Thoughts on Mendeley and Elsevier

Elsevier In Advanced Talks To Buy Mendeley For Around $100M To Beef Up In Social, Open Source Educ... tcrn.ch/W8L5io by @ingridlunden

— TechCrunch (@TechCrunch) January 17, 2013

The rumour that Elsevier is buying Mendeley has been greeted with a mixture of horror, anger, peppered with a few congratulations, I told you so's, and touting for new customers:

Oh FFS, nooooooo! MT @phylogenomics: Elsevier In Advanced Talks To Buy Mendeley For Around $100M techcrunch.com/2013/01/17/els… via @techcrunch

— Siouxsie Wiles (@SiouxsieW) January 17, 2013

.@srp @dancohen I imagine a coin flip deep within the Elsevier Headquarters Cave, using a gold, custom-minted BUY OR SUE coin.

— Jason Priem (@jasonpriem) January 17, 2013

By the way, over here @ Zotero headquarters (@chnm) we welcome all Mendeley users to a truly open platform for research zotero.org

— Dan Cohen (@dancohen) January 17, 2013

Here's some probably worthless speculation to add to the mix. Disclosure: I use Mendeley to manage 100,000's of references, and use the API for various projects. I'm not paying customer (but I do pay for some Internet services such as DropBox, BackBlaze, and Spotify, so it's not that I won't pay, it's just that the service Mendeley charge for doesn't interest me). I've published in Elsevier journals (most recently a couple of papers that, thanks to the efforts of Paul Craze, editor of TREE, are "free" in the sense you can download the PDF for free), and I took part in the Elsevier Grand Challenge.

So, given that I'm suitably compromised, here are some thoughts.

Elsevier suck

Elsevier are big, ugly, and at the corporate level are doing things that actively make researchers angry (see The Cost of Knowledge).

Elsevier rocks

Elsevier are one of the most innovative science publishers around. They fund challenges, are investing heavily in interactive and semantic markup of papers (for example, interactive phylogenies), and have built an app ecosystem on their publishing platform.

Mendeley sucks

Mendeley is suffering some from serious failings, most of which could be addressed with sufficient resources. The API sucks, mostly because Mendeley themselves don't actually use it. The Desktop client communicates with Mendeley's database using a different protocol, hence the API lacks the functionality needed to make truly great apps on the platform. The algorithms Mendeley use to de-duplicate their catalogue are flawed, occasionally creating entirely fictional entries.

Mendeley rocks

The way Mendeley engineered the creation of a bibliographic database in the cloud is genius, as is their recognition that the object around which scientists will cluster is the article, not the author. They helped foster the altmetrics movement, and have a great presence on Twitter and at conferences (i.e., you can talk to actual people who write code).

What happens next?

Let's assume that Elsevier does, indeed, buy Mendeley, and wants to do interesting things with Mendeley, and that Mendeley doesn't become one of the many startups that have a successful "exit" for the founders but ends up dying in the bosom of a larger company. Here are some possibilities.

Mendeley becomes iTunes for papers

Forget the "Last.fm" of papers, what about the "iTunes of papers"?. Big publishers are facing a revolt over the cost of institutional subscriptions, and journals are increasingly irrelevant as aggregations. The literature that people read is widely scattered across different outlets. Journals are archaic in the same way that music albums are mostly a thing of the past, people mix and match singles.

In the recent fight between UC Davis and Nature, Nature estimated that "CDL will be paying roughly $0.56 per download". So, why not charge a buck a paper? Mendeley's web interface is practically crying out for a "BUY THIS PAPER" button. Under this model, Elsevier has an outlet for its content that doesn't force people to subscribe to large amounts of stuff they don't want. Mendeley could be used to establish a relationship directly with paying customers, rather than institutions.

Mendeley becomes the de facto measure of research impact

But combining Mendeley's readership data with citations, Elsevier could construct powerful measures of research impact, bringing altmetrics into the mainstream. Couple this with links to institutions, and Elsevier could provide universities with all the data they need to evaluate academic performance (gulp).

Mendeley becomes an authoring tool

Managing references and inserting citations into manuscripts is one of the basic tasks facing an academic author. Authoring tools are evolving in the direction of being online, and embedding more semantic markup (e.g., these are taxon names, this is a chemical compound, this is a statement of causality). In a sense reference lists are the one form of structured markup we are already familiar with. Why not build on that and create an authoring platform?

Mendeley becomes the focus of post-publication review

Publishers have failed to crack the problem of post-publication review. Several provide the ability for readers to comment on an article online, but this has failed to take off. I think this is because the sociology is wrong, if you want a conversation you need to go where the people are, not expect them to come to you. Given that people are bookmaking papers in Mendeley, the next step is to get them to comment, or aggregate their annotations (in the same way that Amazon's Kindle can show you passages that others have highlighted).

