Data-round-tripping: wherein the future?

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor used to place them into a context (say Microsoft office), via an intermediate storage area known as the clipboard. The round trip between the Macintosh (OS X) versions of these programs had been broken a little while, but it is now fixed! A small victory. This blog reports what happened when such a Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa).

As you might have guessed, the molecular diagram arrives largely dead, and not re-usable. Opening the .docx archive (it is nothing more than a zip file) reveals only a JPEG file residing inside. Nothing that can be chemically repurposed. If the reverse process is undertaken, of creating a chemdraw diagram, and pasting it into Word on Windows, one finds in the .docx two components; a bit-mapped image linked to an active object containing the data. Only the first of these is recognised if the file makes its way to a Macintosh; i.e. the same story, the data is again lost. So the bottom line is that Mac users and Windows users cannot, after all, exchange repurposable molecular diagrams using Word documents using this combination of programs. This is not good.

But let me remind what happened around 1993. The word processor was joined by a program called the Web browser. In 1996, the underlying content carrier, HTML, became XHTML (an instance of XML). Right from day 1 almost, such XHTML could, and frequently was repurposed. A memorable example is that search engines could use it to index the Web. The XHTML easily survived trips to and from clipboards. In 1996, CML joined HTML as a way of carrying chemical information capable of round-tripping without loss (if need be). There are other chemical XML languages in use nowadays, including CDXML used by the ChemDraw program. Word itself now uses XML (the x in .docx). So, after 14 years, why am I still describing the difficulties above? I am frankly at a loss to explain why there is still a need to write this post.

All is not entirely lost. The CML4Word approach is designed to enable (chemical) data round tripping from the outset. Although I do not yet know if the CML created and stored in the Word document using this mechanism is recognised anywhere outside of Word 2007 on Windows?  If anyone can let me know of examples where such a CML-enabled Word document can be used in other environments, I would be very grateful (but not on  OS X, as I know already).

And as I might have mentioned in the previous post on this topic, things may not however be getting better in that other carrier of information and data, the mobile phone/iPad, as exemplified by operating systems such as iOS or Android. Watch this space, as they say.

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