linking papers to open data – Science in the Open

July 17, 2008December 30, 2009

Policy and technology for e-science – A forum on on open science policy

I’m in Barcelona at a satellite meeting of the EuroScience Open Forum organised by Science Commons and a number of their partners.Â Today is when most of the meeting will be with forums on ‘Open Access Today’, ‘Moving OA to the Scientific Enterprise:Data, materials, software’, ‘Open access in the the knowledge network’, and ‘Open society, open science: Principle and lessons from OA’. There is also a keynote from Carlos Morais-Pires of the European Commission and the lineup for the panels is very impressive.

Last night was an introduction and social kickoff as well. James Boyle (Duke Law School, Chair of board of directors of Creative Commons, Founder of Science commons) gave a wonderful talk (40 minutes, no slides, barely taking breath) where his central theme was the relationship between where we are today with open science and where international computer networks were in 1992. He likened making the case for open science today with that of people suggesting in 1992 that the networks would benefit from being made freely accessible, freely useable, and based on open standards. The fears that people have today of good information being lost in a deluge of dross, of their being large quantities of nonsense, and nonsense from people with an agenda, can to a certain extent be balanced against the idea that to put it crudely, that Google works. As James put it (not quite a direct quote) ‘You need to reconcile two statements; both true. 1) 99% of all material on the web is incorrect, badly written, and partial. 2) You probablyÂ haven’t opened an encylopedia as a reference in ten year.

James gave two further examples, one being the availability of legal data in the US. Despite the fact that none of this is copyrightable in the US there are thriving businesses based on it. The second, which I found compelling, for reasons that Peter Murray-Rust has described in some detail. Weather data in the US is free. In a recent attempt to get long term weather data a research effort was charged on the order of $1500, the cost of the DVDs that would be needed to ship the data, for all existing US weather data. By comparison a single German state wanted millions for theirs. The consequence of this was that the European data didn’t go into the modelling. James made the point that while the European return on investment for weather data was a respectable nine-fold, that for the US (where they are giving it away remember) was 32 times. To me though the really compelling part of this argument is if that data is not made available we run the risk of being underwater in twenty years with nothing to eat. This particular case is not about money, it is potentially about survival.

Finally – and this you will not be surprised was the bit I most liked – he went on to issue a call to arms to get on and start building this thing that we might call the data commons. The time has come to actually sit down and start to take these things forward, to start solving the issues of reward structures, of identifying business models, and to build the tools and standards to make this happen. That, he said was the job for today. I am looking forward to it.

I will attempt to do some updates via twitter/friendfeed (cameronneylon on both) but I don’t know how well that will work. I don’t have a roaming data tariff and the charges in Europe are a killer so it may be a bit sparse.

May 11, 2008December 30, 2009

More on the science exchance – or building and capitalising a data commons

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Following on from the discussion a few weeks back kicked off by Shirley at One Big Lab and continued here I’ve been thinking about how to actually turn what was a throwaway comment into reality:

What is being generated here is new science, and science isnâ€™t paid for per se. The resources that generate science are supported by governments, charities, and industry but the actual production of science is not supported. The truly radical approach to this would be to turn the system on its head. Donâ€™t fund the universities to do science, fund the journals to buy science; then the system would reward increased efficiency.

There is a problem at the core of this. For someone to pay for access to the results, there has to be a monetary benefit to them. This may be through increased efficiency of their research funding but that’s a rather vague benefit. For a serious charitable or commercial funder there has to be the potential to either make money, or at least see that the enterprise could become self sufficient. But surely this means monetizing the data somehow? Which would require restrictive licences, which is not at the end what we’re about.

The other story of the week has been the, in the end very useful, kerfuffle caused by ChemSpider moving to a CC-BY-SA licence, and the confusion that has been revealed regarding data, licencing, and the public domain. John Wilbanks, whose comments on the ChemSpider licence, sparked the discussion has written two posts [1, 2] which I found illuminating and have made things much clearer for me. His point is that data naturally belongs in the public domain and that the public domain and the freedom of the data itself needs to be protected from erosion, both legal, and conceptual that could be caused by our obsession with licences. What does this mean for making an effective data commons, and the Science Exchange that could arise from it, financially viable? Continue reading “More on the science exchance – or building and capitalising a data commons”

May 5, 2008December 30, 2009

Attribution for all! Mechanisms for citation are the key to changing the academic credit culture

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Once again a range of conversations in different places have collided in my feed reader. Over on Nature Networks, Martin Fenner posted on Researcher ID which lead to a discussion about attribution and in particular Martin’s comment that there was a need to be able to link to comments and the necessity of timestamps. Then DrugMonkey posted a thoughtful blog about the issue of funding body staff introducing ideas from unsuccessful grant proposals they have handled to projects which they have a responsibility in guiding. Continue reading “Attribution for all! Mechanisms for citation are the key to changing the academic credit culture”

February 6, 2008December 30, 2009

Connecting Open Notebook data to a peer reviewed paper

One thing that we have been thinking about a bit recently is how best to link elements of a peer reviewed paper back to an Open Notebook. There are a number of issues that this raises, both technical and philosophical about how and why we might do this. Our first motivation is to provide access to the raw data if people want it. The dream here is that by clicking on a graph you are taken straight through to processed data which you can then backtrack through to get to the raw data itself. This is clearly some way off.

Other simple solutions are to provide a hyperlink back to the open notebook, or to an index page that describes the experiment, how it was done, and how the data was processed. Publishers are always going to have an issue with this because they can’t rely on the stability of external material. So the other solution is to package up a version of the notebook and provide it as supplementary information. This could still provide links back to the ‘real’ notebook but provides additional stability and also protects the data against disaster by duplicating it.

The problem with this is that many journals will only accept pdf. While we can process a notebook to provide a package which is wrapped up as pdf this has a lot of limitations particularly when it comes to data scraping, which after all we want to encourage. An encouraging development was recently described on the BioMedCentral Blog where they describe the capability of uploading a ‘mini website’ as supplementary information. This is great as we can build a static version of our notebook, with lots of lovely rich metadata built in. We can point out to the original notebook and we can point in from the original notebook back to the paper. I am supposed to be working on a paper at the moment which I was considering where to send. I hope we can give BMC Biotechnology or perhaps BMC Research Notes a go to test this out.