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)?

Failure

Success is the ability to go from failure to failure without losing your enthusiasm -- Winston Churchill

I learnt today that my Elsevier Challenge entry didn't make the final cut. This wasn't unexpected. In the interests of "open science" (blame Paulo Nuin) here is the feedback I received from the judges:

Strengths
Beautiful presentation, lovely website. Page clearly made his case for open access to metadata/full articles in order to allow communities to build the tools they want. The judges would have enjoyed seeing more elements from the original abstract (tree of life). Great contribution so far to the discussion; Page made his point very well.

Weaknesses
Given that no specific tool was proposed, this submission is somewhat out of scope for the competition. Nonetheless, in support of his point, Page could have elaborated on the kinds of open formats and standards for text and data and figures that would support integrated community-wide tool-building. Alternatively, if the framework and the displayed functionalities were to be the submission, there could have been more discussion of how others can integrate their plug-ins and make them cross-referential to the plug-ins of others. The proposal for Linked Data should utilize Semantic Web standards

Elements to Consider for Development
How many, and which types of, information substrates? How much work for a new developer to create a new one, and to make this work? How to incentivize authors to produce the required metadata? Or to make the data formats uniform?

I think this is a pretty fair evaluation of my entry. I was making a case for what could be done, rather than providing a specific bit of kit that could make this happen right now. I think I was also a little guilty of not following the "underpromise but overdeliver" mantra. My original proposal included harvesting phylogenies from images, and that proved too difficult to do in the time available. I don't think having trees would have ultimately changed the result (i.e., not making the cut), but it would have been cool to have them.

Anyway, time to stomp around the house a bit, and be generally grumpy towards innocent children and pets. Congratulations to the bastards fellow contestants who made it to the next round.

Elsevier Challenge

Stata Center. MIT
Originally uploaded by Roderic Page

Quick post about the Elsevier Challenge, which took place yesterday in the wonderful Stata Center at MIT. It was a great experience. Cool venue, interesting talks, probing questions (having a panel of judges ensured that everybody got feedback/queries). Some talks (like mine) were more aspirational (demos of what could be done), others, such as Sean O'Donoghue's talk on Reflect, and Stephen Wan's on CSBIS (see "In-Browser Summarisation: Generating Elaborative Summaries Biased Towards the Reading Context") were systems that Elsevier could plug in to their existing Science Direct product (and hence are my picks to go forward to the last round).

I was typically blunt in my talk, especially about how useless Science Direct's "2collab" and "Related articles" features were. Rafael Sidi is not unsympathetic to this, and I think despite their status as the Microsoft of publishing (for the XBox crowd, that's a Bad Thing™), the Elsevier people at the meeting were genuinely interested in changing things, and exploring how best to disseminate knowledge. There's hope for them yet! Oh, and special thanks to Anita de Ward and Noelle Gracy for organising the meeting, and the smooth running of the Challenge.

Challenge entry

I've submitted my entry for the Elsevier Grand Challenge. The paper describing the entry is available from Nature Precedings (doi:10.1038/npre.2008.2579.1). The web site demo is at http://iphylo.org/~rpage/challenge/www/. I'm now officially knackered.

Elsevier Grand Challenge Video

Elsevier have released this video about the challenge, featuring a few of the contestants. I couldn't get my act together in time to send anything useful, and having seen the 16 gigabytes song (full version here), I'm glad I didn't -- there's just no way I could compete with Michael Greenacre and Trevor Hastie.

Elsevier Article 2.0 Contest

Chris Freeland's tweet alterted me to the Elsevier Article 2.0 Contest:

Elsevier Labs is inviting creative individuals who have wanted the opportunity to view and work with journal article content on the web to enter the Elsevier Article 2.0 Contest. Each contestant will be provided online access to approximately 7,500 full-text XML articles from Elsevier journals, including the associated images, and the Elsevier Article 2.0 API to develop a unique yet useful web-based journal article rendering application. What if you were the publisher? Show us your preference!

Elsevier are clearly looking for ideas (they also have their Grand Challenge), and there's been some interesting commentary on the Article 2.0 contest.
The site provides some sample applications (written in XQuery), which you can play with by going to the list of journals that are included in the challenge and clicking down through volume and issue until you get to individual articles.

Challenge data

Just to provide a sense of how much data I want to analyse for the Challenge, I have the XML, PDF, and images for 1687 articles from Molecular Phylogenetics and Evolution to play with.

Hell is other people's data

Starting to get serious about the Grand Challenge. First step is to parse the XML data Elsevier made available. Sadly this is only for Molecular Phylogenetics and Evolution for 2007, I would have liked the whole journal in XML to avoid hassles with parsing PDF. However, XML is not without it's own problems. I'm slowly getting my head around Elsevier's XML (which is, it has to be said, documented in depth). Two tools I find invaluable are the oXygen XML editor, and Marc Liyanage's TextXSLT application.

As a first attempt, I'm converting Elsevier XML into JSON (being a much simpler format to handle). I'm just after what I regard as the core data, namely the bibliography, and the tables (rich with GenBank accession numbers, specimen codes, and geocoordinates). There are a few "gotchas", such as misisng namespaves to add, and HTML entities that need to be added. Then there's the fact that the XML describes both the document content and it's presentation. Tables can get complicated (cells can span more than one row or column), which makes tasks such as identifying cell contents by using the heading of the corresponding column a bit harder. I hope to put a XSLT style sheet online once I'm happy that it can handle most, if not all the tables I've come across. Then the fun of trying to extract the information can begin.

Elsevier Grand Challenge

Elsevier recently announced the 10 semi-finalists for their Grand Challenge. To my consternation, I'm one of them. I wrote a proposal entitled "Towards realising Darwin’s dream: setting the trees free" (I have uploaded a copy to Nature Precedings, it should be available shortly see doi:10.1038/npre.2008.2217.1). The "setting the trees" free is a reference to my oft expressed view that much of our knowledge of evolutionary history is locked up in the pages of Molecular Phylogenetics and Evolution.

Of course, writing a proposal is one thing, making something useful is quite another. I envision something along the lines of this, but *cough* better. Meantime, the other semi-finalists look scarily good.