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MMDS for iPhone, iPod and iPad can share molecular data by integration with iTunes file sharing, email attachments and web downloads. These techniques are described. |
Overview
The Mobile Molecular DataSheet for iOS devices (iPhone, iPod and iPad) is designed to create and organise molecular data. Content is stored on the device itself, and does not require any network connectivity to operate. If this were the end of the story, MMDS would not be very useful. There are a variety of ways for communicating the data.
MMDS allows file sharing through the iTunes service. Molecular structures and datasheets that have been "exported" are placed in the app's sharing directory, in multiple formats, and can be copied onto a Mac or PC using iTunes. MMDS can be used to initiate emails which contain attached data in a variety of formats. Through integration with the iOS attachment handler, whenever an incoming email contains a recognised filetype, it can be opened using MMDS. The same file types can also be opened by MMDS when downloaded using the Safari mobile browser.
In addition to data sharing capabilities, MMDS also supports access to webservices. For more information, see the example: Searching ChEBI (iPhone). The remainder of this article describes the iTunes, email and attachment handling techniques for sharing data.
iTunes File Sharing
File sharing with iTunes is a one-way technique for migrating data off the mobile device. Molecules and datasheets can be exported, which means that the data is written into files within the app's home directory, using all available formats. These files can be accessed using iTunes, when the device is connected:
In the example shown above, all of the files in the root directory are those which have been exported from MMDS. These files are created by MMDS, but are not used for its internal content, so they can be copied, moved, deleted, renamed etc. Files stored in subdirectories, particularly data, should not be tampered with.
Exporting from the Main Menu
The opening screen for MMDS provides menu entrypoints for exporting whole datasheets, or individual molecules or reactions.
Any kind of datasheet can be exported in its entirety, whether it is the scratch sheet, a user defined datasheet, template group, reaction datasheet, webservice results etc. The export feature can be found underneath the Interoperability submenu:
Select Export DataSheet, and a dialog will appear, which prompts for a base filename:
The default filename has been constructed from the datasheet title. Do not add a file extension, because this will be done automatically. As the text above indicates, two files will be exported: one using the native XML format (.ds) and another using the industry standard MDL SDF format (.sdf).
After pressing Accept, both of these files will be created, and may be accessed using iTunes.
When exporting a reaction datasheet, the process is the same, except that the MDL RDF (.rdf) format is used instead of MDL SDF. The MDL RDF format is designed to store reactions and associated data, while the MDL SDF format only allows a single molecular structure.
To export an individual molecular structure or reaction, bring up the menu for an individual entry by press-and-hold:
The same export dialog will be presented. For exporting molecular structures, the two formats used are SketchEl molecule (.el) and MDL MOL (.mol). When exporting a single reaction, the data is exported as an excised single row from a datasheet, which uses the same formats as for a whole datasheet, i.e. native XML and MDL RDF.
Exporting from Command Banks
The datasheet viewer, molecule editor and reaction editor screens all have a command bank icon for interoperability:
When the export command is selected, the export dialog is brought up. The process is the same as for when it is activated from the main screen.
Email Attachments
Datasheets, molecules and reactions can be sent and received using attachments. This form of data sharing is two-way. It is typically more convenient to interchange data between two users of MMDS (either iOS or BlackBerry), but the sender/receiver can be using any email client, as long as standard file extensions or MIME types are used.
Outgoing
Initiating an email with data attachments is analogous to the export process described above: the main menu Interoperability submenu contains an entry for sending an email:
All kinds of datasheets, molecules and reactions can be sent as email attachments. Once the email process is initiated, the mail app will appear:
As with exporting files, the outgoing email will contain all appropriate dataformats. For communication between two instances of MMDS, it is highly recommended that the native formats be used preferentially (.el and .ds file extensions), because they are guaranteed to preserve all data. Interconverting between industry standard MDL dataformats is generally safe, but does have the potential for data loss.
When emailing a single molecule, an additional image attachment is included in the outgoing message:
When emailing an individual reaction, the preferred formats are the same as for the whole reaction datasheet, but with just one row, i.e. a single reaction. For compatibility with third party sketcher applications, such as ISIS/Draw and ChemDraw, an additional attachment with the RXN (.rxn) filetype is included.
Incoming
MMDS registers attachment handlers for datasheet and molecule filetypes that it can import:
| Extension | MIME type | Description |
|---|---|---|
| .el | chemical/x-sketchel | Molecular structure (native) |
| .mol | chemical/x-mdl-molfile | Molecular structure (non-native) |
| .ds | chemical/x-datasheet | Molecular or reaction datasheet (native) |
| .sdf | chemical/x-mdl-sdfile | Molecular datasheet (non-native) |
| .rdf | chemical/x-mdl-rdfile | Reaction datasheet (non-native) |
Whenever a device with MMDS installed recognises one of these filetypes as an attachment, it offers the chance to open the attachment using MMDS:
When the attachment is opened, MMDS will receive the content and add it to its data collection. For molecule data, the new structure will be added to the scratch sheet. For datasheets and reaction datasheets, a new datasheet will be created.
Browser Downloads
iOS uses the same attachment recognition for files that are encountered by Safari when browsing the web. When downloading one of the recognised file types (see above), an option is presented to use MMDS to open it:
There is one caveat: some websites that serve up chemical data that is generated on-the-fly, such as results from search requests, do not provide sufficient information to identify the file type. The web server must either provide the right MIME type, or a recognised extension. If the URL is something like http://molecules.acme.com/search.cgi?id=10, it may not be possible to open it with MMDS, even if the content is valid.
Summary
The Mobile Molecular DataSheet for iOS provides a number of ways to share data, which includes iTunes file exporting, email sending and receiving, downloads from a web browser, in addition to a chemically-aware webservices client. With the exception of file sharing, all of these options are truly mobile, allowing data to pass in and out of MMDS, whenever the device is connected to the internet.
See Also
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| © 2010-2011 Molecular Materials Informatics Inc. All rights reserved. Last modified 27-Nov-2010 |
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