The Tamboti Tree Use Case (Bioclipse meets OpenTox)

While in Zululand in December working on conservation monitoring work in the bush, I learned about an interesting tree called the Tamboti Tree.  The leaves of this tree were traditionally used to cure toothache.  But it seemed like ingredients in this tree can cause severe nerve damage. For example, we were told that it was quite dangerous to use its wood in a fire, as inhaling the fumes could cause brain damage, if not death.  Without such local knowledge, how would I have known that?  I could easily have just assumed this wood was like any other wood and burnt it!

 

And so this provided the seed to me for what I will call The Tamboti Tree Use Case.  In this case the individual moving about in the environment will be provided advice on such risks.  Such advice could be provided from the future distributed semantic knowledge base we would have in predictive toxicology that we have been working to develop on OpenTox.  The advice could be delivered to the individual's mobile device which would recognise this biological object and then query the knowledge base and return the risk warning.  This could apply to many other situations in the bush e.g., if you encounter a lion "don't run" or indeed many contexts in society e.g., "don't buy this product, you are allergic to it" to shoppers in the supermarket.

 

So this Tamboti Tree Use Case can serve as an inspiration for us to work towards in our efforts to create this future semantic web of predictive toxicology knowledge and services.

 

What can we do now? Once back at my computer I searched on google, found information on the tree on wikipedia and even some sentences on its toxicity.  However the active ingredient chemcial structure mentioned, the diterpene excoecarin, had no chemical information or structure linked.

 

I go back to google and search around and finally find a chemical string as a SMILES. I paste this into the new Bioclipse application, see the structure, and click play. Bioclipse then starts running local predictive models on the toxicity of the molecule which I can start examing. BUT it also goes out on the web and starts to bring in predictions and alerts for the distributed set of OpenTox services available. I can also edit the structure, click play again, and the models and predictions are recalculated.

 
 

You can see a Bioclipse-OpenTox movie of my activities on this "early version of the Tamboti Tree Use Case" at:

http://www.opentox.org/data/documents/development/tambotitree/tambotitreebioclipseopentoxfeb2011/view

We still have lots of work to do, but you can see the directions for progress. 

This promising interoperation between Bioclipse and OpenTox was achieved in Autumn 2010 by Ola Spjuth (blogging at http://bioclipse.blogspot.com/), Egon Willighagen, and OpenTox developers, and first demoed at the OpenTox-EBI industry forum workshop on ontology and interoperability at Hinxton (16, 17 November).  It is I think a good early practical example of the value of ontology and interoperability and the applications it enables linked with the nascent semantic toxicology web, and has much promise for further development in the months and years ahead.

You can download the Bioclipse application that interoperates with OpenTox and try it out yourself using one of the following downloads for PC, Mac or linux:

http://pele.farmbio.uu.se/dl/bioclipse2.4.1.OT-linux.gtk.x86_64.zip

http://pele.farmbio.uu.se/dl/bioclipse2.4.1.OT-linux.gtk.x86.zip

http://pele.farmbio.uu.se/dl/bioclipse2.4.1.OT-macosx.cocoa.x86_64.zip

http://pele.farmbio.uu.se/dl/bioclipse2.4.1.OT-win32.win32.x86_2.zip

http://pele.farmbio.uu.se/dl/bioclipse2.4.1.OT-win32.win32.x86.tar.gz

 

 

 

Comments

[inexpensive bicycle clothes]

In this case the individual moving about in the environment will be provided advice on such risks. Such advice could be provided from the future distributed semantic knowledge base we would have in predictive toxicology that we have been working to develop on OpenTox. The advice could be delivered to the individual's mobile device which would recognise this biological object and then query the knowledge base and return the risk warning.