Monthly Archives: April 2009

CML – semantic representation of molecular structure

Posted on April 6, 2009 by pm286

I have been asked by Rich Apodaca to show how the various styles of representing ferrocene are possible within CML. Let me stress that these are different connection tables which the community variously uses to represent a single compound. There … Continue reading →

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Why we need chemistry ontologies

Posted on April 6, 2009 by pm286

Mat Todd is an example of the new generation of organic chemists who is concerned about the broader picture of information. Here’s a recent comment, which I address: Mat Todd says: April 5, 2009 at 11:09 pm (Edit) Peter, I … Continue reading →

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Chem4Word – why semantics are necessary

Posted on April 6, 2009 by pm286

I was asked to explain how Chem4Word and CML could encode ferrocene. I’ll start by using Wikipedia to give a clear and accurate picture. Sorry for the cut-and-paste mess. WP: Ferrocene is the organometallic compound with the formula Fe(C5H5)2. It … Continue reading →

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CML – a semantic approach to chemistry

Posted on April 5, 2009 by pm286

Rich Apodaca has asked me to show how CML can deal with metallocene compounds – and I’m happy to do this – it comes at a very good time. He points to Metallome blog and I’ll copy some of the … Continue reading →

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CAS and InChI – who can assign identifiers?

Posted on April 5, 2009 by pm286

I’ve had two useful comments on CAS and InChI identifiers which have updated my knowledge (a feature of closed organizations and authorities is that updates often trickle out in small amounts, particularly if they represent an unwelcome progress towards openness). … Continue reading →

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Identifiers: why we need them and when CAS and InChI don't mix

Posted on April 4, 2009 by pm286

I have tried to write this without needing to know chemistry as there is an important political point. I have been involved in InChI since the beginning and I am a great supporter of it. But it’s not a simple … Continue reading →

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Chem4Word – aspects of Openness

Posted on April 4, 2009 by pm286

I’ll now reply to the second part of Rich’s question Rich Apodaca says: April 4, 2009 at 4:49 pm (Edit) Metallocenes? Axial Chirality? Apache/MIT/BSD License? OpenOffice? GitHub? My current understanding is that C4W will be posted on CodePlex when we … Continue reading →

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Chem4Word + CML representational power

Posted on April 4, 2009 by pm286

Rich Apodaca is an original member of the Blue Obelisk and has developed his own chemical authoring tool (ChemWriter 299USD). He’s just posted the rather enigmatic comment… Rich Apodaca says: April 4, 2009 at 4:49 pm (Edit) Metallocenes? Axial Chirality? … Continue reading →

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A ramble through alternative chemistry

Posted on April 4, 2009 by pm286

For many years I used to have a small patch of weeping scalp, but when I came to Cambridge I went to Ray’s barber shop in All Saints’ Passage – he was about 75 and got his politics from the … Continue reading →

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Chem4Word – the journey so far

Posted on April 4, 2009 by pm286

We’ve been very silent about Chem4Word (C4W) for several reasons, but a major one is that I don’t like vapourware. I’ve spent too long in the pharma industry getting high-pitch sales including (ca. late 1980s, all true): “We have a … Continue reading →

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