HCLSIG/PharmaOntology/Meetings/2010-02-04 Conference Call

Conference Details

• Date of Call: Thursday February 4 2010
• Time of Call: 12:00am - 1:00pm 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

• Drug Ontology
  • VA NDF-RT - Rich
  • ChEBI - Janna
  • Drug Ontology Requirements - Susie, Elgar
• Other Update
  • TMO changes - Colin
  • Structuring inclusion/exclusion criteria - Michel
  • Mapping drug codes - Michel
  • UI discussions - Chris
• Outreach
  • AMIA TBI update - Susie
  • JBI paper - Colin
  • CSHALS - Elgar
  • BioOntologies SIG - Susie
  • UPenn Translational Medicine (ITMIT) - Chris
• AOB

Minutes

Attendees: Chris, Lee, Susie, EricP, Elgar, Joanne, Bosse, Eric Miller, Rich, Janna

Apologies: Colin

• Drug Ontology
• <boycer> Blog entry about NDF-RT: http://www.pitt.edu/~rdb20/bhi-scholar-blog/NDF-RT.psp.html
• <ElgarPichler> Rich: on VA NDF-RT
• <ElgarPichler> since 2001 rough drug classification terminology
• <ElgarPichler> RxNorm is one of the braches of that work
• <ElgarPichler> to cover mostly US approved drug
• <Joanne> Joanne asked Susie, Michel, Elgar, Colin to read the email relating to the i2b2 data access and get back to her - pref with fax of form
• <ElgarPichler> http://www.nlm.nih.gov/research/umls/rxnorm/
• <ElgarPichler> for chem ingredients good mapping to MeSH
• <boycer> http://bioportal.nci.nih.gov/
• <boycer> Mitoxantrone
• <boycer> http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?mode=&index=8572&view=concept
• <ElgarPichler> [start session at bioportal then look for Mitoxantrone]
• <ElgarPichler> discussion of racemic compounds
• <ElgarPichler> in MeSH no distinction between racemates; better granularity in Chebi
• <ElgarPichler> NDFRT iavailable in OWL-DL
• <ElgarPichler> inferred ontology for it is also provided in distribution
• <ElgarPichler> does not contain explicit defs of relations
• <ElgarPichler> Diana: on ChEBI
• <ElgarPichler> "trying to get Chemistry right"
• <boycer> Early paper describing NDF-RT: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=pubmed&term=12463798
• <ElgarPichler> each distinct chemical substance is a distint entity in ChEBI
• <ElgarPichler> root term for isA hierarchy is "molecular structure"
• <ElgarPichler> role ontology describes how chemical interacts in various contents
• <ElgarPichler> [for more detailed discussion of ChEBI structure and discussed examples see
• http://esw.w3.org/topic/HCLSIG/PharmaOntology/Meetings/2010-02-04_Conference_Call?action=AttachFile&do=get&target=Drugs_in_ChEBI.pd
• <ElgarPichler> Rich: on VA NDF-RT
• <ElgarPichler> some annotation of brand names
• <ElgarPichler> but no annotation of dose, indication, etc.
• <ElgarPichler> this could be provided by links to RxNorm
• <ElgarPichler> hard to link to MeSH because of problems with MeSH classifications
• <ElgarPichler> chemical might have role; 'role' could be reinterpreted as 'mode of action'
• <ElgarPichler> ad maintenance: suggestions, corrections can be submitted; no way to do bulk submission of comments ...
• <ElgarPichler> interface: query interface exists; often users just download a distribution and then mine data
• <ElgarPichler> ... discussion of enantiomers, importance to distinguish between chiral forms for clinical usecases ...
• <ElgarPichler> Susie: thinking about usecase for TMO: how could pharma companies exchange chemical information with collaborators? ChEBI looks like it might be appropriate for small molecules ...
• <ElgarPichler> ... problem for ChEBI with large molecules
• <ElgarPichler> Diana: if, e.g., contraindication is based on chemical feature it might be possible to include this info in ChEBI
• <ElgarPichler> Lee: how easy is drug to synthesize, would like to record that somehow
• <ElgarPichler> Susie: what else could be in drug ontology: information on inlicensing, formulation, ...
• <ElgarPichler> mentioning of Pistoia collaboration, coordination between W3C and Pistoia, how?
• <ElgarPichler> Lee: one workstream in Pistoia is on vocabularies
• <ElgarPichler> about 10 pharma companies in Pistoia
• <ElgarPichler> ontologies would fit into higher level Pistoia workstream
• <ElgarPichler> topic: TMO
• <ElgarPichler> Bosse: interface discussion
• <ElgarPichler> have prepared information, put on wiki, get feedback from group in 2 weeks from now
• <ElgarPichler> used usecase to develop high level requirements; Susie to put interface doc on wiki
• <ElgarPichler> topic: outreach
• <ElgarPichler> Susie: need to talk about AMIA poster with Trish and discuss poster at next meeting
• <ElgarPichler> JBI paper: no discussion on acceptance; quite a few comments by 2 reviewers
• <ElgarPichler> reviewers comments: need to better connect data and ontology
• <ElgarPichler> Colin will incorporate review suggestions