The Open Notebook Science property prediction service can be used to predict melting points for chemical structures.

Overview

Summary

Overview


In collaboration with Jean-Claude Bradley (UsefulChem) and Andrew Lang, on behalf of the Open Notebook Science Web Services project, the Open Notebook Science Physical Properties calculation service has been made available as a webservice that can be invoked from the Mobile Molecular DataSheet. The webservice offers access to melting point calculations, which achieve a new level of reliability by making use of well curated training data.

Both the BlackBerry and iOS versions of MMDS have supported a webservices client since version 1.1. The remainder of this article demonstrates how to use the web services interface of the iOS version of MMDS to calculate melting points using Open Notebook Science property prediction.

Setting Up

Before using a webservice, it must be discovered. If you already have MMDS installed, and have used the webservices feature already, you will probably already have the PubChem and ChEBI search services listed. The Open Notebook Science Physical Properties service is the 3rd webservice to be added to the default webservice directory. To ensure that this service is available, tap or touch-and-hold the logo on the top right, then select Discover WebServices from the menu:

A dialog will be presented. If there are currently no discovered webservices, the default URL will be filled in automatically, as shown on the left. If there are already webservices known, then the URL will be blank, as shown on the right:

If the URL is blank, then press the logo button on the right. This will fill in the URL, setting it to http://molmatinf.com/webapp/list.php, which is required in order to refresh the list and make sure the new webservice is added.

Press the Accept button, and after a short delay while the server is contacted, the list of available webservices should be presented:

Press the Accept button again to add these webservices to the available list.

Executing

Opening

Once the required webservices have been discovered, there are two buttons that can be used to initiate the execution process:

The list of webservices will be shown:

Select ONS Properties and press the Open button, or double tap it. The first time a service is opened, there will be a brief delay as the webservice is contacted in order to obtain the specification, which includes the input parameters. Once the specification has been downloaded, the display will appear as follows:

Specifying Input

The current structure is initially blank. It is necessary to provide a chemical structure using any one of the three buttons shown underneath it: Paste to transfer a structure from the clipboard, Scratch to select a structure from the scratch sheet, or Edit to draw a new structure, or to edit the structure that is currently shown, e.g. caffeine:

The checkboxes shown below allow certain functionality to be activated or deactivated. By default, all of the capabilities of the webservice are enabled, which is appropriate for most uses. The webservice is capable of calculating melting points for organic structures, and it also refers to the ChemSpider service in order to lookup experimentally determined melting points, should they be available. If the actual melting point is known, it is generally interesting, either to be used in preference, or simply to compare the efficacy of the calculation. Also, links to the ChemSpider page for the submitted structure are provided when available, as a useful extra feature.

Obtaining Results

Press the Execute button to submit the webservices query. It will be necessary to wait awhile for the service to finish: the calculation process involves some overhead. When the execution has completed, you will be dropped back to the main menu. Observe that there is a new datasheet in the list, called Physical Properties from Open Notebook Science Open Data, which has a blue title banner:

To view the results, open the detail view for the datasheet (the magnifying glass logo, highlighted above):

The properties associated with the structure are shown. The predicted melting point is shown alongside the experimentally determined melting point.

Because this structure was located in ChemSpider, it can conveniently be looked up in the online resource. Touch-and-hold on the structure from within the main menu, and select select the Open URL menu item, which will launch the mobile browser:

Updating the Service

The Open Notebook Science project is rapidly evolving, and it is highly likely that the webservice will be extended in the future to offer other calculations. Because MMDS stores the webservice definition in a cache, so it does not need to download it each time it needs to be used, it will be necessary to refresh the specification when new features become available.

To refresh the list, tap-and-hold on the entry prior to running the webservice, and select Refresh:

This will cause the specification to be re-downloaded next time it is opened.

Summary


The property calculation service from Open Notebook Science has been made available to users of the Mobile Molecular DataSheet. The melting point calculations make use of cutting edge developments in property prediction and high quality open data, and is likely to be the first of many such services that are made available by way of open protocols.

See Also


Demonstration Videos, Mobile Molecular DataSheet (iOS), MolSync Remote Procedure Calls, Products, Searching ChEBI (iPhone), Searching PubChem (BlackBerry), WebService Code Example, WebServices Protocol