Methods and scenarios for sharing molecule data using MMDS for BlackBerry are described.

Overview

Sending

Overview

The Mobile Molecular DataSheet for BlackBerry is a content creation, management and sharing application. DataSheets containing molecular structures and associated data can be created, viewed and manipulated using standalone features. With a connection to any kind of network, MMDS becomes a vehicle for bidirectional exchange of molecular data.

There are three main methods for sharing data using MMDS: email integration, webservices and the SD card filesystem. Each of these methods is discussed below.

Email

Transmitting chemical data via email on a BlackBerry smartphone is a convenient secure way to exchange information with colleagues, and can also be used to transfer data to another device. Because the BlackBerry email server is used for all transmission, it is potentially very secure.

Sending

Sending email from MMDS is very simple. Any document that is selected from the main menu includes the Email... option within its own menu:

When editing any datasheet or molecule, the interoperability bank includes options for sending the datasheet or molecule by email:

When the email command is activated, the BlackBerry email client is opened, and the appropriate data is included as attachments:

The standard email client can be used to add recipients and modify the content to suit.

Note that for this datasheet, two files have been attached to the email, one with the extension .ds, and the other with the extension .sdf. The first file contains the datasheet in the native XML format used by MMDS, while the second file contains the data converted to the MDL SDF format.

MDL SD files can be interpreted by almost any cheminformatics software. When a datasheet is sent to somebody who is not using MMDS, the recipient can save the attachment to disk and open it with any software that can read and understand MDL SD files, of which there are many. Unfortunately the MDL SDF format has a number of limitations, and so it is not always possible to save a datasheet as an SD file then read it back in and obtain the exact same data as the original. The workaround for this is to include both files whenever possible, so the recipient can either: (1) read the industry standard format with third party software, or (2) use the data in its original form, without any translation.

When a single molecule is being transmitted rather than a datasheet, the process is very similar. As for datasheets, two attachments are included: MDL MOL format (.mol) and SketchEl molecule format (.el). The rationale for including both format is the same: the MDL MOL format is an industry standard which works with almost all third party software, and the SketchEl molecule format is the format used natively by MMDS.

Receiving

MMDS can send chemical data as email attachments, and it can also extract chemical data from incoming email attachments. All of the four recognised formats (MDL MOL and SDF, and the native datasheet and molecule formats) can be extracted from incoming emails.

In the example below, a message has been received from a colleague who has sent an attachment called caffeine.mol, using an ordinary email program:

Selecting the attachment and opening up the menu offers the Open Attachment choice. The BlackBerry email system has two slightly different ways of handling email attachments. In some cases they are downloaded to distinct files, so when the MMDS email attachment handler receives the instruction to open the attachment, the attachment has already been written the filesystem. In this case, MMDS adds this file to the external folder, rather than automatically the file to its preferred location:

The file can be moved to the attachments folder with a single menu option.

Other times the BlackBerry email system does not download the attachment and write it to a file, and so MMDS writes the data directly to its own attachments folder:

Either way, the attachment will be immediately viewable and editable with MMDS.

When a user of MMDS for BlackBerry receives chemical data by email from another user of MMDS (either the BlackBerry or iPhone version), there will typically be two attachments:

In this case, a single molecule has been transmitted. Either attachment can be opened, but caffeine.el is preferred, since it uses the native format, rather than the industry standard for compatibility purposes.

WebServices

MMDS provides a webservices client which can be connected with a network service that uses the MMDS API. The service describes the input that it needs, which is some combination of fields which contain molecular data, text, numbers, flags, options, etc. When MMDS presents the service to the user, the fields can be filled in, and molecules and datasheets that are stored on the smartphone can be submitted.

The webservice then acts on the input data, and prepares a new datasheet which it sends back to the client. The returned datasheet can be stored and manipulated just like any other datasheet.

There are many different ways in which these webservices can be used. Immediately useful examples include functionality that is transient as far as the server is concerned, such as searching for molecular structures within an online database (e.g. PubChem, ChEBI), or predicting properties for input molecules.

