The process of configuring MMDS (for iPhone) to include the ChEBI (Chemical Entities of Biological Interest) webservice is described, as are some of the searches that can be carried out.

Overview

Adding the Service

Running the Service

Results

Summary

Overview


Since version 1.1, both the iPhone and BlackBerry versions of the Mobile Molecular DataSheet app have included a webservice client. This allows the app to be connected to a particular web URL which describes some number of available services. Once these services have been discovered and added to the list, they can be called up at any time. Running a webservice brings up a dialog box which provides a way to enter input for each of the parameters that the webservice requires, e.g. structures, text, numbers, flags or lists of options. When the parameters have been set, the webservice can be run. If the execution is successful, then webservice will return a new datasheet, which contains the results of the query. The new datasheet can be viewed, edited, saved and manipulated like any other datasheet.

ChEBI stands for Chemical Entities of Biological Interest, and is a searchable online chemical database hosted by EBI (European Bioinformatics Institute). The data is available through a WSDL/SOAP webservice. Searches can be executed from MMDS by connecting to an intermediate bridge service that is hosted by the MMI website.

ChEBI is the second public database to be made searchable from MMDS. The first was PubChem. This article explains the process of configuring and running the service, using the iPhone version of MMDS. The process is identical for the iPod and iPad, though the iPad layout is different because of the larger screen.

Adding the Service


Before the ChEBI webservice can be accessed, it must be added to the list of webservices available to MMDS. On the main menu, look for the MMI logo at the top left corner:

Tap the logo, or touch-and-hold, then when the menu pops up, select Discover WebServices:

The webservices discovery dialog will then appear:

If there are currently no webservices configured, which is the case for a fresh installation of MMDS, the default URL will be filled in automatically. Otherwise, manually enter the link:

http://molmatinf.com/webapp/list.php

Press the Accept button. The provided URL will be queried, and a list of available webservices will be obtained. When successful, the discovered services will be shown in a list:

Note that the second entry in this case is the ChEBI webservice. Press Accept, which will add these webservices to the list. If any of them were already present, they will be refreshed.

Running the Service


On the main menu, locate the spider-web image at the top right:

Tap it, and the list of available webservices will be shown. Select the entry for ChEBI by tapping twice, or tapping once then tapping Open.

The fields required for the ChEBI webservice are presented in a preparation panel:

Three fields must be provided: structure, search type and the maximum number of results.

The structure field is currently blank, which is denoted by the empty square. There are two ways to provide a structure: either by pasting from the clipboard, or by picking a structure from the scratch sheet.

Tap the Select button, and a list of molecules from the scratch sheet will be shown:

Select the first molecule (caffeine) by tapping once followed by the Select button, or by tapping twice. The molecule will be entered into the appropriate position:

Note that if the query molecule is not already on the clipboard or the scratch sheet, press the Cancel button, and draw the molecule on the scratch sheet, or copy it to the clipboard. When returning to the webservice, the most recently used parameters will be restored to their most recent state, so there is no need to reenter anything.

Now change the search type to Similar90%, which will use a fingerprint comparison to select the structures most similar to caffeine. The third field, which is not shown in the above screenshot, limits the number of results to 20, which means that up to 20 compounds, all of which have a Tanimoto similarity of 0.9 or more, will be returned, ordered by decreasing similarity.

Tap the Execute button, and wait for the webservice to complete:

If the service is taking too long, or a mistake was made, press the Cancel button.

Results


When the webservice request has finished executing, MMDS will return to the main menu.

Notice that a new datasheet has been added underneath the scratch sheet, which has a blue title bar and is called ChEBI Query: Similar90%. This is a special datasheet type which contains the results from the most recent webservice query.

To take a closer look at the results, locate the detail edit button:

Tap it to bring up the detail view:

In the above screen, the third entry has been selected, which corresponds to caffeine, the subject of the search query. The two molecules listed above it have a similarity of 100% to caffeine, due to equivalency of the fingerprint scheme.

For each row in the list, the molecule is shown on the left, and any additional fields are shown to the right. The results from a ChEBI search include the structure, compound name, and a URL which links to the ChEBI website, which provides further details.

The most convenient way to find out more information about a search result from the ChEBI website is to return to the main menu, locate the molecule of interest, and touch-and-hold:

From the popup menu, select Open URL, which is an option that is made available whenever a datasheet row contains a text field which starts with the http:// prefix.

Opening a URL will launch the Safari browser and direct it to the appropriate page:

The webservice query result datasheet is always shown with a blue title, and is a special datasheet, of which there can only be one at a time. If a webservice is executed successfully, and there is already a webservices result datasheet present, then the old one will be overwritten. Webservice results are assumed by default to be temporary.

To preserve the results from a webservice query tap, or touch-and-hold, the menu icon for the datasheet:

Select the Convert to DataSheet option, which will change the result into an ordinary datasheet. From this point onward, it is not in danger of being clobbered by subsequent webservice queries.

Summary


Access to the ChEBI online database has been made available to users of MMDS. The free online data is a valuable resource for chemists working in life sciences industries.

See Also


Demonstration Videos, Mobile Molecular DataSheet (iOS), MolSync Remote Procedure Calls, Products, Property Calculations via Open Notebook Science, Searching PubChem (BlackBerry), WebService Code Example, WebServices Protocol