Category Archives: XML

Egon on SMILES InChI CML and RSS

Posted on December 10, 2006 by pm286

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?

Posted on December 10, 2006 by pm286

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

Posted on November 29, 2006 by pm286

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

Posted on November 18, 2006 by pm286

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?

Posted on October 25, 2006 by pm286

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 →

Posted in chemistry, data, XML | Leave a comment

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

Posted on October 17, 2006 by pm286

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 →

Posted in XML | Leave a comment

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

Posted on October 17, 2006 by pm286

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 →

Posted in "virtual communities", XML | Leave a comment

Hamburgers and Cows; The Cognitive Style of PDF

Posted on September 10, 2006 by pm286

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

Posted on September 8, 2006 by pm286

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 →

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

ACS presentation Part I

Posted on September 8, 2006 by pm286

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 | 4 Comments