Hello:

This is Asish from Calgary and a new member to the Open tox community. I am
associated with Toxipedia and World Library of Toxicology. Recently, I
authored a book with Steve Gilbert of Toxipedia, Phil Wexler and Bert
Hakkinen of NIH-NLM. If you want any information related to Toxipedia,
please let me know. I can forward them to Steve or ask Steve directly to
talk to you about potential collaborations (if any).  Some of my current
collaborative project are in the applied areas of computational toxicology,
toxicity data integration, data fusion for health risk assessments. I am
also interested in semantic web applications in these areas.

Sincerely,

Asish Mohapatra, MSc, MPhil (pre-doctoral), EMC, Risk Cert. (Harvard)
Regional Health Risk Assessment and Toxicology Specialist (Alberta Region)
Contaminated Sites Division (CSD), Safe Environments Directorate (SED)
Regions and Programs Branch (RAPB), Healthy Environments and Consumer Safety
(HECS)
Health Canada
Suite # 282, 220-4 Avenue SE (Harry Hays Building)
Calgary, Alberta, Canada
T2G 4X3
Tel: 403-221-3284
Fax: 403-221-3422
Email: asish_mohapatra at hc-sc.gc.ca

On Wed, Oct 7, 2009 at 10:47 AM, sunil chawla <sunil at seascapelearning.com>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
> >>
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >Development mailing list
> >Development at opentox.org
> >http://www.opentox.org/mailman/listinfo/development
> >
> >
>
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>