[MOBY-l] Re: BIoinformatics Protocols Ontological KnowledgeBase?

[Elia Stupka]

Hello all,

> What you're talking about is an ontology of bioinformatics services.

So sorry I didn't explain myself clearly... while I will be happy to help
with Moby and MyGrid, we were no talking about bioinformatics services but
prtocols A-Z to achieve X. To make it clearer bioinformatics services would
be yet another way to do point C in the *protocol* but not the protcol
itself.
What Shawn and I were really hoping to establish was a resource of
scientific protocols in bioinformatics, e.g. Wolfe published a method of
building gene families which can be abstracted into a series of programs and
parameters, that is the sort of protocol we were talking about. It doesn't
matter whether I do my blast locally or via a Moby-enabled service....
unless I have misunderstood Moby I didn't think at the moment it was aimed
at capturing complex bioinformatics protocols but rather at becoming a
standard for providing services... the same goes for MyGrid, as far as I
understand....

That is why we found that the connection would work well with a book such as
current protocols, because it is really about a review of scientific methods
used in research. With the difference that developing a service ontology,
input data ontology and reusing SO one can better define the protocol and
make it "executable" with a bit of BioPipe magic on top of the ontology.

> This is  similar to what we've been talking about for MOBY, and also
> similar to the  (much more ambitious) MyGrid project.

Again, correct me if I am wrong but I think these are all about *services*.
  I definitely agree both BioMoby and what we are trying to propose will
need to work off an ontology system on which we can work together.

> As far as the connection to Current Protocols goes, I'm on the
> editorial board  at Current Protocols in Bioinformatics, and can
> introduce the idea of a  relationship at the next board meeting on June
> 13.  Do you think you might  have a concrete proposal or discussion
> paper ready by then?

I think we can put something together by then with Shawn, but before we
start, hoping that now I clarified what the intent is, I would still like
some feedback to see what others think of it...

Elia

-- 
Bioinformatics Program Manager
Temasek Life Sciences Laboratory
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