Category Archives: chemistry

Pubchem and Thomson – two cheers

Posted on November 8, 2006 by pm286

Noted in Peter Suber’s Blog: Additional 2.2 Million Structures Now Searchable in Freely Available Database Thomson Scientific, … provider of information solutions to the worldwide research and business communities, today announced the deposit of 2.2 million chemical structures from Thomson … Continue reading →

Posted in chemistry, open issues | 4 Comments

Mystery Molecule!

Posted on November 7, 2006 by pm286

This is a detective story. If you know the answer, please don’t reveal it (though I’d be pleased that you announce that you know it). (Anyone remember when Psycho came out? Hitchcock made the audience promise not to tell). Many … Continue reading →

Posted in chemistry | 8 Comments

Do we really need discovery metadata?

Posted on October 26, 2006 by pm286

Many of the projects we are involved in and interact with are about systematising metadata for scientific and other scholarly applications. There are several sorts of MD; I include at least rights, provenance, semantics/format, and discovery. I’ll go along with … Continue reading →

Posted in chemistry, open issues | 3 Comments

Rich Apodaca: Closed Chemical Publishing and Disruptive Technology

Posted on October 26, 2006 by pm286

Rich Apodaca, a founder member of the Blue Obelisk, has a thoughtful blog, DepthFirst. Besides the interesting stuff on programming – especially Ruby – there are useful injections from outside chemistry and IT. Here’s one: The Directory of Open Access … Continue reading →

Posted in "virtual communities", chemistry, open issues | Leave a comment

Silicos contributes Commercial Open Source – thank you

Posted on October 25, 2006 by pm286

It is very uncommon for commercial organizations in chemoinformatics to make any of their material Open Source. (Unlike the contributions of many IT companies – e.g. Eclipse, Netbeans, etc.) So I was very pleased to see an announcement of open … Continue reading →

Posted in "virtual communities", chemistry, open issues, programming for scientists | 1 Comment

Chemistry Theses: How do you write them?

Posted on October 25, 2006 by pm286

As I have shown it is hard and lossy to recover information from theses (or anything else!) written in PDF. In unfavourable cases it fails completely. I have a vision which I’ll reveal in future posts, but here I’d like … Continue reading →

Posted in chemistry | 3 Comments

Inorganic InChIs

Posted on October 25, 2006 by pm286

Mark Winter – who has done an enormous amount to promote web-based chemistry such as WebElements – makes an important point: Mark Winter Says: October 18th, 2006 at 10:18 am eOK – having carefully and rather too obviously written in … Continue reading →

Posted in chemistry | 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

Blogging and the chemical semantic web

Posted on October 15, 2006 by pm286

This post will explain how chemically-aware blogs can be indexed and searched. If you’re not a chemist, but still interested in the semantic web, this may be interesting. I revealed in recent posts that molecules in blogs can be indexed … Continue reading →

Posted in "virtual communities", chemistry | 10 Comments

The mystery unfolded – the molecules have been (and can be) found

Posted on October 14, 2006 by pm286

I think this was delayed by WordPress.) Jean-Claude and his students cracked a bit of it. Egon has explained it fully and provided the motivation… Egon Says: October 14th, 2006 at 7:55 pm eI have not been able to track … Continue reading →

Posted in "virtual communities", chemistry, open issues | 3 Comments