Show me the data!

just a quick post…

I’m pretty shocked at the poor indexing service given by Thompson Reuters Web of Knowledge (or ISI Web of Science as you might know it).

I’ve unashamedly bashed them before and I’ll bash them again here. (They deserve criticism because they’re paid a lot of money to do this as a commercial for-profit enterprise, and I don’t think they’re doing it as well as they could be.)

I performed a very simple search today looking for the articles containing the word ‘cladistic’ but NOT ‘phylogen*’ for articles published in the year 2010.

Topic=(cladistic) NOT Topic=(phylogen*) AND Year Published=(2010)

Below is a screenshot of just one of many of the disappointing results. I’ve refined the search to just the PLoS paper, to clearly show that it does come-up in this search:

It’s an Open Access paper, so we can all go see for ourselves the FULL content of the paper

Na, B.-K., Bae, Y.-A., Zo, Y.-G., Choe, Y., Kim, S.-H., Desai, P. V., Avery, M. A., Craik, C. S., Kim, T.-S., Rosenthal, P. J., and Kong, Y. 2010. Biochemical properties of a novel cysteine protease of plasmodium vivax, vivapain-4. PLOS NEGLECTED TROPICAL DISEASES 4.

In which we find the text caption for figure 1 mentions ‘phylogen*’ twice!

from Na, B.-K., Bae, Y.-A., Zo, Y.-G., Choe, Y., Kim, S.-H., Desai, P. V., Avery, M. A., Craik, C. S., Kim, T.-S., Rosenthal, P. J., and Kong, Y. 2010. Biochemical properties of a novel cysteine protease of plasmodium vivax, vivapain-4. PLOS NEGLECTED TROPICAL DISEASES 4. CC-BY licenced

so at the very least I suspect Web of Science (WoS) is systematically NOT indexing the caption text of figures (if you know more than I about this, please do comment). Academics rely on services like this to effectively and accurately search the literature, to perform comprehensive reviews and such. If all the textual content of science isn’t actually being indexed by WoS, that’s clearly going to lead to bad science at some point (e.g. a vital missing paper, not picked up in an otherwise well designed literature search). I could forgive them for not being able to OCR the text within the images of figures, but NOT for the fully machine-readable text captions like this one. Furthermore, it’s Open Access and fully-digital – why aren’t they indexing figure caption text?



It appears it’s not just figure caption text they don’t index. Do they index only titles and abstracts?

many of the other 81 results (papers) of that search for ‘cladistic’ but NOT ‘phylogen*’ contain the word-stem ‘phylogen*’ in the full text of the paper!


Wilts, E. F., Arbizu, P. M., and Ahlrichs, W. H. 2010. Description of bryceella perpusilla n. sp (monogononta: Proalidae), a new rotifer species from terrestrial mosses, with notes on the ground plan of bryceella REMANE, 1929. INTERNATIONAL REVIEW OF HYDROBIOLOGY 95.

Echeverry, A. and Morrone, J. J. 2010. Parsimony analysis of endemicity as a panbiogeographical tool: an analysis of caribbean plant taxa. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 101.

Stutz, H. L., Shiozawa, D. K., and Evans, R. P. 2010. Inferring dispersal of aquatic invertebrates from genetic variation: a comparative study of an amphipod and mayfly in great basin springs. JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY 29

Campo, D., Molares, J., Garcia, L., Fernandez-Rueda, P., Garcia-Gonzalez, C., and Garcia-Vazquez, E. 2010. Phylogeography of the european stalked barnacle (pollicipes pollicipes): identification of glacial refugia. MARINE BIOLOGY 157.

Choiniere, J. N., Clark, J. M., Forster, C. A., and Xu, X. 2010. A basal coelurosaur (dinosauria: Theropoda) from the late jurassic (oxfordian) of the shishugou formation in wucaiwan, people’s republic of china. JOURNAL OF VERTEBRATE PALEONTOLOGY 30.

Caldwell, M. W. and Palci, A. 2010. A new species of marine ophidiomorph lizard, adriosaurus skrbinensis, from the upper cretaceous of slovenia. JOURNAL OF VERTEBRATE PALEONTOLOGY 30.

Hastings, A. K., Bloch, J. I., Cadena, E. A., and Jaramillo, C. A. 2010. A new small short-snouted dyrosaurid (crocodylomorpha, mesoeucrocodylia) from the paleocene of northeastern colombia. JOURNAL OF VERTEBRATE PALEONTOLOGY 30.

