(only to the Blue Obelisk and OpenTox mailing list)

Hi Barry,

On Tue, Oct 26, 2010 at 8:05 PM, Barry Hardy
<barry.hardy at douglasconnect.com> wrote:
> I also think there is a great current opportunity to connect some of your
> work, CML, CDK, Blue Obelisk initiatives, Bioclipse etc. with the new
> OpenTox initiative and we have the possibilities to make "quite startling
> progress" in coming months.

Yeah, a lot pieces are coming together...

> But we must also critically link OpenTox with
> pathways, systems biology and bioinformatics too, at least for supporting
> the growing integrated service and analysis needs of advancing the field of
> predictive toxicology.

Indeed... bioinformatics and cheminformatics are not enough integrated yet.

> How do we best leverage current knowledge and methods with regards to
> biological pathway analysis to design improved approaches to predictive
> toxicology that increase our ability to characterise the potential of
> chemicals to cause adverse human health effects and including an
> understanding of mode of action, mechanisms involved in the mode of action
> and the interaction of biological entities, pathways and networks in the
> perturbations introduced by the chemicals?/

I think two major aspects here are:

* linking the pathway databases back to literature
* quality improvement of these databases

Work is ongoing in these areas, but need tighter linking to cheminformatics...

<snip>

> So we really have a Grand Interoperability Challenge almost demanding the
> benefits of a consensus-based Open & Public
> Standards/Ontology/Dictionary/Source/Data/Access approaches.  (All the good
> stuff Peter has been driving for in cheminfo for many years!!)

Open Standards play a key role here. Both CML and OpenTox have done
great things here.

> We ("OpenTox & Partners") are organising some workshop activity near
> Cambridge at EBI 15-17 November to discuss interoperability, data exchange
> standards, public ontologies, and a collaborative ontology development
> roadmap for the field of predictive toxicology.  In addition to good science
> & engineering, there is also an increasingly strong business case driver, so
> we also have the collaboration and involvement of the EBI Industry Forum and
> Pistoia Alliance.  We will also communicate outcomes aggressively with
> policy makers and program designers. Quo Vadis R&D progress and success in
> such scientific challenges without community, flexible infrastructure and
> interoperability?

I will be in the area, and if people like to talk about Oscar, please
let me know.

Predictive toxicology is one area that can benefit from text mining,
and I hope I can help the opentox community start Oscar and other
tools developed in Cambridge at some point.

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers