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I read some sad news on Twitter recently. The Ecological Society of America has decided to publish its journals with Wiley:

Whilst I think the decision to move away from their old, unloved publishing platform is a good one. The move to publish their journals with Wiley is a strategically poor one. In this post I shall explain my reasoning and some of the widespread dissatisfaction with the direction of this change.

Society journals should not be a profit-driven business

The stated goals of The Ecological Society of America (ESA) are noble and I reproduce them here below to help you understand what the society in theory aims to do:

  • * promote ecological science by improving communication among ecologists;
  • * raise the public’s level of awareness of the importance of ecological science;
  • * increase the resources available for the conduct of ecological science;
  • * ensure the appropriate use of ecological science in environmental decision making by enhancing communication between the ecological community and policy-makers

Source: http://www.esa.org/esa/about/

Reading those four bullet points, it strikes me that a society with this stated mission should be a vanguard of the open access movement. An efficient, well-implemented open access publishing system, supported (and thus empowered) by the ESA would positively address all four of those goals.

Do I need to explain how open access would improve communication among ecologists? It should be obvious to most. Some facts:

Universities around the world do not have access to all subscription journals, not even Harvard. Wiley’s big journal bundle of subscriptions is no exception to this rule. Brock University in Canada is one such notable example. ‘Ecology and Evolution’ is one of two “main themes” of Brock’s Biology Department yet it does not have access to the Wiley bundle of subscription journals.

Furthermore, as the above tweet demonstrates many ecologists are not based at universities. Not all uses or readership of ecology journals is by ecologists, it’s absolutely not sufficient to just provide access to ecologists (alone). It’s vital that policymakers and the public have access to the latest research, no embargoes. Want evidence that policymakers lack access to research? Look no further than this blog post from a recent intern at the UK Parliamentary Office for Science & Technology (POST):

The level of access to journals was far lower than I had expected (it was actually shocking) – I ended up using my academic access throughout my placement.

Source: https://therostrumblog.wordpress.com/2015/01/12/why-all-phd-students-should-do-a-policy-placement/ (2015-01-12)

If the ESA seriously wants to “ensure the appropriate use of ecological science in environmental decision making by enhancing communication between the ecological community and policy-makers” then making it easier for policymakers like those at POST to access research published in ESA journals would surely be a great way of doing that. How does the ESA expect to “raise the public’s level of awareness of the importance of ecological science” if most of the science that they themselves publish in their own journals is behind an expensive paywall? $20 for 30 day access to one article? Admittedly that’s cheaper than many but it’s simply not supportive of ESA’s mission.

Does this help raise the awareness of ecological science?

Does this unnecessary paywall help raise the awareness of ecological science?

 

Lastly, with respect to increasing “resources available for the conduct of ecological science” the ESA urgently needs to consider the big picture here. Wiley, Springer Nature, Elsevier and other legacy publishers are a major drain on the financial resources available for research. With their big bundle deals they ransom/rent access to libraries for sums that can be up to many millions of dollars, every year, per institution. Money should instead be diverted into efficient, high-quality publishing systems like JMLR, Open Library of Humanities, PeerJ, Pensoft and Ubiquity Press to name but a few. All of these not only provide open access, but also high-quality publishing services at a significantly lower cost. Many provide added extras such as semantically-enhanced full-text XML which would make synthesis of ecological science easier. Wiley does not provide direct access to per article full-text XML even to its paying subscribers! They do half the job for thrice the price. Why would ESA want to help to sustain and enhance Wiley’s famous 42% profit margin? These legacy publishers are strategically merging, and acquiring journals in order to make it harder for libraries to cancel their dross-laden ‘big bundle’ subscription packages. It doesn’t seem like a logical decision to me or others.

Comparing this to other recent journal publishing changes

To put into context the ESA move to Wiley, let’s look at three other recent examples of academic societies changing publisher:

1.) Museum für Naturkunde Berlin journals (flipping to open access)

In 2014 all of their journals moved away from being published with Wiley. Their two zoological journals which have been around since before the ESA was even formed(!) transferred to open access publishing with Pensoft. Their Earth Science journal Fossil Record also moved away from Wiley, to open access publishing with Copernicus Publications. Guess what? The sky didn’t fall. I predict the articles in these journals will start being read, downloaded and cited more now that they are open access to everyone.

2.) Paleontology Society journals (switching to arguably a more benign, less profit-driven legacy publisher)

In 2015 PalSoc journals switched to be published with Cambridge University Press (CUP). I’m not super enthusiastic about CUP but if a society really wants to do legacy publishing, without worsening the stranglehold of the big publishing companies over libraries then CUP, or other university presses (Oxford, John Hopkins, Chicago) seem like safer custodians of academic intellectual property to me.

3.) American Society of Limnology and Oceanography (moving to Wiley)

To provide a fair comparison it’s important to look at what happens when a society journal joins Wiley. I know of one such case recently: ASLO journals. The transfer to Wiley was far from smooth or professional. In the few months that Wiley had the ASLO journals, they managed to ‘accidentally’ paywall thousands of articles that should have been available for free (as per ASLO’s wishes) and charged actual readers for reading these older should-be-free articles.  I paid $45.60 for access to one such ASLO article at Wiley – it should have been made available to all for free. Both Springer and Elsevier have also been caught doing this. The ESA currently makes some articles in its subscription journals ‘free to read’ to all, so I shall be closely monitoring the new Wiley-ESA journal websites when they launch, to see if they make the same conveniently profit-generating ‘mistakes’ again.

How did this happen? Who was consulted? Why was this choice made?

I for one was completely unaware that ESA were looking for a new publisher. I would have tried to help if I had known. I have many unanswered questions over the consultation process. For example, the ESA has an Open Science section and mailing list, its members are extremely knowledgeable about the academic publishing landscape and publishing technology.

Was the ESA membership in it’s entirety specifically and clearly asked which publisher they would like the ESA to publish with? Did they ask their membership what features they wanted from their new publishing platform? I would have requested a platform that provides access to semantically-enriched full text XML – Wiley does not provide this. Given a choice, and the vital context and information given above I think few ESA members, policymakers, or members of the public would choose Wiley as ESA’s new publisher.

I gather from Twitter that “any and all” were invited to submit a proposal to publish ESA journals and that Elsevier submitted a proposal. But having a lazy tendering process only biases decisions towards major conglomerates who have the time, energy and resources to make slick proposals – I wonder if smaller but high-quality publishing companies were pro-actively approached by ESA to submit a proposal? In the public interest, I think the ESA should publish the names of all organisations who submitted proposals to publish ESA journals – I think just that data alone might potentially reveal flaws in the tendering process. I’m finding it really hard to reconcile the goals of ESA and shareholder-profits motivation of Wiley. I genuinely think the leadership of ESA is out of touch with its membership and that they may not have been properly consulted about this major change to the society.

This is a long post, and I’ve said enough, so I’ll leave it to a professional scholarly communications expert (Kevin Smith, Duke University), to have the last word about Wiley, and the recent trend towards cancelling Wiley subscriptions:

I don’t know if Wiley is the worst offender amongst the large commercial publishers, or whether there is a real trend toward cancelling Wiley packages.  But I know the future of scholarship lies elsewhere than with these large legacy corporations.

Source: http://blogs.library.duke.edu/scholcomm/2014/12/16/cancelling-wiley/

Postscript

But perhaps we can turn this negative into positive by creating resources and impartial educational guides for academic societies on how to negotiate better publishing deals, and how to start a tendering process with an eye towards the inevitable future of open access? If SPARC or SPARC Europe already provides these resources please do point me at them!

With a first commit to github not so long ago (2015-04-13), getpapers is one of the newest tools in the ContentMine toolchain.

It’s also the most readily accessible and perhaps most immediately exciting – it does exactly what it says on the tin: it gets papers for you en masse without having to click around all those different publisher websites. A superb time-saver.

It kinda reminds me of mps-youtube: a handy CLI application for watching/listening to youtube.

Installation is super simple and usage is well documented at the source code repository on github, and of course it’s available under an OSI-approved open source MIT license.

An example usage querying Europe PubMedCentral

Currently you can search 3 different aggregators of academic papers: Europe PubMedCentral, arXiv, and IEEE. Copyright restrictions unfortunately mean that full text article download with getpapers is restricted to only freely accessible or open access papers. The development team plans to add more sources that provide API access in future, although it should be noted that many research aggregators simply don’t appear to have an API at the moment e.g. bioRxiv.