Karanovic, I. and McKay, K. 2010. Two new species of leicacandona karanovic (ostracoda, candoninae) from the great sandy desert, australia. JOURNAL OF NATURAL HISTORY 44.

(and more, these are just some of the articles I’ve looked at the full-text of so far… I think it’s safe to say now this is NOT a one off phenomenon)

I’ve now found through manual inspection that at least 47 of the ‘hits’ for this search actually contain a ‘phylogen*’ word within the main text of the paper (excluding the reference list)

I guess I’m probably not the first to realise this but… wow. Is this not *really* poor service? I’m pretty sure my desktop software could do a better job of indexing than this. All it is, is simple string matching!

…and of course I can do a better job of this myself with Open Access papers. All one need do is download the OA corpus from UKPMC and index the *FULL* text including figure caption text and reference lists yourself. I wonder how many more relevant papers I might ‘find’ with my searches if I did this rather than relying on Web of Science?

I realise thus far, I may not have explained too clearly exactly what I’m doing for my Panton fellowship. With this post I shall attempt to remedy this and shed a little more light on what I’ve been doing lately.

The main thrust of my fellowship is to extract phylogenetic tree data from the literature using content mining approaches (think text mining, but not just text!) – using the literature in its entirety as my data. I have very little prior experience in this area, but luckily I have an expert mentor guiding me: Peter Murray-Rust (whom you may often see referred to as PMR). For those of us biologists who may not be familiar with his work, whilst trying not to be too sycophantic about it, PMR is simply brilliant, it’s amazing what he and his collaborators have done to extract chemical data from the chemical literature and provide it openly for everyone, in spite of fierce opposition at times from those with vested interests in this data remaining ‘closed’.

Now he’s turned his attention to the biological literature for my project and together we’re going to try and provide open tools to extract phylogenetic data from the literature. Initially I proposed trying to grab just tree topology and tip labels – a kind of bare minimum, but PMR has convinced me that we should be ambitious and all-encompassing, and thus our aims have expanded to include branch lengths, support values, the data-type the phylogeny was inferred from, and other useful metadata. And why not? We’re ingesting the totality of the paper in our process, from title page to reference list, so there’s plenty of machine-readable data to be gleaned. The question is, can we glean it off accurately enough, balancing precision and recall?

So for starters, we’ve been using test materials that we’re legally allowed to, namely Open Access CC-BY papers from BMC & PLoS to test our extraction tools, specifically focusing on a subset of all ~8500 papers containing the word-stem phylogen* from BMC. It’s a rough proxy for papers that’ll contain a tree, and it’s good enough for now – we’ll need to be able to deal with false positives along with all the positive positives, so it’s instructive to keep these in our sample.

We’ve been working on the regular structure of BMC PDFs, getting out bibliographic metadata, and the main-text for further NLP processing downstream to pick out data & method relevant words like say PAUP* , ML , mitochondrial loci etc… But the real reason we’re deliberately using PDFs rather than the XML (which we also have access to) is the figures – where all the valuable phylogenetic tree data is. If this can be re-interpreted with reference to the bibliographic metadata, the figure caption and further methodological details from the full-text of the paper, then we may be able to reconstruct some fairly rich and useful phylogenetic data.

To make it clear, in slight contrast to the Lapp et al iEvoBio presentation embedded above, we’re not trying to just extract the images, but rather to re-interpret them back into actual re-useable data, probably to be provided in NeXML (and from there on, whatever form you want). We’re pretty sure it’s an achievable goal. Programs like TreeThief, TreeRipper, and TreeSnatcher Plus have gone some way towards this already, but never before been incorporated in a content mining workflow AFAIK.

Unfortunately I wasn’t at iEvoBio 2012 (I’m short on money and on time these days) but it’s great to see from the slides the growing recognition of the SVG image file format as a brilliant tool for communicating digital science. I also put a bit about that in my Hennig XXXI talk slides too (towards the end). Programs like TNT do output SVG files, so there’s scope to make this a normal part of any publication workflow. Regrettably though, rather few publisher produced PDFs contain SVG formatted images – but if people, and editorial boards (perhaps?) can be made aware of their advantages, perhaps we can change this in future…?

the very same file, opened as plain-text. It’s fairly easy to reconvert back into re-useable machine-readable data.


