Show me the data!

Open Access discussed on the radio

August 20th, 2012 | Posted by rmounce in Open Access - (0 Comments)

[I’m cross posting this from the OKFN version so I can embed the audio of the show in the post]

Last Friday (17/08/12), representing the Open Knowledge Foundation, I had the pleasure of discussing the new Research Councils UK (RCUK) plan for all UK publicly-funded research to be published Open Access, on a special half hour Voice of Russia UK broadcast radio discussion.

I have written about this policy before and am very supportive of it, just as I am with Open Access in academia in general. I personally believe it will aid transparency and equality in research – so that no researcher has an unfair advantage over another through greater/easier access to vital research literature (just one of many worthy benefits arising from Open Access). But there are certainly also vocal opponents to this plan – mostly those with vested interests in keeping the obscene profits of the traditional subscription access publishing system alive (which commonly generate >30% profit margins largely derived from the taxpayer-spending of the world’s research libraries on journal subscriptions). Whilst others express vague and often unspecified “concerns” about Open Access and further still many academics are notably apathetic towards it, or are even proudly agnostic on the issue.

Thus a publicly-broadcast discussion of this new open policy is well warranted.

No secret science
[wpaudio url=”″ text=”Voice of Russia UK radio Open Access discussion hosted by Daniel Cinna” ]
I won’t say anything about the discussion itself, only that you should listen to it (embedded above; alt link here) if you are at all interested in the future of science, and the benefits of the new RCUK Open Access policy.

The members of the discussion panel included Rita Gardner, the Director of the Royal Geographical Society, noted for her concerns about the potential effects of Open Access on UK Learned Society income and revenue [paywalled link]; Ross Mounce, Panton Fellow promoting open data in science (myself) from the Open Knowledge Foundation; Bjorn Brembs, Professor at the Department of Genetics at the University of Leipzig, noted critic of for-profit publishers and their lack of ‘value-add’ amongst other issues; and Timothy Gowers, the Rouse Ball Professor of Mathematics at Cambridge University, instigator of the popular academic-led boycott of the academic for-profit publisher Elsevier.

The ensuing discussion was ably guided by VoiceofRussia radio presenter Daniel Cinna, and recorded by a backroom team with an impressively professional studio setup (Timothy & Bjorn were joining the debate via phone from abroad almost seemlessly, whilst Rita and I were in the London studio). As noted by Rita off-air, it would have been nice to have had a publisher representative in the discussion to add their unique viewpoint but apparently the VoR production team had asked, but no for-profit publisher they had asked was willing to take part. So one cannot attribute any blame to the VoR team if the discussion panel lacked representational balance.

About Voice of Russia (adapted from their own website):

The Voice of Russia is the world’s oldest international broadcaster and is among the world’s top five radio broadcasters today which include the BBC, the Voice of America, Deutsche Welle and Radio France International. The London-based team produces programs for VoR that bring our listeners a Russian perspective on our two countries and the world. VoR broadcasts to 160 countries in 38 languages using short and medium waves, FM, satellite and the global communications network. In London we are now also available online and via DAB radio. We aim to welcome a new British audience to our 109 million listeners worldwide.

Panton Fellowship updates: July (month 4)

August 4th, 2012 | Posted by rmounce in Content Mining | Panton Fellowship updates - (Comments Off on Panton Fellowship updates: July (month 4))

It’s the Olympics now so this work update is a) late and b) short


As ever progress has been exciting – look what we can extract from some PDFs:

(click to enlarge each) Attribution: The left panel is from Cánovas et al. BMC Evolutionary Biology 2011 11:371 doi:10.1186/1471-2148-11-371

On the left is the original figure, and on the right we have an SVG representation of the data we can extract automatically from this figure. We have the topology, the taxon labels AND the support values 100% correctly interpreted! Obviously we can’t reclaim phylogenetic data with this much precision and recall from all papers. But it’s a promising example, automatically generated – no manual guidance or tweaking needed – just feed it the PDF. [My WordPress server won’t let me upload the original SVG copy of this for “security reasons” so the image on the right is a .jpg copy of the original .svg]


I should also note this was achieved completely independently of previous image-based tree-extraction softwares like TreeSnatcher Plus, TreeRipper & TreeThief. This is a great example of why it’s very important for editors and publishers to strictly stipulate that diagrams in figures containing data such as this be uploaded and produced in the final PDF version as lossless vector graphics rather than lossy bitmaps such as .png .jpg or .bmp – only vectors keep the fidelity of the underlying data. We note that there are many publishers out there who regularly seem to produce figures in their PDFs that are NOT on the whole very good quality wrt this. Difficult to know whether the authors or the publishers are to blame in each case but either way standards need to be improved.


By mining PDFs we can re-extract and re-release far more than just phylogenetic data from the literature – we’re fairly sure we can reliably identify the rough type of figure depicted in PDFs by machine methods using certain diagnostic features such as number & proportion of horizontal and vertical lines.



Peter Murray-Rust & I now are looking for a collaborator to help us implement machine learning methods to classify scientific figures into discrete categories e.g. bar charts, scatter plots, network diagrams (including phylogenies), pie charts, box & whisker plots etc… in an automated way.

If you’re interested please contact myself or Peter.

That’s all for now.

PS If you’re watching the London 2012 Olympics Volleyball tomorrow morning you may well just see me in the crowd. Managed to snaffle some returned tickets by setting up an alert for new tickets using a combination of (to alert me to page changes on the ticket website) and to email me as soon as the RSS feed gets a new item (updated ticket information). Without this nifty trick I very much doubt I’d have got any tickets.