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
>>
>>
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>
>
>
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