Agapornis phylogeny.svg from Wikipedia (PD)










Gathering phylogenetic data from beyond PLoS, BMC and other smaller Open Access publishers is going to be hard, not for technical, but purely legal reasons:

The scope and scale of phylogenetic research (using ‘phylogen*’ as a proxy):

There’s a lot of phylogenetic research out there… but little of it is Open Access – which is problematic for content mining approaches – particularly if subscription-access publishers are reticent to allow access.

Some facts:

  • with a Thomson Reuters Web of Science search, SCI-EXPANDED database (only), Topic=(phylogen*) AND Year Published=(2000-2011) this returns 101,669 results (at the time of searching YMMV)
  • 91,788 of which are primary Research Articles (as opposed to Reviews, Proceedings Papers, Meeting Abstracts, Editorial Materials, Corrections, Book Reviews etc…)
  • Recent MIAPA working group research I contributed to (in review) quantitatively estimates that approximately 66% of papers containing ‘phylogen*’ report a new phylogenetic analysis (new data).
  • Thus conservatively assuming just one tree per paper (there are often many per paper), there are > 60,000 trees contained within just 21st century research articles.
  • As with STM publishing as a whole, the number of phylogenetic research articles being published each year shows consistent year-on-year increases
  • Cross-match this with publisher licencing data and you’ll find that only ~11% of phylogenetic research published in 2010 was CC-BY Open Access (and this % probably decreases as you go back before 2010)
So the real fun and games will come later this year, when I’m sure we’ll have the capability (software tools) to do some amazing stuff, having first perfected it on OA materials… but will they let us? Heather Piwowar’s experience earlier this year didn’t look too fun – and that was all for just one publisher. Phylogenetic research occurs in and beyond at least 80 separate STM publishers by my count (let alone the >500 journals it occurs in!) – so there’s no way anyone would bother trying to negotiate with them all! I’m sticking by the intuitive principle that The Right to Read Is the Right to Mine but I’ll have a think about that some more when we actually get to that bridge.

Finally, it’s also worth acknowledging that we’re certainly not the first in this peculiar non-biomedical mining space – ‘biodiversity informaticists’ have been doing useful things with these techniques for a while now in innovative ways largely unrelated to medicine e.g. LINNAEUS from Casey Bergmann’s lab, and a recent review of other projects from Thessen et al (2012) [hat-tip to @rdmpage for bringing that later paper to the world’s attention via Twitter]. Literally all areas of academia could probably benefit from some form or another of content mining – it’s not just a biomed / biochem tool.

So, I hope that explains things a bit better. Any questions?


Some references (but not all!):

Gerner, M., Nenadic, G., and Bergman, C. 2010. LINNAEUS: A species name identification system for biomedical literature. BMC Bioinformatics 11:85+. [CC-BY Open Access]

Thessen, A. E., Cui, H., and Mozzherin, D. 2012. Applications of natural language processing in biodiversity science. Advances in Bioinformatics 2012:1-17. [CC-BY Open Access]

Hughes, J. 2011. TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics 12:178+.  [CC-BY Open Access]

Laubach, T., von Haeseler, A., and Lercher, M. 2012. TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinformatics 13:110+. [CC-BY Open Access, incidentally I was one of the reviewers for this paper. I signed my review, and made a point of it too. Nor was it a soft review either I might add]

Running TNT in parallel

July 14th, 2012 | Posted by rmounce in Conferences | Phylogenetics | TNT - (6 Comments)

Building upon the instructions given here and here I thought I’d write up one of the many useful things Pablo Goloboff kindly taught us at the TNT scripting workshop after the Hennig XXXI meeting.

It’s actually not the easiest thing to setup if you’re using Ubuntu… Pablo had to help me do it – I would never have got it up and running on my own.


You’ll need to install the pvm package either from the repositories with

sudo apt get install pvm

or download and compile from source

It’s actually better to compile from source because the pvm package in the Ubuntu repositories is out of date – they provide only version 3.4.5, whilst the latest version of pvm, released way back in 2009 is 3.4.6 ! I guess the packaging team have other priorities…

Then you’ll need to configure pvm on your machine:

  • edit your bashrc file  nano ~/.bashrc  and insert this line:

export PVM_ROOT=/usr/lib/pvm3

save & close the bashrc file. Now  source ~/.bashrc and then test the path with echo $PVM_ROOT this should now return


  • in your user home directory (for me this is /home/ross/ ) create a plaintext file called hostlist (the exact name doesn’t matter but remember it) and write one line within this file:

rossnetbook ep=/usr/bin/

(replace ‘rossnetbook’ with your computer hostname – if you’re not sure what this is then nano /etc/hostname will tell you) save and close this file.

