Using MMDS to enter chemical structures and associated data.

Overview

Data Source

Setting Up

New DataSheet

Title and Description

Adding Columns

Entering Data

Drawing Structures

Activity Data

Using the DataSheet

Overview


The Mobile Molecular DataSheet (MMDS) application is based around groups of datasheets, each of which is a spreadsheet-like document which contains columns of molecular structures, text, numeric and other auxiliary data. Organising structure and activity data in this highly typed tabular format is one of the most effectively straightforward ways to collect chemical information so that it can be perused by people using a variety of different media, and used as source data for cheminformatics applications.

This article describes the steps involved in curating pharmaceutical data, using the BlackBerry version of MMDS.

Data Source


Consider a table of structure-activity data from the printed literature. The following clipped section shows part of a group of molecules whose activities were measured for their ability to inhibit the Enoyl Reductase enzyme of Toxoplasma gondii:


McLeod et al: , J. Med. Chem. 53, 6287-6300 (2010) link

Setting Up


Before any data can be entered, a new datasheet must be created. The columns should be configured to be able to accommodate the necessary data fields, though they can be modified later as necessary.

New DataSheet


From the main screen, move the selection cursor over the heading for the Archive folder. Open the BlackBerry menu, and pick Create New...:

Enter the name for the new datasheet. The name that is entered will initially be used to form the filename and the title:

When the Archive folder is opened, the new datasheet will be listed:

Title and Description


When the new datasheet is opened, the header and top few rows are shown. The header line shows the title of the datasheet. When it was created, a single column ("Molecule") and a single empty row were created automatically:

The current selection cursor is positioned over the header, which is denoted by the title being highlighted in green. To edit the header, simply click with the trackpad. The title and description of the datasheet can be modified:

Adding Columns


To select the columns, move the cursor down by one unit, so that the "Molecule" column is highlighted. Then, press the BlackBerry button to bring up the command bank:

Select and click the add new row/column action, and a dialog box for creating a new column will be shown:

For this data collection, just one of the data fields from the source material will be entered: IC50. Because the source data includes a numeric value and a comparator, it is necessary to create two new columns, one called "IC50_mod" and the other called "IC50_value":

The "IC50_mod" field is a string which can contain arbitrary data, so it can be used to hold whatever qualifiers were included within the printed table, such as "<" or ">". The "IC50_value" field is a numeric value. While MMDS does not have an explicit unit tracking system, the column description is a good place to indicate the measurement units.

The datasheet is now ready to enter structures and activity data.

Entering Data


For most datasheets, there is one row of data for each conceptual entity, which is in this example a single molecule and its associated activity data. Sometimes it is easier to complete the data for each row one at a time, but othertimes it is preferable to skip ahead. Because all of the molecules are based on the same scaffold, we will be making use of copy'n'paste to save a significant amount of work.

Drawing Structures


Select the first (and only) row, and the first column. Press space or use the menu to open up the structure editor, and draw the common substructure fragment which is common to all 5 of the structures that are being entered:

While the cursor is still positioned over the molecular structure, activate the copy action from the main command bank. Then, press the add new row/column action four times, each of which will append a blank row to the end of the datasheet:

Move the cursor over each of the blank molecule cells, and activate the paste action for each of them. There will now be 5 identical rows, each containing the common framework structure:

Edit each of the molecule structures in turn, to add the additional adornments as indicated in the source data. To fit all of the rows onscreen, select the resize to small scale action from the main command bank:

Activity Data


To add in the activity data, move the cursor over each of the cells, and either press space or select the edit action:

Once the data entry is complete, the results will look like:

The datasheet should now be saved and closed.

Using the DataSheet


The datasheet was created in the Archive folder, which means there is a corresponding file on the SD card:

The file has the extension .ds, which means that it is an XML datasheet. The SD card, or the BlackBerry itself, can be connected to a PC and the file can be viewed or edited with any software that can parse the format.

Alternatively, the data can be exported. Select the datasheet from within the main screen, open the BlackBerry menu and select Export...:

The default format is the native DataSheet XML format, but for most interoperability purposes, it should be changed to MDL SDfile. The export dialog allows any file location to be selected. On completion, the new file will be created.

To transmit the datasheet by way of email attachment using the BlackBerry email service, select the the datasheet from within the main screen, open the BlackBerry menu and select Email...:

The recipient, subject and text content of the message can be filled in as necessary. Note that the email contains two attachments. The first file has the extension .ds, which is the datasheet in its native XML format, while the second file has the extension .sdf. If the recipient uses MMDS, or other software which can interpret the XML format, then the first file should be used. Since the MDL SDfile format can be understood by almost all cheminformatics software, the second file is included in order to ensure that the data can be accessed by the recipients.

If the email recipient uses MMDS for BlackBerry that has an attachment which contains molecules or datasheets that are recognised by MMDS, they can be opened using MMDS. Other email clients, or BlackBerry smartphones which do not have MMDS installed, can handle the attachments as ordinary files, which can be extracted, modified and/or transmitted. MMDS can also open files of these types sent using software other than MMDS.

See Also


Demonstration Videos, Mobile Molecular DataSheet (iOS), Products