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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