HCLS IG weekly: HCLS Pharmceutical in Clinical Research

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

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 proteins
... 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 geeks)

vbulusu: overlap with Sylventa's 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 http://www.w3.org/2012/02/21-HCLS-minutes.html#action01]

ACTION: ericP to connect Dave Hau to Helena [recorded in http://www.w3.org/2012/02/21-HCLS-minutes.html#action02]

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 http://www.w3.org/2012/02/21-HCLS-minutes.html#action03]

michel: IO-Informatics might be interested

Helena: will reach out to Eric Gombocz

Pharmacogenomics

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

recruitment

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, 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 Exceleris

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.

strawman research pipeline document

<michel> http://www.sciencedirect.com/science/article/pii/S1359644609000737

michel: met Jeremy Fray (S'Hampton) has been working on chem lab notebooks
... 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 connections

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)) .

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Found ScribeNick: ericP
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WARNING: No "Present: ... " found!
Possibly Present: Bosse Helena IPcaller achille_z ericP matthias_samwald matthias_samwald1 michel mscottm2 scribenick vbulusu
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Got date from IRC log name: 21 Feb 2012
Guessing minutes URL: http://www.w3.org/2012/02/21-HCLS-minutes.html
People with action items: ericp vbulusu