  • now start pvm from your user home directory with pvm hostlist  this tells pvm your hostname and the path. Unfortunately you’ll need to start-up pvm this way every time you restart your computer. Perhaps there’s a better way? Let me know if so…

Finally, make sure you’ve copied the 64-bit TNT binary to both /usr/bin/ & to your user home directory and make sure that they’re executable.

Now you should be ready to go…

if you get an error message like this from TNT:

tnt*>ptnt begin ajob2 2 = mult 5; return ; ptnt wait . ;
Macro language is ON
Macros: 50.5 Kb in use, 51.8 Kb free
libpvm [pid7539] /tmp/pvmd.1000: No such file or directory
libpvm [pid7539] /tmp/pvmd.1000: No such file or directory
libpvm [pid7539] /tmp/pvmd.1000: No such file or directory
libpvm [pid7539]: pvm_config(): Can’t contact local daemon

Can’t enter parallel interface (make sure PVM is running)

you’ve probably forgotten to start pvm with pvm hostlist

see the video I uploaded below for demonstration of the speed-up possible by performing tasks in parallel:

the video shows me performing a simple search on the zilla dataset of Chase et al. (1993) using traditional heuristic settings (60 reps) performed first in serial, then in parallel (starting after 2:00) 20 reps x 3 slaves.

100 seconds for search 1, down to just 48 seconds for search 2 (in parallel). YMMV

Neither of these searches found the shortest length trees btw!

mxram 100; /* increase memory */
p zilla.tnt; /* read in the data */
hold 20000; /* increase the maximum number of trees held */
mult 60; /* perform a traditional search with 60 replications */
le; /* tree lengths */

/* parallel tnt job, called ‘ajob’ using 3 slaves performing ‘mult 20’ on each slave */
ptnt begin ajob 3 = mult 20; return ; ptnt wait . ;

basically just insert what you want your slaves to do in between the ‘=’ and the return; commands.

ptnt get ajob; /* get data back from slaves to master */

This was just the tip of the iceberg of the course. I can’t even begin to write-up the rest of the course in this much detail! But I hope this helps…

many many thanks Pablo, and all the organisers of this workshop AND the conference – it was *much* appreciated

After sending a letter to my local MP, urging him to support the recommendations of the Hargreaves Report on Intellectual Property reform in parliament nearly a month ago (sent on the 17th June 2012) – I finally have a reply!

Sadly, it’s not the reply I wanted. Don Foster does not appear willing to support the Early Day Motion on Intellectual Property law reform to further enable research, that I explicitly asked him to sign.


Below is a verbatim copy of his letter as was emailed to me earlier (12th July 2012), which I am posting here so all his constituents can see, for their own satisfaction (or not, as in my case), his position with respect to IP reform.



12 July 2012

Mr Ross Mounce

Flat 3, Rochfort Court

Forester Avenue



Our Ref: Moun010/1

Dear Mr Mounce


Thank you for writing to me in reference to the exceptions for digital content proposed by the Hargreaves Review. I had in fact received your letter, so I apologise the confusion on Twitter and the delay in replying; life has been rather hectic recently not least because of the impending Olympics and my role as a member of the Olympic Board. Adding this to the very large amounts of correspondence received in my office each day, I’m sorry to say that I cannot always respond as quickly as I’d like.


As you may know, I have been involved in these issues for some time. I am currently working within Government on the development of the Communications White paper (which will touch on these issues when it is published in early 2013), I helped initiate – and serve as a member of – the Creative Industries Council (which, among other issues, is reviewing the Hargreaves Report) and am a member of the All Party Parliamentary Group on IP (which is currently reviewing the work of the IPO and its various recent pronouncements).


Inevitably I am somewhat constrained in responding in detail to your letter since some of the work I am involved in is not yet public and, more importantly, because final conclusions haven’t been reached.


