HCLSIG BioRDF Subgroup/Meetings/2007-11-12 Conference Call

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Conference Details

  • Date of Call: Monday November 12, 2007
  • Time of Call: 11:00am Eastern Time
  • 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: 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: Jonathan Rees

Agenda

  • Review of F2F meeting
  • Meeting Updates (SfN, ISWC BOF, WWW2008) - Susie
  • URI note - Jonathan
  • Knowledgebase extensions - Alan
  • Clinical data set assessment - All
  • AOB

Minutes

  • Don [Don@70.20.65.111] has joined #biordf
  • <Susie> Regrets from Jonathan, Alan, & David
  • mscottm [marshall@81.69.36.208] has joined #biordf
  • matthiassamwald [a@85.127.78.35] has joined #biordf
  • <Susie> Review of F2F meeting.
  • <Susie> F2F meeting agenda: http://esw.w3.org/topic/HCLS/F2F/2007/11/Agenda
  • <Susie> 40 people at the meeting
  • BillBug [chatzilla@69.242.28.112] has joined #biordf
  • <Susie> The first day focused on the Clinical Observations Interoperability task.
  • <Susie> EricN and Tonya started the meeting with a high level overview.
  • <Susie> Vipul then described our interest in COI.
  • <Susie> Rachel then gave a good overview of the use case.
  • <Susie> Tom Oniki (GE), Chimezie (Cleveland Clinic) and Chintan (Columbia) presented on their work.
  • <Susie> Finished with a round table where folks indicated their level of support and resources that they could contribute to the task.
  • <Susie> Scott: Aligning ontologies / terminologies were identified as a bottleneck in many presentations.
  • <Susie> Scott: this was in the area of the clinical medical records.
  • <Susie> Scott: May make sense to talk to RIF about some of the practical issues of KR.
  • <Susie> Scott: Adrian P is a member of HCLS and RIF.
  • <Susie> Scott: Need a rule interchange format as identified by Scott, Chimezie, Adrian, Vipul
  • <Susie> Scott: SWRL fits into this nicely.
  • <Susie> Scott: Rule discussions were primarily done during the coffee breaks, as not part of the formal agenda.
  • <Susie> Scott: Co-locating a RIF F2F with a HCLS F2F would be interesting.
  • <Susie> Scott: Think Chimezie uses the Fuxi rule language.
  • <Susie> Scott: COI focused on presenting what has been done, rather than discussing which approach is best.
  • <Susie> Scott: No direct mention of UMLS, although other terminologies/ontologies were mentioned.
  • <Susie> Scott: FAO have got help from people at ISWC to align food ontologies.
  • <Susie> Susie: This has been written up as a SWEO use case.
  • <Susie> Day 2 started with a brief welcome from EricN and Tonya, and then moved to reviews of the groups.
  • <Susie> Susie presented on BioRDF. Described progress against the initial charter.
  • <Susie> Chimezie presented on the rule work that he has done in the ACPP group with Helen.
  • <Susie> EricN presented on the DSE work that he has been doing with Pfizer, AstraZeneca and others. He showed nice results of integrating genetic information with clincial information in Exhibit.
  • <Susie> Vipul the work that was undertaken in BIONT, and the move towards the COI task.
  • <Susie> EricP gave an overview of where we are in the charter process.
  • <Susie> He described how the group created a questionnaire to solicit feedback.
  • <Susie> He discussed how feedback was gained from over 70 people.
  • <Susie> The questionnaire was qualitative, but a scheme was used to convert feedback into a numerical system for analysis.
  • <Susie> Feedback was compared for pharma vs health care vs academia vs vendor. Results were also compared for those who are current members vs those who aren't vs all responders.
  • <Susie> It was clear that were 3 groups of responders, namely, academia, pharma, and HC.
  • <Susie> Co-chairs for the next group have been selected who have strengths in all of these areas: Alan Ruttenberg, Susie Stephens, Chimezie Ogbuji.
  • <Susie> Results also highlighted a need for a stronger focus on outreach, and EricN will take that role.
  • <Susie> Bill: Many academics interested in links between genetic data and the clinic.
  • <Susie> Bill: Many are interested in semantic integration of data, including comparing mouse and human.
  • <Susie> Susie: The 3 chairs will work together in all areas, as we recognize the importance of linking between genetic information and the clinic.
  • <Susie> Susie: There was some discussion of the CTSA grants at the meeting too.
  • <Susie> Alan gave an overview of the KB, and also discussed his approach for designing ontologies.
  • <mscottm> Alan mentioned wanting to look at OWLIM http://www.ontotext.com/owlim/big/index.html
  • <Susie> TN Bhat presented on INCHI.
  • <Susie> Jonathan presented on challenges with URI, ways to overcome them, and recommendations for minting URIs.
  • <mscottm> From Jonathan's presentation (for a chuckle): http://www.thenewyorkerstore.com/product_details.asp?mscssid=17QPRB0R3MS68L95JT1W2NDRNSTJ41JB&sitetype=1&did...
