HCLSIG/PharmaOntology/Meetings/2010-03-04 Conference Call

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Conference Details

  • Date of Call: Thursday March 4 2010
  • Time of Call: 12:00am - 1:00pm ET
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (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


  • TMO
    • Data - Michel
    • Ontology - Colin
    • Interface - Bosse
    • Outreach - Trish, Michel, Colin
  • Inclusion/exclusion criterion - Michel, Bosse
  • Drug Ontology update - Susie
  • Other Outreach
    • UPenn Translational Medicine (ITMIT) - Chris
    • Other opportunites (AAAI)
  • AOB


Attendees: Chris, EricP, Peter, Julia, Matthias, Elgar, Bosse, Susie

Apologies: Michel, Trish

Susie: Michel is working on aligning data with ontologies – he is not here today.

Susie: next, TMO. Colin is absent. Elgar, is the ontology complete?

Elgar: it needs more terms. We need to revisit some missing terms. Cannot give a development update. Last version is from Oct/Nov – no new submissions since on google code. Not sure if Colin’s been working on some terms he’d proposed in Jan. If he has a new version, it hasn’t been published and reviewed. Another editing iteration is due.

Susie: can Elgar and Colin get the current status and decide how we can incorporate new terms. How about ‘biomarker’? Some medical records seem to have them.. If some terms are not obvious, a group discussion can fill in the gaps.

Elgar: the first round was towards the paper deadline. Need more mapping of ontologies to data set classes. And we need to review the terms (missing, not fitting, clinical vs. pharma terms to add to make it more useful etc.)

Action item: Elgar to get in touch with Colin and the rest to submit terms/issues/etc to Elgar or Colin.

Susie: in an upcoming call, Elgar will present the latest ontology and we will discuss new terms. Also, we might need new datasets.

Elgar: use email to make suggestions, don’t wait for TC. Make more written comments on google code (TMO.owl, TMO_external.owl – load into Protégé to see , and a ‘DOC’ directory for comments)

Matthias: should we use the ‘issues’ functionality of google docs for comments?

Elgar: either way, let’s have a written record, and make sure all new ontology versions are submitted.

Susie: next item. Can Bosse present an update on the UI work with Eric and Chris? Susie posted the latest version of the doc in the wiki.

Bosse: did you also put the storyboard there?

Susie: still looking for it.

Eric Miller: will post it to the wiki and the link the IRC.

Bosse: the document does not replace the previous one, but is a response to last week’s questions. It has more concrete details. Eric, Chris and Bosse met and came up with more concrete details. The aim is to demo two different cases to demonstrate using the data for either research (in a pharma), or for a physician to provide better care to a patient. We won’t worry too much about legal or technical issues, stick to e-health records. Talked about GoogleHealth or MicrosoftHealth: if they can be persuaded of research value of the data, it would be valuable – future discussion. Not a brand new UI, but just enough to demo the power of TMO and the value of the data. Will start with Eric’s mock-up, then discuss within this group and finalize it into a demo for one use case If resources are available, we could go for a pilot. IF not, just another mock-up for the second use case. The new story board is easier to understand.

Chris: we changed direction while developing the mock-up. The important part is not the appearance, but to highlight the distinct uses. GoogleHealth is a good example of various functions being able to access the records for various reasons. However, the data is not easily mineable or accessible to the academic research. Microsoft also has as system which accesses data for different provision of care purpose.

Eric: people might wonder why storyboard instead of app? But this process helps break the system into ‘interaction chunks’ and differentiate between different types of usage, and understand when and how the system would be used. Once that’s clearer, we can suggest changes to EHR systems or provide req’s for researchers to use the system

Susie: what is more productive right now (talk through, read, feedback later?)

Susie: why don’t we walk through now, and send more feedback later. (http://www.squishymedia.com/client/W3CTMO/ )

Chris: each part is a moment in time of where someone is interacting with the data (‘interactive touch points’). The terminology is still imprecise. The green boxes is the process (what people are doing), the blue is the technology (implementation). #4 is slightly less specific and needs an instance of improving quality of care (access to specific trial data not available on standard EHR systems). Please provide feedback.

Action Item: everyone should read through and send feedback at the next call.

Susie: next item. Outreach. Trish couldn’t make it, but we hope to get a look at the poster to provide comments for the meeting next week. One suggestion is to put the list of names into the wiki, to make more room on the poster, and put a link to the wiki. Pharma people do need to get approval, so the link is easier and faster.

Susie: will suggest to Trish to include the link to the wiki (and all names are on the abstract) as a solution to not having enough time to get approval.

Susie. Outreach item #2. Last call we decided that a lot of paper feedback was due to the paper trying to cover too much ground in not enough detail. If we pull out the ontology info to submit to BioOntologies SIG at ISMB separately, we can include more details. Michel will do that. This leaves the original paper that can now be more focused on use cases. Perhaps we can do yet another “thought piece” paper (2 pager or so) on how semantics could play a role in various uses of health data. And perhaps we can re-submit the original paper to other places? So, do people think we should write the thought piece?

Susie: will send a copy of Susie’s latest commentary piece and other example pieces as starting points. Perhaps we can also submit to Nature Review Drug Discovery.

Action item: Chris will take the lead on the paper effort by the end of the month. If both the thought paper and the ontology details come out before the re-submit of the original paper, this might help.

Chris: the problem is that the paper is too medical for ontology/informatics people, and too technical for JAMA-type medical people. We didn’t have enough time to develop enough for both.

Susie: With more time, we can make the technical stuff (linkage, queries, ontologies) cleaner.

Susie: where else we can submit? Briefings in Bioinformatcs? BMC Bioinformatics? The Journal of Web Semantics (too IT)? Drug Discovery Today? Another re-submit to JBI? Science Journal of Translational Medicine?

Elgar: was it completely rejected?

Susie: yes, we think so, because it was a special issue. We can try to argue that we improved the paper and maybe it can go into a regular JBI issue? Kei is affiliated, perhaps he can act as an advocate?

Susie: For Nature Review Drug Discovery, we can submit the thought piece? W3C note from HCLS? (description of the work, asking for feedback from the community, then publishing as a W3C document). Probably better to be in a health-related.. Chris – thoughts?

Chris: looking for something a bit “middle of the road” – major medical journal reader will not get the technical detail.. Need a technical publication (like JBI).

Susie: Nature Drug Discovery seemed interested in the general topic – worth contacting editors by email to see if there is interest. They might have good pointers.

Susie: don’t want to make final decisions without Colin’s input.

Susie: Elgar presented TMO at CHALS 2010 last week, and there is an article in Genome Web briefly referring to TMO. However, the journalist wants to do more articles on the HCLS group.

Susie: does it make sense to keep separating LODD and TMO calls? The data and the ontologies need to be closely tied together. Everyone should think about merging the calls?

Susie: we made good progress when we had a deadline with weekly longer calls. Should we go back to weekly calls?

Question: if we merge calls, we can use the Wed slot (easier for Europeans and not in conjunction with the Thu general HCLS call)

Susie: will discuss timing next week (also, remember the US clocks change 2 weeks before Europe).

Susie: done.