The speed of the overall process is very impressive. I ran the below search & download command and it executed it all in 32 seconds, including the download of 50 full text PDFs of the search-relevant articles!

You can choose to download different file formats of the search results: PDF, XML or even the supplementary data. Furthermore, getpapers integrates extremely well with the rest of the ContentMine toolchain, so it’s an ideal starting point for content mining.

getpapers is one of many tools in the ContentMine toolchain that I’ll be demonstrating to early career biologists at a FREE registration, one-day workshop at the University of Bath, Tuesday 28th July. If you’re interested in learning more about fully utilizing the research literature in scalable, reproducible ways, come along! We still have some places left. See the flyer below for more details or follow this link to the official workshop registration page: bit.ly/MiningWrkshp

mining-flyer

To prove my point about the way that supplementary data files bury useful data, making it utterly indiscoverable to most, I decided to do a little experiment (in relation to text mining for museum specimen identifiers, but also perhaps with some relevance to the NHM Conservation Hackathon):

I collected the links for all Biology Letters supplementary data files. I then filtered out the non-textual media such as audio, video and image files, then downloaded the remaining content.

A breakdown of file extensions encountered in this downloaded subset:

763 .doc files
543 .pdf files
109 .docx files
75 .xls files
53 .xlsx files
25 .csv files
19 .txt files
14 .zip files
2 .rtf files
2 .nex files
1 .xml file
1 “.xltx” file

I then converted some of these unfriendly formats into simpler, more easily searchable plain text formats:

 

Now everything is properly searchable and indexable!

In a matter of seconds I can find NHM specimen identifiers that might not otherwise be mentioned in the full text of the paper, without actually wasting any time manually reading any papers. Note, not all the ‘hits’ are true positives but most are, and those that aren’t e.g. “NHMQEVLEGYKKKYE” are easy to distinguish as NOT valid NHM specimen identifiers:

 

Perhaps this approach might be useful to the PREDICTS / LPI teams, looking for species occurrence data sets?

I don’t know why figshare doesn’t do deep indexing by default – it’d be really useful to search the morass of published supplementary data that out there!

Progress on specimen mining

June 14th, 2015 | Posted by rmounce in Content Mining - (0 Comments)

I’ve been on holiday to Japan recently, so work came to a halt on this for a while but I think I’ve largely ‘done’ PLOS ONE full text now (excluding supplementary materials).

My results are on github: https://github.com/rossmounce/NHM-specimens/tree/master/results – one prettier file without the exact provenance or in-sentence context of each putative specimen entity, and one more extensive file with provenance & context included which unfortunately github can’t render/preview.

 

Some summary stats:

I found 427 unique BMNH/NHMUK specimen mentions from a total of just 69 unique PLOS ONE papers. The latter strongly suggests to me that there are a lot of ‘hidden’ specimen identifiers hiding out in difficult-to-search supplementary materials files.

I found 497 specimen mentions if you include instances where the same BMNH/NHMUK specimen is mentioned in different PLOS ONE papers.

Finding putative specimen entities in PLOS ONE full text is relatively automatic and easy. The time-consuming manual part is accurately matching them up with official NHM collection specimens data.

I could only confidently link-up 314 of the 497 detected mentions, to their corresponding unique IDs / URLs in the NHM Open Data Portal Collection Specimens dataset. Approximately one third can’t be confidently be matched-up to a unique specimen in the online specimen collection dataset — I suspect this is mainly down to absence/incompleteness in the online collections data, although a small few are likely typo’s in PLOS ONE papers.

In my last post I was confident that the BM Archaeopteryx specimen would be the most frequently mentioned specimen but with more extensive data collection and analysis that appears now not to be true! NHMUK R3592 (a specimen of Erythrosuchus africanus) is mentioned in 5 different PLOS ONE papers. Pleasingly, Google Scholar also finds only five PLOS ONE papers mentioning this specimen – independent confirmation of my methodology.

One of the BM specimens of Erythrosuchus is more referred to in PLOS ONE than the BM Archaeopterx specimen

Now I have these two ‘atomic’ identifiers linked-up (NHM specimen collections occurrence ID + the Digital Object Identifier of the research article in which it appears), I can if desired, find out a whole wealth of information about these specimens and the papers they are mentioned in.

My next steps will be to extend this search to all of the PubMedCentral OA subset, not just PLOS ONE.