  • <mscottm> http://www.iscb.org/cshals2008/#
  • <Susie> Don: 32,000 folks at the SfN meeting.
  • <Susie> Don: It was an especially good meeting for informatics.
  • <Susie> Don: We had our poster on Saturday.
  • <Susie> Don: We had a steady stream of interest.
  • <Susie> Don: About 20% of folks from Library Sciences
  • <Susie> Don: Most were bench neuroscientists.
  • <Susie> Don: They were interested to see that we could query across databases.
  • <Susie> Don: They want to know how they can use it on a day to day basis.
  • <Susie> Don: They want a nice interface.
  • <Susie> Don: A lot of people wanted to know how they can keep up with what's going on/
  • <Susie> Don: We should be getting some people lurking on the web site, and maybe even joining in.
  • <Susie> Bill: Don got quite a lot of traffic, especially compared to bench science related posters.
  • <Susie> Don: Too much going on to see everything, even in informatics.
  • <Susie> Bill: Ongoing effort called PubMedPlus.
  • <Susie> Bill: NIH bringing folks together to talk about new publishing approaches.
  • <Susie> Bill: Aim to minimize work, and turn around time for the 'bibliome'
  • <Susie> Bill: More community work needed around minimal metadata, like MIAME for instance
  • <Susie> Bill: Possibility of shared reviewing knowledgebase across journals
  • <Susie> Bill: How do we deal with all of the supplementary material.
  • <Susie> Bill: 9 supplementary articles with 2 page nature document on Allen Brain Atlas last year.
  • <Susie> Bill: EricN, EricM, John Wilbanks are involved in this effort.
  • <Don> http://www.newsweek.com/id/68221
  • <Susie> Don: Andy Grove (former Intel CEO) did a critique of LS
  • <Susie> Don: Covered NIH and current motivating factors.
  • <Susie> Don: He talked about information life cycle
  • <Susie> Don: And how new information get incorporated quickly into chip design.
  • <Susie> Don: This needs to happen in life sciences.
  • <Susie> Don: Andy Grove has been diagnosed with Parkinson disease which clearly gives this topic immediate and very significant importance to him.
    • Andy Grove's talk at the SfN 2007 meeting
    • <BillBug> His take home message is there really needs to be significant effort invested in altering the organization/management of research grant awards and research project organization to make more rapid progress in both directing and integrating basic research studies with the disease treatment needs out there in the population. This is obviously a plea for more effective translational research direction. When asked specifically whether Pharma does it better than government funded projects, his answer was no, since their primary goal of making a profit doesn't always coincide with providing the best and most rapid Rx to the diseases that cause the most damage to individuals and society. From the POV of maximally leveraging the power of the $$$$ they invest in biomedical research, he felt there was also significant waste in the pharmaceutical industry as well.
  • <Susie> Don: Expect to see more people from Michael J Fox foundation
  • <BillBug> Michael J Fox Foundation (MJFF) for Parkinson's Research - article by Michael J. Fox "Who's Finding the Cures?"
    • Michael T. Rogan (Associate Director, PD Research Consortium and the Research Programs Director for the MJFF) I believe was the person Don spoke with and who came by the BIRN booth at the SfN meeting
    • If you read the MJFF material - and look at some of the efforts they are funding - you get the sense - just as with Andy Grove's plea - their focus is on improving our ability to translate research findings into a relevant clinic context - AND - on better directing basic research projects to more immediately serve the needs of treating disease (in their case, Parkinson's Disease).
  • <Susie> HCLS BOF agenda at: http://esw.w3.org/topic/HCLS/ISWC2007/BOF
  • <Susie> Although take up was initially slow, it looks like the meeting will go OK.
  • <Susie> We have 12 folks signed up to participate so far, and we should get more as the BOF is listed in the conference program.
  • <Susie> We have 5 very interesting presentations lined up.
  • <Susie> Progress is being made on the HCLS workshop at WWW.
  • <Susie> The CFP has been written. A PC has been selected. We have a list of mailing lists to reach out to.
  • <Susie> We also have a Web page at: http://ccnt.zju.edu.cn/hcls2008/index.php?title=Main_Page
  • <Susie> A tutorial proposal has been submitted to WWW.
  • <Susie> It'd be very good if this is accepted, as it will encourage us to write up detailed notes on the construction and use of the KB.
  • <Susie> It's important to be aware of conferences, so that we can present, participate, and feedback news to the group.
  • <Susie> Please add conferences we should participate in at: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Conference_Possibilities