Southampton’s Blog3 and ScholarlyHTML


There were several exciting things to come from the recent workshops (World University Network Lab note book, and OREChem) at PNNL; this post is on Southampton’s Blog3 ( (Jeremy Frey, Simon Coles, Mark Borkum and others). They’ve been using blogging as a means to provide an “electronic lab notebook” (a term which I think is rather dated and where the Soton work goes much beyond).

They’ve been doing it for some years but I think the progress over the last year or so has been important. Originally blog technology was very flaky (and still is). They’ve written their own which creates a better semantic platform. I’m not sure what the interoperability is and the issues in using this beyond Soton, but hope to find out.

It has convinced me that blogging is the way to go for capturing and enhancing scientific work – at least for academia and probably for companies as well. There is so much common ground with established practice on the web. Obviously if strong AAA (Authorisation, Authentication, Accounting) is required this takes a LOT more effort whatever technology is required – there are no easy answers (and academia is a hotchpotch of so many different problems in that area).

This reinforces my conviction that HTML5, not PDF, is the way to go for science. (It always was until PDF lost us ten years of progress). ScholarlyHTML fits perfectly into this. It helps to define what convention(s) a blog should emit and what it can consume. If, for example, the blog has created a chemical compound record, then we should use a convention that supports and constrains this in ScholarlyHTML (/pmr/2011/03/14/scholarly-html-%E2%80%93-major-progress/ ). Of course we can and should embed CML in this where appropriate – e.g. for molecules, crystals, calculations, etc.

If we all adopt ScholarlyHTML for our science – and the relatively modest discipline it imposes – then we can have something close to semantic interoperability.

And where we can’t it’s because we don’t fully understand the science, not because we cannot manage the syntax.

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