HCLSIG/PharmaOntology/Meetings/2010-03-18 Conference Call
Conference Details
- Date of Call: Thursday March 18 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: Elgar
- Scribes: Bosse, Elgar
Agenda
- TMO
- Data - Michel
- Ontology - Elgar, Colin
- Interface - Bosse
- Outreach - Trish, Michel, Colin, Chris
- Inclusion/exclusion criterion - Michel, Bosse
- Other Outreach
- UPenn Translational Medicine (ITMIT) - Chris
- Other opportunites (AAAI)
- Upcoming F2F
- AOB
Minutes
Attendees: Bosse Andersson (B), Colin Batchelor (Co), Chris Domarew (Ch), Michel Dumontier (M), Elgar Pichler (E), Trish Whetzel (T)
Apologies: Susie Stephens (S)
TMO
- Ontology:
- E:
- noticed new version of TMO has been uploaded to TMO Google project
- review of recent ontology work?
- M:
- went back to comments of JBI paper reviewers; fixed hanging terms, moved orphan classes as information content entities that define various contextual information (information about drug, patient, etc.)
- Co:
- information entities grouping is interesting, will take a closer look at TMO changes
- E:
- did the comments from mail exchange in December make it into the ontology?
- thought also it was time for a second round of TMO editing;
- wanted to address 3 things: 1. missing concepts?; 2. Cannot display IAO properties labels in an informative way in any ontology editor - IAO annotations rather difficult to figure out for anyone who looks at TMO; 3. How can we make mapping of concepts to other ontologies more dynamic? (i.e., actually enable a TMO to dynamically use part of another ontology if we point to class in it via xrefs; at the moment we just provide xrefs and for some classes a static link to another ontology)
- T:
- we should use SKOS properties for editorial notes
- E:
- there seem to be several choices for annotations: 1. IAO, 2. SKOS, 3. annotations in collaborative Protege, ...; IAO currently has usability issues; SKOS is definitely a choice - could Trish suggest when to use it?
- Co:
- agreed, problems with IAO
- T:
- could use SKOS, e.g., for prefLabel, altLabel (for synonyms); will compile a short list of properties to use from SKOS
- ⇒ T: compile list of SKOS properties which could be used for TMO
- Data
- M:
- had discussion in February about mapping RxNorm - any progress?
- E:
- yes, have completed UMLS install (includes: all unrestricted sources (level 0) + SNOMED)
- now can extract UMLS mappings between all those source vocabularies
- could now extract RxNorm mappings to Alcohol and Other Drug Thesaurus, Metathesaurus FDA National Drug Code Directory, and Veterans Health Administration National Drug File
- ⇒ E: provide RxNorm mappings to M for integration into TMO data triple store
- Inclusion/Exclusion Criteria
- M:
- had conference call last week with Bosse and Vassil (OntoText) and discussed how to extract inclusion/exclusion criteria from LinkedCT
- B:
- work also of interest for LOD project
- M:
- bjective: to be able to query over these "entities" and relationships
- have developed script and RDFiser to download and transform ClinicalTrials.gov to RDF
- Interface
- B:
- presented in last TMO TC a schematic view of interface scenarios (TMO use scenarios) that were developed with Eric; Eric needs comments on these in order to better gauge interface requirements; any comments?
- E:
- if there are no comments now, we all should look at this and comment
- ⇒ all: check out TMO use scenarios and send interface comments to Bosse
Outreach
- Report from AMIA2010 Summit on Translational Bioinformatics, CSHALS 2010
- Ch, T:
- reporting on AMIA2010 Summit on Translational Bioinformatics:
- Ch:
- at conference last week met people from Mayo Clinic [should that be Marshfield Clinic?] and initiated a discussion around collaboration on user interaction.
- they have established eHR system; data dumped into Access; ran into interface issues
- will set up a call next week; will send out meeting information and try to coordinate so that interested TMO members can participate
- ⇒ Ch: to set up call between Mayo/Marshfield Clinic folks and TMO group
- met Vivien Marx who wrote article on TMO
- E:
- yes, Vivien wrote nice article on TMO in GenomeWeb after CSHALS2010
- regarding eHRs: talked with Jonas Almeida and Lynn Vogel (both from MD Anderson Cancer Center) at CSHALS
- they have done very nice work on eHR and clinical data analysis customized for MD Anderson; very impressive informatics organization there; see also Vogel's CHSHALS keynote talk
- Ch:
- work done in this area at University of Minnesota also very impressive
- a lot of parallel activities out there, we can learn from them and demonstrate the strength in our work
- smart way of making data anonymous is to shift the time so that the individual not can be identified
- E:
- seems we could follow different approaches in working with clinical data:
- 1. get clinical data (very hard for US data because of privacy issues, might be easier to get data from countries other than US) and integrate with other TMO data, or
- 2. leave data with owners behind firewalls (e.g. at hospitals) and strike deal with data owners to jointly analyze data with TMO tools
- seems we could follow different approaches in working with clinical data:
- Ch:
- critiscism of ontologies: don't strife forever to model everything; use existing systems; find something that works, apply it, don't reinvent wheel
- ontologies well received and accepted, but goal should be to make them work so that patient care improves
- T:
- other interesting people presentations at conference:
- Allan Halevi [?], Google: why not mine what you got?
- Peter Kos, Harvard: interested in further discussions with TMO
- Sherri De Coronado, NCI: worked on similar project with grid technology
- other interesting people presentations at conference:
- former JBI paper
- Co:
- will talk about this at next TC
Meeting/Communication Logistics
- HCLS F2F
- E:
- 2 F2F meetings planned in April:
- 2010/04/22,23 F2F Meeting: Stata Center, Cambridge, MA; after 2010/04/20-22 BioIT2010 in Boston, MA; sign up at F2F wiki page, if you wish to attend by phone, you can add "(remote)".
- 2010/04/26 Workshop on The Future of the Web for Collaborative Science: Raleigh Convention Center, Raleigh, NC, USA; held in conjunction with WWW2010
- planned for both: "dDD" (discussion, Dinner, Drink)
- ⇒ all: sign up at F2F wiki page, if you plan to attend
- 2 F2F meetings planned in April:
- return to weekly TMO TC meetings
- E:
- so as not to lose momentum, how about return to weekly meetings as previously discussed at beginning of year?; had a productive push last year to get JBI paper done; would be good to go for something similar
- how do people feel about this?
- Co, Ch, M, E, T:
- support weekly schedule
- B:
- would like to have goal to work towards, otherwise meetings can also just take time
- E:
- agreed; but seems we have enough action items for next weeks to necessitate going to weekly meetings; we seem to have general preference for weekly TC schedule
- ⇒ S: to reinstall weekly TMO TC meetings, starting 2010/03/25
- TMO mailing list
- T:
- would be useful to have TMO only email group so that TMO notifications and updates don't have to be sent out to whole HCLS mailing list
- all:
- sounds good
- T:
- ⇒ T: to set up google mailing list for TMO
Action Items
- ⇒ Elgar: provide links for meeting minutes
- ⇒ Trish: compile list of SKOS properties which could be used for TMO
- ⇒ Elgar: provide RxNorm mappings to Michel for integration into TMO data triple store
- ⇒ all: check out TMO use scenarios and send interface comments to Bosse
- ⇒ Chris: set up call between Mayo/Marshfield Clinic folks and TMO group
- ⇒ all: sign up at F2F wiki page, if you plan to attend
- ⇒ Susie: reinstall weekly TMO TC meetings, starting 2010/03/25
- ⇒ Trish: set up google mailing list for TMO