Interesting times...

Elsevier articles have interactive phylogenies

Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post Fabian Schreiber pointed out that Elsevier have released an app to display phylogenies in articles they publish. The app is based on jsPhyloSVGand is described here. You can see live examples in these articles:

Matos-Maraví, P. F., Peña, C., Willmott, K. R., Freitas, A. V. L., & Wahlberg, N. (2013). Systematics and evolutionary history of butterflies in the “Taygetis clade” (Nymphalidae: Satyrinae: Euptychiina): Towards a better understanding of Neotropical biogeography. Molecular Phylogenetics and Evolution, 66(1), 54–68. doi:10.1016/j.ympev.2012.09.005

Poćwierz-Kotus, A., Burzyński, A., & Wenne, R. (2010). Identification of a Tc1-like transposon integration site in the genome of the flounder (Platichthys flesus): A novel use of an inverse PCR method. Marine Genomics, 3(1), 45–50. doi:10.1016/j.margen.2010.03.001

PLoS doesn't "get" the iPad (or the web)

PLoS recently announced a dedicated iPad app, that covers all the PLoS Journals, and which is available from the App Store. Given the statement that "PLoS is committed to continue pushing the boundaries of scientific communication" I was expecting something special. Instead, what we get (as shown) in the video below is a PDF viewer with a nice page turning effect (code here). Maybe it's Steve Job's fault for showing iBooks when he first demoed the iPad, but there desire to imitate 3D page turning effects leaves me cold (for a nice discussion of how this can lead to horribly mixed metaphors see iA's Designing for iPad: Reality Check).

PLoS iPad Demo from PLoS on Vimeo.

But I think this app shows that PLoS really don't grok the iPad. Maybe it's early days, but I find it really disappointing that page-turning PDFs is the first thing they come up with. It's not about recreating the paper experience on a device! There's huge scope for interactivity, which the PLoS app simply ignores — you can't select text, and none of the references. It also ignores the web (without which, ironically, PLoS couldn't exist).

Instead of just moaning about this, I've spent a couple of days fussing with a simple demo of what could be done. I've taken a PLoS paper ("Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila", doi:10.1371/journal.pone.0007516), grabbed the XML, applied a XSLT style sheet to generate some HTML, and added a little Javascript functionality. References are displayed as clickable links inline. If you click on one a window pops up displaying the citation, and it then tries to find it for you online (for the technically mined, it's using OpenURL and bioGUID). If it succeeds it displays a blue arrow — click that and you're off to the publisher's web site to view the article.


Figures are also links, click on and you get a Lightbox view of the image.
You can view this article live, in a regular browser or in iPad. Here's a video of the demonstration page:

PLoS paper on the iPad from Roderic Page on Vimeo.

This is all very crude and rushed. There's a lot more that could be done. For references we could flag which articles are self citations, we could talk to bookmarking services via their APIs to see which citations the reader already has, etc. We could also make data, sequences, and taxonomic names clickable, providing the reader with more information and avenues for exploration. Then there's the whole issue of figures. For graphs we should have the underlying data so that we can easily make new visualisations, phylogenies should be interactive (at least make the taxon names clickable), and there's no need to amalgamate figures into aggregates like Fig .2 below. Each element (A-E) should be separately addressable so when the text refers to Fig. 2D we can show the user just that element.



The PLoS app and reactions to Elsevier's "Article 2.0" (e.g., Elsevier's 'Article of the Future' resembles websites of the past and The “Article of the Future” — Just Lipstick Again?) suggests publishers are floundering in their efforts to get to grips with the web, and new platforms for interacting with the web.

So, PLoS, I challenge you to show us that you actually "get" the iPad and what it could mean for science publishing. Because at the moment, I've seen nothing that suggests you grasp the opportunity it represents. Better yet, why not revisit Elsevier's Article 2.0 project and have a challenge specifically about re-imagining the scientific article? And please, no more page turning effects

Elsevier Grand Challenge paper out

At long last the peer-reviewed version of the paper "Enhanced display of scientific articles using extended metadata" (doi:10.1016/j.websem.2010.03.004), in which I describe my entry in the Elsevier Grand Challenge, has finally appeared in the journal Web Semantics: Science, Services and Agents on the World Wide Web. The pre-print version of this paper has been online (hdl:10101/npre.2009.3173.1) for a year prior to appearance of the published version (24 April 2009 versus 3 April 2010), and the Challenge entry itself went online in December 2008. Unfortunately the published version has an awful typo in the title (that was in neither the manuscript nor the proofs).

Given this typo, the time lag between doing the work, writing the manuscript, and seeing it published, and the fact that I've already been to meetings where my invitation has been based the entry and the pre-print, I do wonder why on Earth would I bother with traditional publication (which is somewhat ironic, given the topic of the paper)?