow = possible explanation
- this is good basis for further work in amsterdam, next we can try these out with some data
- some people are already doing conversions of suitable data to SW format e.g. Olivier http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Entrez_Gene_to_RDF
- right now there are no links to data yet, the data can be asked by e-mail
- some info of work being done in [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks
BioRDF/Tasks section]