Re: [Obi-coord] [Obi-devel] Bio-ontology SIG paper

[Bjoern P. <bp...@li...>]

I am all in favor of such a submission, but it worries me that two of 
the examples chosen ("vaccine challenge assay" and "Decision processing 
in the caudate nucleus") are not currently in OBI. I think it will be 
important to run the modeling of these experiments past the entire group 
before including them as examples for OBI in the manuscript. Otherwise 
we will confuse people if we contradict our own examples.

Would one example = (blood glucose measurement) be enough?

- Bjoern




ls...@ab... wrote:
> Hello everyone,
>
> I would like to let you know the current situation with the paper for
> Bio-ontology SIG/ ISMB.
>
> The volunteers (Oliver, Allyson, Alan, Dirk, James, Larisa ) had a vote:
> option 1 - prepare 4 pages using the material from the main paper. Such a
> paper will be considered as unpublished.
> option 2 - prepare 4 pages about some interesting aspect of OBI, but try
> not to intervene with the main paper. Hope for a journal publication.
>
> The option 2 has won 6:0.
>
> We think that a paper about modelling of experiments would be interesting
> and useful for the intended audience.
>
> We have agreed on an outline (see below, some minor changes are still
> possible). Currently we are assigning responsible people for the sections.
> James and Melanie will be reviewers.
>
> Larisa
> --------------------------------
> Title: ??? The modelling of experiments with OBI
>
> Authors: the OBI Consortium
>
> 1.Introduction [ but not too much of it so we do not interfere with the
> main paper.]
>
> BFO - OBO - IAO - OBI (Larisa, Dirk)
>
> Project goals (Larisa, Dirk)
> ??? Comparison other ontology projects (too domain specific, not easy to
> combine with other formalisms, not great for inference) (Larisa)
> current status (Larisa)
>
> 2.UC
> The modelling of experiments in OBI. Go through the main classes (showing
> versatility)
> Example 1: The blood glucose measurement with detailed explanations. Fig.
> 1 ? Alan?s updated diagram.(Alan)
> ??? Example 2: vaccine challenge assay (by Oliver) with brief
> explanations. (Oliver)
> ??? Example 3: "Decision processing in the caudate nucleus" (Dirk)
>
> discuss some interesting problems, explain solutions.(through examples?)
>
> 3. Conclusion and discussion. Mostly about future work and how such
> descriptions of experiments can be used.
>
>
>
>
>
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-- 
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters