Show me the data!

[Rather than summarise what’s already been said about Elsevier and their for-excessive-profit practices in recent weeks, I’ll just lazily assume you’ve read it all… right then. Here’s what I have to add.]

This post is a real-world anecdote of the problems that Elsevier’s journal bundling & excessive profiteering*** causes. Just one of many reasons which persuaded me to sign my name along with 5,000+ other academics over at The Cost of Knowledge, to register my disapproval of what Elsevier (and other publishers) are doing with scholarly works.

Recently, I discovered to my dismay that my institutional library (University of Bath) had cut it’s subscription (and therefore easy access) to an important journal in my field. Literally, one week I had free access to the journal content, and then the next week I found I didn’t!

The journal is Biology Letters, a general biology journal by Royal Society Publishing [RSP from now on]. **


Intellectual property owned by Royal Society Publishing (taken from Wikipedia)

Interestingly RSP take a relatively enlightened stance on Open Access, and have made some interesting statements in the past, such as this gem [from a statement published way back in 2008]:

“…some companies do appear to be making excessive profits from the publication of researchers’ papers”

I think RSP, is a non-profit organisation (source) and hence it doesn’t surprise me that they have such prescient criticism of Elsevier & co to offer. They aren’t in the business of excessive profiteering like some.

So… RSP’s Biology Letters has been cut from our subscriptions budget. Why? – was the very first question I emailed the subject librarian at my institution. To their credit, I got some wonderfully informative replies from our librarian staff – I have no doubt they’ve done their best, given the limited powers they have. Like all institutions, we don’t have an unlimited budget. Something had to be cut, and unfortunately it was our subscription to Biology Letters. Which by the way, would only have cost us £852 for an institutional online-only subscription.

Why was this journal, of which I read/used at least 15 separate articles of in 2011 alone, cut from our subscriptions instead of a journal like… Elsevier’s ‘International Journal of Coal Geology‘?*

I think this is a fair question to ask. Biology Letters has a higher impact factor, not that the journal Impact Factor is a particularly brilliant metric of quality and would cost a lot less (£1107 [Biol. Lett. print version+online] vs 2540 Euros; the current institutional subscription price for the print version ‘International Journal of Coal Geology’). Most damningly of all, I suspect no-one at my institution ever reads this Elsevier journal, feel free to correct me on this – I’m sure I could find plenty of other Elsevier journals that satisfy this last property.

But the answer to this question is of course not relevant to any of 3 rational above points (unfortunately) – Biology Letters can be cut because it’s vulnerable, as it’s not part of a MegaBundle sold by a large for-profit publisher. The International Journal of Coal Geology cannot be cut because access to it comes as part of a ‘Big Deal’ bundle, in which there are some *vital* journals to which we *must* have access to (and the corporation selling access, knows and exploits this). So despite the fact that no one needs it here, that it’s ~2x more expensive, and it has a lower Impact Factor – I have access to this, and many countless other bundled journals I DON’T need, and I DON’T have access to vital articles from another journal I *do* need for my research.

Welcome to the crazy world of academic publishing! Much of it simply doesn’t make sense in the Digital Age. Of current explanations, I’d say Mike Taylor’s parable explains this most clearly.

I can’t claim to have explained all of the problems and intricacies here – but rest assured it clearly doesn’t make sense to me. Journal mega-bundling is plainly inefficient, and we can’t let this practice continue.

Stop feeding the beast! The Cost of Knowledge

* Through-out this post I use the example of the International Journal of Coal Geology, not out of disrespect for the editorial board, or the scholarly quality of the work presented there-in – I’m sure it’s great if you’re into Coal Geology. I only use it because a) it’s an Elsevier journal to which Elsevier very arguably adds very little value to, and b) I sincerely believe virtually no researchers at my institution make use of this journal.

** Just for the record, I don’t blame RSP or my librarians for this subscription cut happening. It’s out of their control. RSP do a great job IMO, as do my librarians.

*** I just read that one UK institution pays over £1,000,000 (yes, more than a million) every year for Elsevier’s ‘Big Deal’ bundle (source). I think this is a disgraceful ransom.

I’m really pleased this new Open Access paper has just been published.

CC BY 3.0 Zookeys Special Issue

Hagedorn, G. et al. Creative commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information 150, 127-149 (2011).

Some background…

After parading my Open Data t-shirt (pictured below) around the Society of Vertebrate Paleontology meeting this month, I was invited to give an impromptu pitch in front of the great and good of the Mammal AToL project & MorphoBank people. Having pointed out to MorphoBank a while ago that they should really make explicit the terms and conditions [license] under which they make their (?) data available, I naturally advocated CC-BY 3.0 and CC0 licences. I talked about this very subject and pleaded with them NOT to use the NC clause refering to Rod Page & Peter Murray-Rust ‘s [1,2] thoughts on the matter.

Data providers vs Data re-users – need they really be in opposition?

The trouble is, a lot of (data providing) institutions seem hell-bent on ‘protecting commercial interests’, at the expense of research opportunities. So as I understand it, at the moment databases such as these face an awkward problem of either satisfying the restriction requests of data providers OR satisfying permissiveness of re-use by data re-users [such as myself!], and the needs of both camps are seldom entirely met.


I see this paper as an important step in persuading such restriction-minded institutions of the absolute importance of #OpenData / #PantonPrinciples and how NC clauses can genuinely obstruct and impair real academic research.
I just hope people read it and take note!

[Most of this is just a re-post of my spur of the moment G+ post here.
I’m reposting here so that this might hopefully get picked up by Research Blogging to give this paper the publicity it deserves. Much of the content is widely applicable IMO to most of scholarly communications, not just biodiversity informatics, and indeed the whole ZooKeys special issue (Open Access) is well worth a browse.]


[3] Hagedorn, G., Mietchen, D., Morris, R., Agosti, D., Penev, L., Berendsohn, W., & Hobern, D. (2011). Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information ZooKeys, 150 DOI: 10.3897/zookeys.150.2189

Yesterday’s post about haywire RSS feeds, reminded me that I should perhaps share a trick or two I know about RSS feeds.

This post assumes you know what an RSS feed is, and why they’re awesome. I still encounter researchers everyday who have no idea what an RSS feed is. I have no idea how they cope with the sheer volume of literature being produced these days without RSS feeds!

1.) RSS feed filtering

Some journals e.g. PLoS ONE put out a *lot* of new research articles each and every week. So much so that it’s tiresome and time-wasteful to even read just the titles, let alone the abstracts of each and every new article published in this journal.

This should not be taken as a criticism of such high-volume journals. I’m very supportive of Open Access publishing, and the higher the volume of articles in Open Access rather than closed access, the better (for science) as far as I’m concerned. All one needs to do is apply some conservative filtering criteria to such feeds so that one receives only items of interest.

My interest is in phylogenetics. Therefore I filter the PLoS ONE new article (all subjects) alert feed by subject specific keywords using Yahoo Pipes (see below).

If the wildcard filters for ‘phylo*’ and ‘clad*’ work, then the other filters are probably redundant, but just in case y’know.
The resultant output of this feed (here), significantly tames the PLoS ONE deluge to a relevant and manageable trickle.
There are many other ways of filtering RSS feeds, but the graphical nature of Yahoo Pipes IMO makes it very recommendable.

It’s worth noting as well that PLoS provide their own filtered feeds here broken down by subject, but this isn’t helpful for me, as my research interest often pop-ups in many different subject classifications.

2.) RSS feed creation

Perhaps a journal / database / website of interest to you doesn’t provide an RSS feed. So you can’t otherwise easily track updates to it. With research, I think it’s very important to keep up to date with the latest developments. Journals, databases and websites *should* of course always provide RSS feeds for you but a minority in my experience don’t.

The solution for these cases is: DIY!

Again there are a huge swathe of options to help you ‘roll your own’ RSS feed. Some are reasonably complex and highly configurable e.g. Whilst others are really simple, but not so adaptable e.g.

The latter, simple option works very well for me, so I can keep up to date with latest additions to the MorphoBank database.

I’d be interested to know if anyone had any further recommendations for RSS feed creation tools, other RSS-related tips & tricks and/or interesting research related use-cases.

PS Should anyone wish to subscribe to my output, the RSS feed for this blog is here (and in the top right hand corner, I should probably make it a bit more obvious though!)

Further Reading:

FUBAR’d ScienceDirect RSS feeds

October 10th, 2011 | Posted by rmounce in phdchat - (0 Comments)

This is just a short post: to vent my anger at a fair few of my RSS feeds being totally FUBAR‘d at the moment. It’s too long for a tweet, and too short for a full post, but here goes:

At least three of my ScienceDirect journal article alert RSS feeds are totally FUBAR’d at the moment.

1) Paleoworld (CAS):
2) Cretaceous Research:
3) Geobios:

They *used* to serve-up informative alerts to new issues and articles for the palaeontological publications listed. A handy alert system that’s both beneficial to me (interested reader, scientist end-user) AND the publisher themselves – advertising their wares (academic research articles held behind paywalls).

Yet now, I’m getting Biosensors and Bioelectronics from the 1st feed, and Current Opinion in Plant Biology from the 2nd feed.

Finally, I’m getting an entertaining litany of journal article alerts from the 3rd feed, including such COMPLETELY UNRELATED TITLES as Journal of Bodywork and Movement Therapies, Journal of International Money and Finance, Gondwana Research, Journal of Alloys and Compounds, Journal of Crystal Growth, and many more…

The ‘contact us’ page over at ScienceDirect doesn’t inspire me with confidence, so I’ll just blog it here.

ScienceDirect – please sort this out!

A note to publishers who may hopefully read this:

a) Once RSS feed URLs are set, I expect them to stay constant like a DOI URL. It’s a hassle to have to change feed URLs.

b) If RSS feed URLs for whatever reason have to be changed/discontinued, then PLEASE send a message via that RSS feed URL to notify subscribers.

*rant over*

PS It looks like the RSS feed service may even have been discontinued (without any warning!) if the absence of an RSS feed button here is anything to go by.

Has anyone else seen RSS feeds of theirs go haywire? Is it just me?

Resurrected comments from the old blog:

I am actually from the Marketing Communication Dept in Elsevier (part of my role is to monitor social media, blogs etc).

Sorry to hear about all your troubles with RSS Feed etc,

I have asked my colleagues in our First Line Support Team to look into this matter and I will get back to you soon.

A Liked Reply
7 months ago 1 Like

Ross Mounce
Thanks Lizzy. Sorry I was too lazy to report it directly to Elsevier. We’ve also established now that it’s probably not a problem at your end, rather it’s Google Reader’s problem (which is the RSS reader that I guess a good majority of people use). As for contacting them about this… I’ve tried via their Twitter @googlereader. But no useful response so far. Many thanks

Edit Reply
7 months ago in reply to LizzzyZ

I also monitor Twitter and seen your tweet… I am waiting for a response that might be able to shed some light.

Like Reply
7 months ago in reply to Ross Mounce

Ross Mounce
I don’t suppose you got that reply yet?

Just came across another wierd GoogleReader specific problem today too:

The new Palaeontology (PalAss journal) issue got pushed out over RSS today. The titles and abstracts are all fine BUT when one clicks on the link to go see the paper… you get “Error – DOI Not Found”. Actually the DOI’s are fine, and the URL links as supplied on the RSS feed are also fine, it’s just GoogleReader is adding %2F into the valid URL :S

instead of…

simple bug, simple fix…? I wonder where one can report GoogleReader bugs?

Edit Reply
6 months ago in reply to LizzzyZ

I have spoken to the Product Manager, and basically they are currently working on fixing our RSS feeds but don’t have an exact timeline at the moment for when they can release the fixes.

A Liked Reply
6 months ago in reply to Ross Mounce 1 Like

Ross Mounce
hmmm… the official suggested bug reporting forum isn’t that inspiring……

Edit Reply
6 months ago in reply to Ross Mounce

Jason Snyder
You’re not the only one – my Behavioural Brain Research and Biological Psychiatry feeds are filled with geological content…

A Liked Reply
8 months ago 1 Like

Ross Mounce
Excellent! Is there a systematic error at work here?
I got 50 erroneous items posted to each of the feeds on the 2nd of October.
I’m thinking this is perhaps when the problem started…?

Edit Reply
8 months ago in reply to Jason Snyder


I am not sure if this relevant anymore, but the tip given in… would seem to solve the problem with wrong feeds.

I have not found a solution to the “DOI not found” issue though,

Like Reply
4 months ago

Tuomo Kalliokoski
I’ve got the problem with Liferea -feed reader.

I want to read:
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
But I’m getting it mixed with
Computers and Electronics in Agriculture

Like Reply
7 months ago

Andrew Farke
I’m having the same issue. . .it’s annoying!!! And it looks like I occasionally get the same issues as J. Salvador Arias, too. But then, my Cretaceous Research feed has a mix of junk and good stuff. I heard a rumor that the problem primarily affects GoogleReader – anyone have cross-platform experience for comparison?

Like Reply
8 months ago

Jon Tennant
I use the program RSSReader. Sometimes, I have to extract the feed through GoogleReader, and that’s what seems to be creating the problem for me with Cretaceous Research.

A Liked Reply
8 months ago in reply to Andrew Farke 1 Like

Andrew Farke
I just installed Thunderbird and downloaded my RSS feeds; I can confirm that everything works just fine in Thunderbird (i.e., no weird feeds).

A Liked Reply
8 months ago in reply to Andrew Farke 1 Like

Ross Mounce
Looks like I might need to contact @googlereader then! You’re right. It appears to be a Google Reader specific issue, the feeds seem okay when viewed with other readers. Curiouser and curiouser!

Edit Reply
8 months ago in reply to Andrew Farke

J. Salvador Arias
I have the same problem :-/… although from time to time I receive the right feeds… (but with the amount of “spam” I probably miss the real ones x-p)

Like Reply
8 months ago