Milkshake runs a superb blog (Org Prep Daily) which does exactly what it says on the tin. Here is an example of a post (6-amino-4-chloro-2-methylpyrimidine). Take a look – you don’t have to be a chemist to get the idea and the quality. He recently posted:
I will run out of procedures to post in about a week or two. Since the chemistry cannot keep up with posting one decent procedure a day, I will have to revert into a more convenient one-post-per-month frequency. (I think I will also rename Org Prep Daily as The Reactionary Organiker and will proceed to expound my entire worpetermr’s blog › Edit — WordPressld-wiew here.) Only you can prevent it – by submitting a good reproducible scalable procedure to appear here. My Scripps address is tomasv{}edu.
It’s obvious we need to step in and help. So how? There are several aspects:
- a community needs to self-assemble. Posts like this will, I hope, help raise awareness. This could be Internet-mediated diffusion, but I would also suggest it’s a wonderful opportunity for undergraduate projects. These can be of very high quality – I know Henry Rzepa does this (not yet public) and Mark Winter has a splendid site Molbase) which is curated and has an effective mechanism for peer-review
- there needs to be an agreed social procedure. This is a very common process in Open Source where several models have been developed. A common one of Benevolent Dictator For Life (BDFL) which works on a mixture of meritocracy and trust. That’s the current implied models for blogs – the blogmeister is effectively the BDFL. In the Blue Obelisk we have a more federated approach – there are many projects, each with a guru or BDFL, but we share all our experiences. There’s no single solution. There are elaborate social pressures on conformity, forking, etc.
- The blog needs to have a clear purpose. At one level this is very clear – the daily posting of organic syntheses. But I’m not quite sure what the selection policy is – are these just molecules that catch Milkshake’s fancy? or that he has just happened to make – this would be similar to Useful Chem where the blog is the primary scientific record. Or are these particularly valuable synthetic intermediates? If this is clearer I can make more suggestions.
- The technology needs to be agreed. IMO this is increasingly suitable for a Wiki rather than a blog. Several of us are looking into how we create semantic tools for Wikis (blogs are somewhat more difficult) where we can author chemistry directly into the Wiki.
Those of you who are not chemists will know the great value of compendia of reactions. At present these are normally sold (at considerable expense) in paper-based compilations. These are difficult to search and are completely uninfluenced by the Internet revolution. We now have the opportunity for social computing to collect the primary reaction data from the literature in free and universal form.
Most of the problems are solved.
- Much of the chemistry is published as Supplementary Information (i.e. not part of the sacred fulltext). It’s therefore free of copyright. (Not all publishers take this view so now, dear readers, do you see why we need to ask for Open Data.)
- Although the data is normally in PDF Hamburger form, rather than HTML Cow, it’s fairly easy to transform it into text, use OSCAR to create HTML and thence automatically to XML. (I have found that PDFBox does a pretty good job – of course it can’t do the chemical structures which has been mashed into soggy gif horrors – not even hamburgers.)
- The recipe can be created for humans, but it’s also straightforward to create CMLReact – the version of CML that supports reactions. Org Prep daily would be an ideal substrate for this. Most of the software is in place – it needs some simple glueware. The great benefit of this is that molecules can be searched, reactions can be balanced, and the reaction-specific data (e.g. temperatures, etc.) can be specifically searched.
- Increasingly Wikipedia will become the primary reference for chemists – it will be trivial (even automatic) to link OPD to Wikipedia and Pubchem. We’d also see OPD syntheses being added to WP either as entries or links.
- The technology exists within the Blue Obelisk community – it needs some volunteers.
This is a wonderful opportunity for you to change the world of chemical information. I hope very much you support Milkshake.