W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2012

Meeting Record: HCLS Call - Pharmaceutical and Clinical Research 2012-02-21

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 21 Feb 2012 12:25:09 -0500
To: w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <20120221172508.GH1389@w3.org>


            HCLS IG weekly: HCLS Pharmceutical in Clinical Research

21 Feb 2012

   See also: [2]IRC log


          Vijay Bulusu



     * [3]Topics
         1. [4]Vijay introduction
         2. [5]Systems Biology for Drug Discovery
         3. [6]Pharmacogenomics
         4. [7]recruitment
         5. [8]task force for rendering experimental information in an
            open manner
     * [9]Summary of Action Items

Vijay introduction

   vbulusu: work in pharma
   ... invited by ericP to chair HCLS
   ... the cochairs and ericP discussed domain-specific calls for:
   ... .. interest to industry
   ... .. task force coodination
   ... there are two TFs in this focus:
   ... .. Systems Bio, chair: Helena Deus
   ... .. Pharmacogenomics, chair: Michel Dumontier
   ... looking for new ideas and use cases for these task forces
   ... will discuss a new task force for which I'm recruiting members

[10]Systems Biology for Drug Discovery

   Helena: in Bio, many things go wrong at the pathway level
   ... e.g. signally pathway failures result in cancer
   ... so we'll look at data made available by TCGA
   ... RDF-izing the 8.3TB of TCGA is unreallistic
   ... instead we'll take data from 8 or 9 interesting proteins
   ... annotate the proteins with results [from TCGA]
   ... we need to look for TCGA resources and extract the 8 or 9 target
   ... first telco this week
   ... at the beginning, we'll be recruiting participants
   ... i've heard lots of interest

   vbulusu: who do you have alread?

   Helena: Jun Zao, ericP, Michael Miller (Institute for Systems Bio)
   ... hoping to recruit more bioinformatisists (as opposed to computer

   vbulusu: overlap with Sylventa's [11]BEL Framework?

   Helena: there's a lot of overlap. expect to use their vocabs
   ... they're not annotating experimental data as far as i know
   ... michel demo'd SBML last week. should be relevent

   ericP: Ted Slater described thinking of BEL in terms of a surface
   syntax for RDF

   ACTION: ericP to connect Ted Slater to Helena [recorded in

   ACTION: ericP to connect Dave Hau to Helena [recorded in

   mscottm2: Sylventa said they wanted to put BEL forward as a standard.
   have they come to W3C?

   ericP: they spoke about the openness in a presentation at the Cambridge
   Semantic Web Gathering

   Helena: my current wiki page is about recruitment
   ... people in this group expect to work bottom-up
   ... people say what they expect to achieve

   michel: would like to see some structure, expected outcomes

   Helena: i can add vision and goals to the wiki

   vbulusu: adding the members will help
   ... do you need pharma folks?

   Helena: desparately

   vbulusu: bioinformatics and systems bio focus?

   Helena: the bioinformatics is just how to glue stuff together
   ... exploring our models to see if we can learn stuff about the biology

   ACTION: vbulusu to recruit in pharma for Systems Biology for Drug
   Discovery [recorded in

   michel: IO-Informatics might be interested

   Helena: will reach out to Eric Gombocz


   michel: we'll be looking at data related to pharmacogenomics
   ... e.g.
   ... .. patient stratification
   ... .. risk assessment
   ... .. dosing
   ... gathering related data, e.g.:
   ... .. clinical trial outcome
   ... .. efficacy
   ... we can marshal data from e.g. PharmGKB, or clinical trial
   ... wherever we can map genotype to phenotype
   ... idea is that we have a pharmacogenomics KB
   ... i got clinical annotation from PharmGKB
   ... PGKB license issue:
   ... .. you need to apply for access
   ... .. you can't redistribute
   ... maybe we can negotiate, but barring that, we can make available the
   [triplifying] scripts
   ... we want to ask questions of the KB, with inference
   ... will support Clinical Decision Support
   ... we have folks from:
   ... .. mayo clinic
   ... .. variety of academic institutions
   ... missing industry, e.g. those interested in clinical trials or FDA
   [,EMA] submissions, adverse event reporting

   vbulusu: looking at use cases, have you looked at how to select a
   smaller set of use cases?

