Posts Tagged ‘XML’

(re)Use of data from chemical journals.

Wednesday, December 22nd, 2010

If you visit this blog you will see a scientific discourse in action. One of the commentators there notes how they would like to access some data made available in a journal article via the (still quite rare) format of an interactive table, but they are not familiar with how to handle that kind of data (file). The topic in question deals with various kinds of (chemical) data, including crystallographic information, computational modelling, and spectroscopic parameters. It could potentially deal with much more. It is indeed difficult for any one chemist to be familiar with how data is handled in such diverse areas. So I thought I would put up a short tutorial/illustration in this post of how one might go about extracting and re-using data from this one particular source.


Data-round-tripping: wherein the future?

Tuesday, December 7th, 2010

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).


Data-round-tripping: moving chemical data around.

Saturday, November 20th, 2010

For those of us who were around in 1985, an important chemical IT innovation occurred. We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was called a Macintosh). Perchance even print the result on a laserprinter. Most students of the present age have no idea what we used to do before this innovation! Perhaps not in 1985, but at some stage shortly thereafter, and in effect without most people noticing, the return journey also started working, the so-called round trip. It seemed natural that a chemical structure diagram subjected to this treatment could still be chemically edited, and that it could make the round trip repeatedly. Little did we realise how fragile this round trip might be. Years later, the computer and its clipboard, the chemistry software, and the word processor had all moved on many generations (it is important to flag that three different vendors were involved, all using proprietary formats to weave their magic). And (on a Mac at least) the round-tripping no longer worked. Upon its return to (Chemdraw in this instance), it had been rendered inert, un-editable, and devoid of semantic meaning unless a human intervened. By the way, this process of data-loss is easily demonstrated even on this blog. The chemical diagrams you see here are similarly devoid of data, being merely bit-mapped JPG images. Which is why, on many of these posts, I put in the caption Click for 3D, which gives you access to the chemical data proper (in CML or other formats). And I throw in a digital repository identifier for good measure should you want a full dataset.


(Hyper)activating the chemistry journal.

Monday, September 7th, 2009

The science journal is generally acknowledged as first appearing around 1665 with the Philosophical Transactions of the Royal Society in London and (simultaneously) the French Academy of Sciences in Paris. By the turn of the millennium, around 10,000 science and medical journals were estimated to exist. By then, the Web had been around for a decade, and most journals had responded to this new medium by re-inventing themselves for it. For most part, they adopted a format which emulated paper (Acrobat), with a few embellishments (such as making the text fully searchable) and then used the Web to deliver this new reformulation of the journal. Otherwise, Robert Hooke would have easily recognized the medium he helped found in the 17th century.