Dear Vladimir, All:

On 1. At least as a first draft process to kick off discussion, we could 
work like this:
a. we place no restriction on the entry of a term and its definition 
within the context of the community based vocabulary development, i.e., 
the entrant solely needs domain knowledge of the term and definition 
context alone (I know and can define the meaning of "reconstructed 
epidermis" within then context of the EST-1000 assay, but may have no 
idea how OpenTox classifies such an assay e.g., IS A A [in vitro -> skin 
-> corrosion] and IS A B [ECVAM -> validated  - > 2009, ... etc.])
b. if such a term entrant has some knowledge of the ontology hierarchy 
and relationships, they could optionally specify classification and 
relationship information, "IS A A" etc.
c. Certain activities not done during activity b, could be added as part 
of the "vocabulary curation" process, e.g., addition of synonyms, links 
to other terms, definition corrections and clarifications...
d. Certain activities not done during activity b, could be added as part 
of the "ontology development" process, e.g., mapping to concept 
hierarchy and level, introduction of predicates, or possibly 
introduction of new concept in tree for brand new assay or artificial 
organ etc.

There may be other processes that work better/improvements 
(suggestions?), but we should at least reflect on and agree such a 
process, and taking practices and experiences elsewhere into account.

Even if new concepts and relatinships are introduced over time, I 
suspect it is also key that we should first define the intial high level 
concepts and scope for both the vocabulary and ontology work, and then 
start mapping out the relationships to lower levels and and links to 
neighbouring ontologies and initiatives.

Collections within Plone could be used to provide multiple views e.g., 
across different ways to classify in vitro assays. However I suspect 
this may not be worth putting effort into, as we should move the 
vocabulary work asap over to a more appropriate tool such as the 
Semantic Media Wiki one Micha is looking at.  (Anyone have experience on 
any import/export difficulties/restrictions between Rest Services, SMW 
and Protege?)

2. looks straightforward at first sight to me, but again, perhaps 
someone with prior experience can guide on what worked well for 
them/what did not with recent SMW projects such as those pointed out by 
Micha.  An area for ... go research more, setup a trial sandbox for us 
to play with in coming days...!?

Barry


Poroikov V.V. wrote:
> 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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>> http://www.opentox.org/mailman/listinfo/development 
>>     
>
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