I am also conscious that we have to work within – while seeking, potentially, to change – relevant EU legislation. As you will know, this includes the InfoSoc Directive (Directive 2001/29/EC; see


You will know better than I, that the development of “exceptions” is never easy. An exception for “format shifting” may be alright and reasonable for, say, the music industry but the situation is very different for the UK Video Industry. Similarly, an exception for “parody” could make sense for small snippets used in a comedy show, but would not necessarily be appropriate for a situation where one artist does a complete performance of another artist’s song and claims it to be a parody. Some of the proposed exceptions for the copying of educational works seem to worryingly disregard the importance of copyright/IP protection in ensuring the flow of new works. 

Whilst Don Foster MP will treat as confidential any personal information which you pass on, he may need to allow his staff and authorised volunteers to see it if this is needed to help and advise you. Don may pass on all or some of this information to agencies such as DWP, Inland Revenue or Local Council if this is necessary to help with your case. We may write to you from time to time, to keep you informed on issues that you might find of interest. Please let us know if you do not wish him to contact you for this purpose

— page break —

In your letter you argue that the exceptions proposed in relation to “data mining” should be accepted.


I am well aware of the strength of feeling among some on this issue. But, as the IPO’s summary of the responses to consultation on the issue makes clear, proposals to enable researchers to use computerised techniques to read information contained in journal articles without infringing publishers’ rights have drawn “strongly divided” views from the industry.


Certainly it is true that, as the IPO puts it, “Researchers and research institutions generally supported the proposed exception. They argued that copyright was not established to restrict the use of data, and the added value of these technologies was provided by the actions of researchers, not publishers.”


However, there is also a strongly held opposing view; one which suggested that it was “too soon to seek a regulatory solution in a new and fast-developing sector, ” that “a copyright exception would prevent publishers from ensuring security of content and stability of provision,” and that “an unremunerated exception would remove the incentive for publishers to make the considerable investments needed to convert content into the right forms, to develop their own services, and to support the application of services by researchers or third parties.”


In the light of these arguments we are currently working to find a way forward. I am not yet in a position to give you assurances that I will press from the exceptions you seek as they are currently formulated (although, I am more inclined to support them than to oppose them).


I hope you will understand, and again, apologies for the delay in replying.

With best wishes,

Yours sincerely,

Rt Hon Don Foster MP

Please reply to 31 James Street West, Bath, BA1 2BT

Tel: 01225 338 973 Fax: 01225 463 630


I have also forwarded Don’s letter to all the staff in my department, as this is about research, and their local parliamentary representative’s views with respect to research, and thus concerns them:


Dear all,

Last month, I sent a formal letter to our local MP Don Foster, urging him
to sign his support for recommendations in the Hargreaves report[1] on
Intellectual Property law reform as it relates to research, particularly
the proposed exceptions to copyright to enable text-mining of otherwise ‘closed
access’ content. (You can read the full letter I sent here[2] it’s fairly short.)
The legal obstructions to text-mining research were also recently described in a Nature news piece[3].

This directly relates to my fellowship research project, as I’m using
content mining techniques to re-extract phylogenetic data from the
literature. At the moment I can only legally mine just ~13% of UKPMC
literature (the XML of which is just 5.5Gb[4] btw, let me know
if you want a copy). This is a great shame, as we have the tools and
capability to make use of ALL of the research literature and more with
current techniques. Only legal barriers prevent this.

I have attached his reply. At best he is sitting on the fence. At worst I
think he has failed to critically evaluate the meekness of the
counter-arguments given such as it being “too soon to seek a regulatory

So, is anyone here interested in sending a further letter in support of
enabling text-mining research? This is perhaps our one and only chance to
directly influence government policy on this research issue. I feel a more
senior scientist from the University of Bath would perhaps help convince
Don to lend his support to this issue. The parliamentary motion already has
the support of 27 MPs[5], but will need more.

Please feel free to contact me offlist about this. I will not contact this
list about this issue again.

Many thanks for your time,



Having invested some time in this already, there seems little point in giving up now. I will wait and see over the weekend if there is anyone else from my department (or the University as whole), that wants to pursue this further before I try again.

The subscription-access segment of the STM publishing industry that is protesting the recommendations of the Hargreaves report undoubtedly has paid lobbyists dedicated to this issue, and they have clearly done a good job here. I am unpaid and inexperienced with respect to arguing this from the research perspective, and probably outnumbered. But I will not stop trying to further enable research.