Services do not need to be stateless. An MMDS-compatible webservice could be used as a compound registration system, with one mode of operation for submitting new structures and data, and another mode for querying the data. Or if the fields were arranged in terms of reactants and products, a crude electronic laboratory notebook could be constructed.

The MMDS webservices client is a very new feature, but its potential scope is large. Publicly hosted services, such as those provided by MMI for general use, can be combined with private services hosted behind the company firewall. The API is straightforward to implement, and to integrate with existing cheminformatics software.

File Sharing

BlackBerry smartphones have an SD card with a significant amount of storage space, typically measured in gigabytes. The SD card is organised in a filesystem hierarchy, and contains an arbitrary collection of folders and files, which is a familiar arrangement to anyone who has used a desktop operating system.

The MMDS app stores some of its molecular data within the internal memory of the device, such as configuration settings, the scratch sheet and templates, in order to ensure that they are not lost if the card is changed. All other molecules and datasheets are stored on the SD card, with a single file for each entity. The files that are considered to be "owned" by MMDS are stored within the folder:

/SDCard/BlackBerry/MMDS

This directory contains subfolders Archive, Attach and WebResults. These are directly mapped to three of the folders that are available from the main menu:

Each of these three folders is scanned by MMDS every time the user interface is used to toggle open the folder. Any file that is discovered, and has a recognised extension, is included within the available content. Files can be copied to and from these folders using the BlackBerry Desktop Software.

The Archive and WebResults folders only recognise files that are stored within the native datasheet format, which is an XML dialect, with a file extension of .ds. The Attach folder can contain files with a variety of formats, including MDL MOL and SDF.

Because most cheminformatics software recognises the MDL MOL and SDF formats, and MMDS works best when it is using its own data formats, the most effective way to share files is by using the import and export mechanisms.

Exporting

From the main menu, highlight any datasheet or molecule, and press the BlackBerry button. One of the menu options that shows up will be Export....

For example, select a datasheet from the archive folder:

The export dialog will be presented. First, change the filetype to SDF:

Then select a file to write to:

Entering a file extension is optional, as the .sdf suffix will be added automatically. The default location is /SDCard/BlackBerry, which can be easily located using the BlackBerry Desktop Manager when the phone is plugged into a PC:

Molecules can be exported as well as datasheets, and can be saved as MDL MOL files (.mol) or using the SketchEl molecule format (.el). Both datasheet and molecule exporting can also be done from within the datasheet editor and molecule editor:

Importing

Any file that is placed onto the BlackBerry SD card that has a recognised file extension can be accessed from MMDS. The available types are:

Extension Format

.ds Native XML datasheet

.sdf MDL SDF datasheet

.el Native SketchEl molecule

.mol MDL MOL molecule

MMDS can access any file on the SD card, but it does not scan the entire SD card looking for files which it might recognise. Files have to be selected and added to a list of external files. An external file is any file that MMDS knows about, but does not reside in the usual locations.

Consider that a file called imported.sdf has been copied to onto the SD card. To access this file from MMDS, locate the external folder from the main menu, press the BlackBerry button, and select Add File...:

After the file is selected, it will be added to the list of files referenced from within the external folder:

The newly added file can be edited and saved just like any other datasheet. The full path of the file is shown in the list, as well as the filetype. Modifications to this particular file will be saved in its original format, i.e. MDL SDF.

There are menu items which can be used to copy or move the file into the archive folder. Files can be added to the external list either individually, as described above, or by adding all valid files in a directory, using the Add Directory... menu option.

Summary

MMDS supplements its suite of standlone features for managing chemical data with open-ended options for exchanging data with other devices, colleagues and network services. Anywhere that the BlackBerry smartphone can get reception, the MMDS user can be connected to a variety of chemical resources, and can share data with anyone else who has access to email or custom designed webservices.

Overview

Email

Sending

Receiving

WebServices

File Sharing

Exporting

Importing

Summary

See Also