I’m at a Talis Research Day today looking at a number of issues that are ‘hot topics’ in education and research at the moment. The program for the day looks great, with presentations by Peter Murray-Rust from the University of Cambridge, who is a proponent of opening up research and research data – I’d recommend his blog to catchup with the latest work in this area. Peter is talking about ‘Data-driven research’. Following this Andy Powell from Eduserv is talking about Web 2.0 and repositories.<\/p>\n
First up – Peter M-R:<\/p>\n
Peter presents using HTML – although it’s hard work, he believes that the common alternatives (Powerpoint, PDF) destroy data. I think the question of ‘authoring tools’ – not just for presentations, but in a more general sense of tools that help us capture data\/information – is going to come to the fore in the next few years.<\/p>\n
Peter has a go at publishers – claiming that publishers are in the business of preventing access to data, rather than facilitating it (at this points asks if there are any publishers in the audience – two sheepish hands are raised). Peter, also mentioning that Chemistry is particularly bad as a discipline in terms of making data accessible – with the American Chemical Society being real offender.<\/p>\n
Peter’s talk tend to be pretty impromptu – so he is just listing some topics he may (or not) touch on today:<\/p>\n
Peter demonstrating how a graph without metadata is meaningless – showing a graph on the levels of Atmospheric Carbon Dioxide. If this was in paper form and we wanted to do some further analysis – it would take a lot of effort to take measurements off the graph – but if we have the data from behind the graph, we can immediately leap to doing further work.<\/p>\n
Peter now noting that a scholarly publication looks very much now as it would have done 200 years ago. Showing a pdf of an article from Nature – and making the point that all looks great (illustrations of molecules, proteins and reactions etc.) but completely inaccessible to machines.<\/p>\n
Peter noting that most important bio-data that is published is publicly accessible and reusable – but this is not true in chemistry. This means in the article, the data about the proteins is publicly accessible, but the information on chemical molecules is not – although covered in the same article.<\/p>\n
Peter illustrating how there is a huge industry based on moving and repurposing data (e.g. taking publicly available patent data, and re-distributing in other formats etc.)<\/p>\n
Peter now showing how a data rich graph is reduced to a couple of data points to ‘save space’ in journals – a real paper-based paradigm – we need to get away from this. Similarly experimental protocols are reduced to condensed text strings.<\/p>\n
Peter now showing ‘JoVE’ – Journal of Visualised Experiments. In this online publication where scientific protocols are published in both textual and audio-visual format – so much richer in detail than the type of summarisation that journals currently support. Peter notes – this is really important stuff – failure to provide enough detail to recreate an experiment, it can have a huge impact on your reputation and career.<\/p>\n
Peter now moving onto ‘big science’ – relating his visit to CERN – how the enormous amounts of data generated by the Large Hadron Collider is captured, as well as relevant metadata. However, most science is not like this – not on this scale. Peter is relating the idea of ‘long tail’ science (coined by Jim Downing) – this is the small scale science, that is still generating (over all activity) large amounts of data – but each from small activities. This is really relevant to me, as this is exactly the discussion I was having at Imperial yesterday – looking at the approach taken by ‘big science’ and wondering if it is applicable to most of the research at Imperial.<\/p>\n
So in Long-tailed Science, you may have a ‘lab’ that will have a reasonably ‘loose’ affiliation to the ‘department’ and ‘institution’. Peter noting that most researchers have experience data-loss – and this can be a real selling point for data and publication repositories.<\/p>\n
Peter showing a thesis with many diagrams of molecules, graphs etc. Noting there is no way to effectively extract the information about molecules from the paper, as it is a PDF. He is demonstrating a piece of software which extracts data from a chemical thesis – demonstrating this from a thesis authored in Word, and using OSCAR (a text-mining tool tuned to work in Chemistry) – and shows how it can extract relevant chemical data, can display it in a table, reconstruct spectra (from the available data in the text – although these are not complete).<\/p>\n
Peter asking (rhetorically) what are the major barriers – e.g. Wiley threatened legal action against a student who put graphs on their website.<\/p>\n
Peter now demonstrating ‘CrystalEye’ – a system which spiders the web for crystals – reads the raw data, draws a ‘jmol’ view (3d visualisation) of the structure, links to the journal article etc. This brings together many independent publications in a single place showing crystal structures. Peter saying this could be done across chemistry – but data is not open, and there are big interests that lobby to keep things this way (specifically mentioning Chemical Abstracts lobbying the US Government)<\/p>\n
Peter now talking about development of authoring tools – pointing out that this is much more important that a deposition tool – if the document\/information is authored appropriately, it is trivial to deposit (it occurs to me that as long as it is on the open web, then deposit is not the point – although there is some question of preservation etc – but you could start to take a ‘wayback machine’ type approach). Peter is demonstrating how an animated illustration of chemical synthesis can be created from the raw data.<\/p>\n
Peter now coming on to Repositories. Using ‘Sourceforge’ (and computer code repository) as an example. Stressing the importance of ‘versioning’ within Sourceforge – trivial to go back to previous versions of code. Need to look at introducing these tools for science. He is involved in a project called ‘Bioclipse’ – a free, open-source, workbench for chemo- and bioinformatics using a ‘sub versioning’ approach (based on Eclipse which is a software subversioning package) – Bioclipse stores things like spectra, proteins, sequences, molecules etc.<\/p>\n
Peter mentioning issues of researchers not wanting to share data straightaway – we need ‘ESCROW’ systems that can store information which is only published more openly at a later date. The selling point is keeping the data safe.<\/p>\n
Peter dotting around during the last few minutes of the talk, mentioning:<\/p>\n
Me: Economic costs of capturing data outside ‘big science’<\/p>\n
PMR: If we try to retro-fit costs are substantial. However, data capture can be marginal cost if done as part of research. Analogy of building motorways and cyclepaths – very expensive to add cyclepaths to motorways, but trivial to build at the same time.<\/p>\n
Some interesting discussion of economics…<\/p>\n