HCLSIG/PharmaOntology/Meetings/2010-01-21 Conference Call

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Conference Details

  • Date of Call: Thursday January 21 2009
  • 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


  • Ontology Update
    • TMO changes - Colin
    • Drug Ontology report - Colin
  • Other updates
    • Structuring inclusion/exclusion criteria - Michel
    • Mapping drug codes - Michel
    • UI discussions - Chris
  • Outeach
    • AMIA TBI update - Susie
    • JBI paper - Colin
    • CSHALS - Elgar
    • BioOntologies SIG - Susie
    • UPenn Translational Medicine - Chris
  • AOB


Attendees: Rich, Colin, Joanne, Matthias, Elgar, Chris

Apologies: Michel, Bosse, Eric

<jluciano> colin update on status of ontology

<jluciano> re: clinical part of the ontology (ifomis)

<colin> ifomis saarbruecken

<colin> mattias brochhausen

<jluciano> I heard that Barry needs to reconnect with Barry Smith and company

<jluciano> there's an ongoing discussion about symptoms

<jluciano> colin needs the sparql endpoint for symptoms

<jluciano> it's not yet clear to colin how symptoms are represented

<jluciano> and the triple store -

<colin> http://tm.semanticscience.org/sparql

<jluciano> Colin is seeking to understand how Michel stored patient data in the triple store so that he could have conversations with Barry Smith and Ifomis

<jluciano> Biomarker data would be very helpful. Susie said it is there within the medical record, SNPs and individual gene varianants.

<jluciano> Cytochrome p450, for example is used for Warfin dosing

<jluciano> There was one patient who suffered side effects in the data, but that may not be enought to incorporate the notion of side effects driven by the data (colin said this would be data driven)

<jluciano> Elgar wrt whre to go next: barry smiths work in

<colin> OGMS

<colin> http://code.google.com/p/ogms/source/browse/trunk/src/ontology/ogms.obo

<colin> http://code.google.com/p/ogms/source/browse/trunk/src/ontology/ogms.owl

<jluciano> barry smith's - a specific group

<jluciano> It's not clear yet how the drug ontology is related to the queries - need to invest time in coordiate the integration

<jluciano> because of the time constraints, we didn't use the ontology as much as we would have liked in the paper. Michel is mapping terms that we used with RxNorm which will help us use the ontology more

<jluciano> Michel is traveling now

<jluciano> Elgar will be presenting at CSHALS

<jluciano> and as it is a month away, considering a call in the interim

<jluciano> will pick this up beginning

<jluciano> of month

<jluciano> Elgar will reach out to set up a meeting and susie will use the mailing list to inform others who may be interested in joining.

<colin> Albert G-ldfain

<jluciano> Discussing whether to invite someone from Barry's group (name above)

<jluciano> I think it will be useful.

<jluciano> I do too

<jluciano> Colin will take this as an AI to contact Albert for next call

<jluciano> Colin's not heard back about the paper

<jluciano> As pharmas are moving to more cooperation among them, there appears to be a need for a drug ontology.

<jluciano> Colin's researched looking for a public drug ontology

<jluciano> Mereology that the Spanish Drug Industry is using - Seems to be a bit more like RxNorm

<jluciano> The TMO paper cited the Neon ontology

<jluciano> ChEBI - lots of useful vocabulary in exactly that space (drug)

<jluciano> They would be willing to add further terms

<jluciano> For example - small molecules and things small molecules do -

<jluciano> eg. being a solvent, an acid or down regulates nervous sys act

<jluciano> what's missing is the mapping to GO but that mapping is clear how to be done

<jluciano> Pharmas looking for a standard way to exchange drug info - e.g. compound because freeing up IP that's sitting on their shelf - setting up a co-development/partnership would have probably filed a patent on it already

<colin> ChemBL

<jluciano> so info about chemcial structure and high througpt screening and strucure activty --- colin says alot covered already

<jluciano> and will be beefing it up because of ChemBL

<jluciano> ChEBI small molecules

<jluciano> --> i'm also wondering about the pistoia group

<jluciano> pistoia - possible area where they can work together precompetitively and are interested in data standard definition

<jluciano> Scott and Eric had a call with them re: areas of alignment. one area is the ontology - they would put their requirements in a doc and share with us. we tend to be more techy

<jluciano> looks like there is interest in collaborating - susie reports

<jluciano> there is some concern among the stakeholders to keep the shared work in the precompetitive space

<jluciano> it woudl be easy in the semweb to keep private bits within extension

<jluciano> feeling "yesterday" was that RDF's time had come

<jluciano> now involved with PRISM (new blood). Looking into areas they should be focused and are interested in data standards (they wouldn't create themselves) but would want to be aligned with to enable the standards to be developed

<jluciano> Next steps in a drug ontology: given ChEBI exists, should we work to extend? Yes, we need to identify areas that are not already covered.

<jluciano> Need to understand the recommendations Colin is suggesting... those thoughts are in the PDF Colin sent to Susie

<jluciano> >> u Pitsberg NDF-RT

<jluciano> multiaxial class hierarchy

<jluciano> Been adopted by FDA (VA NDF-RT)

<jluciano> there's an owl version and other formats

<jluciano> we need to check this out

<jluciano> Susie suggests Rich give an overview and Colin of ChEBI - they accepted

<jluciano> Another area Susie suggests - if primary use case is to share info around compounds, then we need to list the specifics of the info captured and shared.

<jluciano> which then can be compared by (VA?) and ChEBI to see which one would be better to extend

<jluciano> also - how implemented? are they using a consistent upper ontology?

<matthias_samwald> OWL version of NDF-RT: http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT_OWL_Inferred.zip

<jluciano> Chris Domarew - will upstate meeting with Eric and Bosse

<jluciano> Susie askes Elgar to include what AZ would want to share

<jluciano> Chris said that they are creating a google doc descrbing a web-based interface. looking to determine whetehr to use an existing system or something new

<jluciano> Summer or Fall may be able to trial or roll out something

<jluciano> currently in brainstorming mood

<jluciano> AMIA was acceped as poster, Trish taking lead, poster finished in time for Pharma's to get reviewed for legal

<jluciano> still wating on JBI paper

<jluciano> Elgar doing C-SHALS

<jluciano> Followup wiht Call with Michel to make better use

<jluciano> talking about BioOntology

<jluciano> call for papers not out yet for BioOnt SIG, but we should go for it

<jluciano> UPENN - Joanne put in inquiry, have not heard back. should pin them again

<jluciano> discussion about week vs bi-weekly

<jluciano> Re: other ISMB - susie not interested, others can go forward

<jluciano> bi weekly until end of this month

<jluciano> then weekly

<jluciano> adjourned