Something that has been bothering me for quite some time fell into place for me in the last few weeks. I had always been slightly confused by my reaction to the fact that on UsefulChem Jean-Claude actively works to improve and polish the description of the experiments on the wiki. Indeed this is one of the reasons he uses a wiki as the process of making modifications to posts on blogs is generally less convenient and in most cases there isn’t a robust record of the different versions. I have …

…is knowing what you mean…
I posted last week about the spontaneous CMLReact hackfest held around Peter Murray-Rust’s dining room table the day after Science Blogging in London. There were a number of interesting things that came out of the exercise for me. The first was that it would be relatively easy to design a moderately strict, but pretty standard, description format for a synthetic chemistry lab notebook that could be automatically scraped into CMLReact.
Automatic conversions from lab book to machine readable XML
CMLReact files have (roughly) three sections. In …

Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress. However here I wanted to pick up on …

And other big words I learnt from mathematicians…
The observant amongst you will have realised that the title of my previous post pushing a boat out into the area of semantics and RDF implied there was more to come. Those of you who followed the reaction [comments in original post, 1, 2, 3] will also be aware that there are much smarter and more knowledgeable people out there thinking about these problems. Nonetheless, in the spirit of thinking aloud I want to explore these ideas a little further because they underpin …

Frank Gibson has continued the discussion that kicked off here and has continued here [1, 2, 3, 4] and in other places [1, 2] along the way. Frank’s exposition on using FuGE as a data model is very clear in what it says and does not say and some of his questions have revealed sloppiness in the way I originally described what I was trying to do. Here I will respond to his responses and try to clarify what it is that I want, and what I want it to …