Requirements for citations to be treated as First-Class Data Entities In my introductory blog post, I listed five requirements for the treatment of citations as first-class data entities.  The second of these requirements is that they must have metadata structured using a generic yet appropriately detailed data model.

I'm trying to get my head around the data model used by ZooBank to store taxonomic names. To do this, I've built a graph for the species Belonoperca pylei described by Baldwin &

I talk a lot about building tools that make it easy capture all the objects that we create as part of the research process and then connect all of these up together. Thus far there have been small and limited demonstrators. This is a proposal to build something that demonstrates the general principle at this coming weekend’s Science Hack Day in London.

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.

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.

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.

This started out as a comment on Peter Murray-Rust’s response to my post and grew to the point where it seemed to warrant its own post.

More on the discussion of structured vs unstructured experiment descriptions. Frank has put up a description of the Minimal Information about a Neuroscience Investigation standard at Nature Precedings which comes out of the CARMEN project. Neil Saunder’s has also made some comments on the resistance amongst the lab monkeys to think about structure. Lots of good points here. I wanted to pick out a couple in particular; From Neil;

Frank Gibson of peanutbutter has left a long comment on my post about data models for lab notebooks which I wanted to respond to in detail. We have also had some email exchanges. This is essentially an incarnation of the heavyweight vs lightweight debate when it comes to tools and systems for description of experiments.

I’ve been mulling over this for a while, and seeing as I am home sick (can’t you tell from the rush of posts?) I’m going to give it a go. This definitely comes with a health warning as it goes way beyond what I know much about at any technical level. This is therefore handwaving of the highest order. But I haven’t come across anyone else floating the same ideas so I will have a shot at explaning my thoughts.