It has a glossary that could be of use (and which we could potentially 
collaborate on).  But I think we need quite a bit more for OpenTox 
ontology needs e.g., our web services, our automatically generated 
reports, REACH requirements etc.
Barry

sunil chawla wrote:
> Barry
>
> Did you see http://toxipedia.org/ that Nina surfaced......your thoughts 
> on it?
>
> Sunil
>
> Barry Hardy wrote:
>
>   
>> Dear Vladimir:
>>
>> First, thanks for the useful summary on vocabulary from our 
>> discussions in Rome.  Some feedback:
>> - I vote that our OpenTox vocabulary/ontology should be a public 
>> community resource (why keep it non-public?)
>> - We should reuse/collaborate/integrate etc. other relevent and 
>> quality ontologies (but we still will need to develop an approach that 
>> will work for OpenTox, e.g., web services implementing REACH-relevent 
>> use cases and reporting (containing vocabulary terms) etc.)
>> - We will need a review mechanism (especially for a core ontology used 
>> by OpenTox services).  As regards "management" we have an ontology 
>> working group (which could grow) and have development/curation 
>> responsibility.
>> - Whereas Plone has content management and review workflows, it is not 
>> specifically designed for ontology development and management, so we 
>> should research different alternatives against our requirements, e.g., 
>> the SW should be able to handle development, synonyms, relationships, 
>> levels, evolution...   (perhaps there are suggestions from the list 
>> based on their experiences?)
>> - Perhaps we can also have a public wikipedia style vocabulary area 
>> which has greater scope than a core ontology but contains it?  (I 
>> would like to see different views, managed hyperlinking and advanced 
>> search possible)  (Can the same SW handle this?)
>>
>> best regards
>> Barry
>>
>> new.pass wrote:
>>
>>     
>>> Dear Colleagues,
>>>  
>>> Sorry for the delay with submitting of my notes & comments on 
>>> ontology: it appears that during the past week I should do urgent 
>>> preparations for a meeting in Russian Ministry of Education and 
>>> Science. Currently this is already accomplished, and I could take 
>>> part in the discussion concerning the Ontology in the framework of 
>>> the OpenTox project.
>>>  
>>> During the discussions at our Rome’s meeting two points were 
>>> considered: (1) Controlled vocabulary; and (2) Open Toxipedia.
>>>  
>>> 1. Controlled vocabulary.  
>>> It was proposed that we have to move from model to ontology services 
>>> using the vocabulary prepared in the electronic form with special 
>>> computer programs. Question to Nina: Unfortunately I missed the names 
>>> and links to these Programs. Could you, please, remind this 
>>> information? It is reasonable to make a mapping between the different 
>>> fields and construct the correspondence between different databases 
>>> using the ECHA hierarchy of end points 
>>> (http://echa.europa.eu/home_en.asp). Biological and toxicological 
>>> ontologies should correspond to the ECHA ontology.  ToxML scheme was 
>>> suggested to be used for mapping despite it does not cover currently 
>>> all relevant issues (its development is continuing). There exists 
>>> also the Open Biomedical Ontologies (http://www.obofoundry.org/), 
>>> which experience should be taken into account.
>>> As to the chemical ontology, it was suggested that the CHEbi 
>>> (http://www.ebi.ac.uk/chebi/) experience should be taken into 
>>> account. See also the paper: Colin Batchelor (2008). An Upper-Level 
>>> Ontology for Chemistry.
>>>  
>>> 2. Open Toxipedia.
>>>  
>>> It was suggested that the terms should be arranged in alphabetical 
>>> order in addition (or instead?) the categorical order. The reasons 
>>> for that are: (1) terms in all known Wikipedias could be browsed by 
>>> an alphabetical order; (2) some terms are belonging to several 
>>> categories; (3) the comprehensive list of terms related to categories 
>>> could not be determined finally. Also, the hyperlinks between the 
>>> different terms should be established automatically, which provides 
>>> the option for user to surf between the terms. In particular, the 
>>> same approach could be also applied to general terms described the 
>>> categories, which can be used for additional arrangement of terms in 
>>> categorical order.  
>>> Question to Micha and Nina: which software could be used for the 
>>> appropriate organization of terms in Open Toxipedia?       
>>> Later, Nina sent to us the link on the Toxipedia 
>>> (http://toxipedia.org/) that is supported since June 2006. This 
>>> resource looks quite general, covering broad range of toxicological 
>>> terms. The terms are arranged in alphabetical order, and there is 
>>> also a possibility to search for certain items using Boolean queries. 
>>> This resource could be used for creating the Open Toxipedia as a 
>>> collection of terms with the explanations, jointly with many other 
>>> relevant Internet resources.
>>>  
>>> ADDITIONAL QUESTIONS, WHICH REQUIRE THE ANSWERS.   
>>> 1. What should be the content of the OpenTox Toxipedia, which 
>>> differentiate it from many other similar resources in the Internet?   
>>> - From my point of view, we have to concentrate on Chemical Safety & 
>>> Predictive Toxicology issues. 2. Are we going to make Toxipedia a 
>>> public resource, where any (registered?) user can add new terms & new 
>>> categories, and edit the existing explanations?   - If “yes”, we have 
>>> to provide the appropriate service at the OpenTox web-site using the 
>>> special software. Which software could be used for this purpose? 
>>> Also, it should be somebody in the Consortium, who will work as the 
>>> “term’s administrator”. It may be either a single person (who?) or a 
>>> special team of people. 3. Are we going to make the Controlled 
>>> Vocabulary a public resource? - If “yes”, the same questions arise 
>>> (see above).
>>> 4. Are we going to give the links on the external web-resources 
>>> related to the ontology problem at the OpenTox web-site?
>>> 5. If somebody is willing to offer his service or data to the 
>>> OpenTox, who will make the mapping? This person? Somebody from the 
>>> Consortium?
>>>  
>>> Your answers, opinions and further questions are appreciated with 
>>> gratitude.
>>>  
>>> Looking forward to hear from you soon.
>>>  
>>> Kind regards,
>>>  
>>> Vladimir
>>>
>>>
>>>       _______________________________________________
>>> Partners mailing list
>>> Partners at opentox.org
>>> http://www.opentox.org/mailman/listinfo/partners
>>>   
>>>       
>>
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