Category Archives: XML

Egon on SMILES InChI CML and RSS

on Planet Blue Obelisk Egon Willighagen (chemblaics) blogged on: Including SMILES, CML and InChI in blogs I agree with everything Egon says and add comments. (Incidentally WordPress and Planet remove the microformats so please read his original for the correct … Continue reading

Posted in open issues, XML | 1 Comment

Why bother with new technology?

Kinasepro has blogged about discussions of new chemoinformatics technology (specifically CML (Chemical Markup Language) and InChI (chemical identifier)). Here's the post and some correspondence. It's basically about the introduction of new technology. Obviously I'm not neutral but I will try … Continue reading

Posted in chemistry, open issues, XML | 5 Comments

RELAX wins

There's been a buzz today about the changing scene in XML. On the XML-DEV list Michael Champion wrote: I see that Elliotte Harold has declared the schema wars over, and Tim Bray, Don Park, and others have piled on. That … Continue reading

Posted in "virtual communities", XML | 2 Comments

The War on Error

There's been a lot of  excitement over Pete Lacey's The S stands for Simple. This Socratic dialogue, which I blogged yesterday has shown the futility of the overengineered madness from the W3C committees. There are other similar postings, summarised in … Continue reading

Posted in programming for scientists, XML | Leave a comment

Organic Theses: Hamburger or Cow?

This is my first attempt to see if a chemistry thesis in PDF can yield any useful machine-processable information. I thank Natasha Schumann from Frankfurt for the thesis (see below for credits). A typical chemical synthesis looks like this (screenshot … Continue reading

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What are the advantages of XML and why should I care? (text)

This is an attempt to explain why XML is important in a scientific context. I shall try to assemble as many reasons as possible, but there are also many other tutorials and overviews. I believe that XML is a fundamental … Continue reading

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What are the advantages of XML and why should I care? (0)

As I have blogged before we are looking at ways of improving the information infrastructure in our Centre. We're all very consicous of how little we know - I know I know very little and I'm quite prepared to admit … Continue reading

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Hamburgers and Cows; The Cognitive Style of PDF

PDF is one of the greatest disasters in scientific publishing - why? I normally give my slides in XHTML rather than Powerpoint and prefix them with the quote which I made up: "Power corrupts; Powerpoint corrupts absolutely" I then searched … Continue reading

Posted in open issues, XML | 15 Comments

ACS Presentation - Part II

The first part of my presentation dealt with the technical issues surrounding semantic chemistry. This page contains predictions - they are general enough that you don't have to be a chemist to appreciate them. I'll probably try to cover some … Continue reading

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ACS presentation Part I

Edward Tufte said in his recent book that one shouldn't use Powerpoint to present information, but Word. Although I am not a fan of Word (see later posts) I agree with the message. So this is the first part of … Continue reading

Posted in chemistry, open issues, XML | Leave a comment