Monday, August 23, 2010

ChemTaverna Workflows of ONS Web Services now on MyExperiment

I'm pleased to report that one of the collaborations initiated at the Berkeley Open Science conference last month is progressing very well.

Carole Goble introduced me to Peter Li who runs the ChemTaverna project. The idea was to use Taverna to construct workflows using the web services developed by Andrew Lang for our Open Notebook Science projects: UsefulChem and the ONS Solubility Challenge.

Peter quickly created several workflows to demonstrate what is possible. Here is a workflow that uses a Google Spreadsheet as input. SMILES for amines, carboxylic acids, aldehydes and isonitriles are entered in the appropriate columns. The workflow first creates a virtual library of Ugi products from all possible combinations of reactants. Then each product is submitted to a web service that predicts the solubility in methanol, the most common solvent for Ugi reactions.

The resulting spreadsheet can then be sorted by predicted solubility to recommend products that are more likely to precipitate from the reaction mixture. In this particular example Ugi products derived from boc-glycine are predicted to have a low solubility in methanol. The least soluble compound is predicted to have a solubility of only 0.07MIn this library, Ugi products derived from boc-methionine are predicted to be too soluble to precipitate. For example this Ugi product has a predicted solubility of 3.7 M.
(note: ChemSpider has a tendency to draw the minor tautomer for some amides and carbamates)

There are a few issues to take into consideration in order to use this particular workflow:

1) This will only work on Taverna Workbench 2.1.2 with these plug-ins installed. At one point it will be made to work on Taverna Workbench 2.2 and uploaded onto MyExperiment. The workflow used here is currently available here.

2) The SMILES in the input Google Spreadsheet must be written in the format of the current example (aldehyde, amine and isonitrile groups on the left and carboxylic acid groups on the right)

3) All of the Ugi products in the virtual library must already exist in ChemSpider. Otherwise, the solubility predictions will fail because of missing descriptors as discussed previously.

Peter has uploaded simpler workflows onto MyExperiment that are compatible with the current version of Taverna Workbench (v2.2).

First, the generation of Ugi product libraries from reactant SMILES in a Google Spreadsheet is available here.

Another workflow handles the prediction of Abraham descriptors.
This workflow processes the prediction of solubility for a given solute and solvent.

The main rationale for incorporating web services derived from our Open Notebook Science projects into Taverna is leverage. MyExperiment already benefits from a vigorous community of developers in the bioinformatics arena. With the growth of the ChemTaverna initiative, the integration of cheminformatics and bioinformatics workflows should become seamless.

By making our solubility and chemical reaction web services available in formats that are convenient for others to use it increases the opportunities that our work will be actually useful. It also makes it easier for us to leverage the resources made available by others for our own applications in drug discovery and reaction design.

Essentially this means that we have extended the reach of the information cascade triggered by the recording of an experiment in a laboratory notebook and a very simple abstraction process to represent that experiment in a semantically addressable format.

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