Dear Colleagues,

Alexey told me about your "local" web-meeting today, and I would like to 
make two principal comments.

1. When we are talking about terms related to the  "OpenTox" area, we have 
to keep in mind that this is really an open space. A new terms will arize 
permanently, particulartly due to the results of postgenomics studies. Some 
of the terms will be related to the multiple categories, and in many cases 
it will not be easy to define the categories at the moment when the term is 
added to the Toxipedia. Therefore, it seems reasonable to organize the input 
of new terms in alphabetical order with simultaneous (or subsequent) 
categorization. As I understand from Alexey, this is already realized 
through the belonging of terms into the "collections", isn't it?

2. If we would like to organize the terms in Toxipedia like it is realized 
in Wikipedia, we have to arrange an automatic indexing of terms in the 
sentences described their meaning with the hyperlinks to the appropriate 
descriptions of the terms, which already included into the Toxicopedia. For 
example, explanation for "Accute hazard" is written as:

"Acute hazard is assessed using observations of accidental human exposures 
or by conducting LD50 tests on experimental animals, usually rodents."

Probably, hyperlinks should be provided at least for such terms as "human 
exposure", "LD50", "rodents".

Certainly, such hyperlinks should be also arranged for the terms that were 
added into Toxipedia earlier if the new terms are related to them.

Yours comments are appreciated with gratitude.

Kind regards,

Vladimir

Vladimir Poroikov, Prof. Dr.
Head of Bioinformatics Department
Head of Laboratory for Structure-Function Based Drug Design
Institute of Biomedical Chemistry of Rus. Acad. Med. Sci.
10, Pogodinskaya Str.,
Moscow, 119121,
Russia
Tel.: +7 499 246-09-20
Fax: +7 499 245-08-57
E-mail: vladimir.poroikov at ibmc.msk.ru


----- Original Message ----- 
From: "Micha Rautenberg" <mr at mrautenberg.de>
To: "opentox development mailing list" <development at opentox.org>
Sent: Monday, November 30, 2009 2:40 PM
Subject: [OTDev] OpenToxipedia Platform suggestions


> Dear All,
>
> as the Plone-based Content Management System on opentox.org will not
> cover every need for OpenToxipedia and the OpenTox ontology, we think
> about use an other software platform.
> some of the main features should be
> - easy usability (or maybe common like wiki-based software)
> - possibility or interface for data-exchange between OpenToxipedia and
> the OpenTox ontology
> - OWL support (import, export)
> - and at least everything an ontology needs
>
> For discussion and in addition to Nina's list of existing ontologies
> (http://www.opentox.org/dev/apis/api-1.1/feature_ontology/ontologies_existing/onto_list)
> I had a short look into the Semantic MediaWiki, which is an extension to
> the  MediaWiki platform used for Wikipedia.
>
> http://semantic-mediawiki.org/wiki/Semantic_MediaWiki
>
> There are some examplary ontologies based on the Semantic MediaWiki
> NeuroLex - the Neuroscience Lexicon
> http://neurolex.org/wiki/Main_Page
> and
> BiomedGT Collaborative Ontology Development Wiki
> http://biomedgt.nci.nih.gov/wiki/index.php/Main_Page
>
> Has anybody some experiences with this platform? Other suggestions?
>
> best,
>
> Micha
>
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