   michel: this [wiki] list is from the relevent TMO use cases
   ... some from IO-Informatics, and mscottm2 had breast cancer use cases
   ... so yes, we need to identify a small set
   ... potentially, each individual can set up a use case which drives
   their personal interests
   ... i expect significant overlap due to the paucity of data
   ... gene expression, DBSNP, performance of (anti-rejection) drugs

   ericP: feel free to be a tyrant

   vbulusu: pharma focused on precision medicine
   ... mostly these folks would be interested in joining the HCLS
   community where it can give them quick answers


   michel: we can ask industry what they need done, and peridically get
   sanity checks
   ... but in the end, we want assurances of adoption

   mscottm2: great if you can find someone in a hospital or pharma setting
   who's not expecting a shrink-wrapped solution
   ... get them to bring us interesting problems
   ... most folks in those settings don't see the prob with working in
   monolithic applications

   <mscottm2> someone who can bring a problem for us to solve and become a
   sort of 'client'

   Helena: have you looked at pharmacoglycomics?

   michel: looked at some sugars when i was an undergrad
   ... know folks at bioCanada who look at e.g. qualitiy of peptides ...

   Helena: if you know the glycosylation pattern, you can predict binding

task force for rendering experimental information in an open manner

   vbulusu: in 2009, [15]Pistoia started an Electronic Lab Notebook
   working group to exploit the info captured in (different) ELNs
   ... also to share info in the pharma with other organizations
   ... looking at what they've done, they worked for a year trying to
   create ELN standards so that e.g. CambridgeSoft data could work with

   vbulusu: they stopped in early 2011 when some members didn't adopt and
   proposed standards
   ... need is still out there.
   ... pharmas need to exchange with Clinical Research Organizations
   ... every pharma will say they need standards in this space
   ... expect to start with medicinal chemistry, not biology

   <mscottm2> ericP: access control in ELN for example for CROs, capture
   somethings in BEL framework.

   [16]strawman research pipeline document


   michel: met Jeremy Fray (S'Hampton) has been working on chem lab
   ... he's got a representation for synthetic chemistry
   ... track whether you are doing stuff in the right order, and what are
   the values you're obtaining

   <mscottm2> Michel mentions Peter Murray-Rust / Cambridge (Open
   Knowledge Foundation) in the context of patents

   michel: Peter Murray Rust validates patents by seeing if the chemical
   processes follow a single transformation

   vbulusu: looked at Rust, and Jeremy's work is definitely in line. good

   michel: i don't think Jeremy focuses on inferencing; just capture for
   later SPARQL query
   ... BEL may be more focused on inferencing

   a(foo) upregulates b(c(bar)) .

Summary of Action Items

   [NEW] ACTION: ericP to connect Dave Hau to Helena [recorded in
   [NEW] ACTION: ericP to connect Ted Slater to Helena [recorded in
   [NEW] ACTION: vbulusu to recruit in pharma for Systems Biology for Drug
   Discovery [recorded in

   [End of minutes]

    Minutes formatted by David Booth's [21]scribe.perl version 1.136
    ([22]CVS log)
    $Date: 2012/02/21 17:22:00 $


   1. http://www.w3.org/
   2. http://www.w3.org/2012/02/21-HCLS-irc
   3. http://www.w3.org/2012/02/21-HCLS-minutes#agenda
   4. http://www.w3.org/2012/02/21-HCLS-minutes#item01
   5. http://www.w3.org/2012/02/21-HCLS-minutes#item02
   6. http://www.w3.org/2012/02/21-HCLS-minutes#item03
   7. http://www.w3.org/2012/02/21-HCLS-minutes#item04
   8. http://www.w3.org/2012/02/21-HCLS-minutes#item05
   9. http://www.w3.org/2012/02/21-HCLS-minutes#ActionSummary
  10. http://www.w3.org/wiki/HCLSIG/SysBio
  11. http://selventa.com/technology/bel-framework
  12. http://www.w3.org/2012/02/21-HCLS-minutes.html#action01
  13. http://www.w3.org/2012/02/21-HCLS-minutes.html#action02
  14. http://www.w3.org/2012/02/21-HCLS-minutes.html#action03
  15. http://www.pistoiaalliance.org/
  16. http://www.w3.org/2012/hcls-resources/pipeline.svg
  17. http://www.sciencedirect.com/science/article/pii/S1359644609000737
  18. http://www.w3.org/2012/02/21-HCLS-minutes.html#action02
  19. http://www.w3.org/2012/02/21-HCLS-minutes.html#action01
  20. http://www.w3.org/2012/02/21-HCLS-minutes.html#action03
  21. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  22. http://dev.w3.org/cvsweb/2002/scribe/
  23. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
  24. http://www.w3.org/2012/02/21-HCLS-minutes.html
  25. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm

Received on Tuesday, 21 February 2012 17:25:45 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:21:05 UTC