Ross Mounce

Elsevier seem to have responded to my criticism yesterday and have stopped selling the article “HIV infection en route to endogenization: two cases” from their ScienceDirect website. Take what you will from that change, but I infer that they have realised that they are in the wrong. Actually, they are still selling it from the ScienceDirect website too. It only looked freely available to me because I myself had paid for access to it &amp;

Another day, another Elsevier website illegally selling articles

*[Update 2015-03-13: I have blogged further about this here and provided a recap here. This post has been viewed over 10,000 times. Clearly some people want to sweep this under the carpet and pretend this is just ‘a storm in a teacup’ but it did happen and people do care about this.

Elsevier illegally sold me a Creative Commons non-commercial licensed article

Considering I emailed him on a Friday, Darin Croft has done well to reply to my questions about the SVP abstract embargo so soon, on Monday. I don’t always get such swift replies, so that is much appreciated.


Answers to questions about the SVP meeting abstract embargo

This is a re-post, originally first blogged by myself on the Open Knowledge Foundation main blog here

Recently Science Europe published a clear and concise position statement titled:

 Principles on the Transition to Open Access to Research Publications

This is an extremely timely &amp; important document that clarifies what governments and research funders should expect during the transition to open access.

Science Europe denounces ‘hybrid’ Open Access [another repost]

Today I received proof that Elsevier are also sending takedown notices to

 UK universities

– asking them to takedown copies of their staff’s academic research papers, hosted on

 university

webpages. The full text is further down this post (in red). It is not just Academia.edu, it is not just the University of Calgary, University of California-Irvine, or Harvard University.

Elsevier is also sending takedown requests to UK universities

This post is about my new preprint I’ve uploaded to PeerJ PrePrints:

 Mounce, R. (2015) Dark Research: information content in some paywalled research papers is not easily discoverable online. PeerJ PrePrints

Needless to say, it’s not peer-reviewed yet but you can change that by commenting on it at the excellent PeerJ PrePrints website. All feedback is welcome.

Dark Research: behind the preprint

[Update: I’ve submitted this idea as a FORCE11 £1K Challenge research proposal 2015-01-13. I may be unemployed from April 2015 onwards (unsolicited job offers welcome!), so I certainly might find myself with plenty of time on my hands to properly get this done…!]

Inspired by something I heard Stephen Curry say recently, and with a little bit of help from Jo McIntyre I’ve started a project to compare EuropePMC author manuscripts

Author manuscripts versus the publisher version of record

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 &amp;

Progress on specimen mining

This is just a quick post of appreciation for PCI Registered Reports. I’ve recently joined the PCI RR community as a ‘recommender’.  One thing that spurred me to join is a rather unsatisfactory experience I had as a peer-reviewer, reviewing a manuscript where the experimental design was deeply insufficient.

Kudos to PCI Registered Reports

In December last year, it was widely publicized e.g. in

 Science

magazine [1], that Scopus has been instrumental in legitimizing publication scams whereby authors pay to bypass real scholarly peer review and have their work published on a website that looks like a real scholarly journal but is in fact not a proper journal, merely an impersonation of one.

Scopus: caught-out and shirking responsibility

Wiley &amp; Readcube have done something rather sneaky recently, and it’s not escaped the attention of diligent readers of the scientific literature. On the article landing page for some, if not all(?) journal articles at Wiley, in JavaScript enabled web browsers they’ve replaced all links to download the PDF file of the article with links that direct you to Readcube instead.

How to Block Readcube and Why

To:

francesca.martin@oup.com, sally.iannacci@oup.com, Jennifer.Boyd@oup.com, rebecca.seger@oup.com, graham.grant@oup.com, chris.holmes@oup.com, andrea.gilbey@oup.com

 From:

Ross Mounce &lt;rcm61@cam.ac.uk&gt;

 Subject:

An Open Letter to Oxford University Press on Publishing

 Cc:

R.VanNoorden@nature.com, Q.Schiermeier@nature.com, Ben.Taplin@jisc.ac.uk, Anna.Vernon@jisc.ac.uk,

An Open Letter to Oxford University Press on Publishing

I’ve written 29 blog posts this year! Still time for one more…  This work relates to my new postdoc at the University of Cambridge in Sam Brockington’s group. I’ve been closely examining IUCN RedList data for plant taxa and found some rather odd things.

When is an ‘extinct’ plant actually extinct?

In a recent series of posts I’ve become fascinated with how unnecessarily fragile the scholarly communications system seems to be in 2017:  Oxford University Press have failed to preserve access to the scholarly record (23-01-2017)  Documenting the many failures across OUP journals (24-01-2017)  Comparing OUP to other publishers (25-01-2107)  As a reminder, academics literally invented the internet, I think we can and should be doing

Monitoring publishing services

[This is my competition entry for the ARCS2015 essay competition hosted at The Winnower. I’m using their excellent WordPress plugin to automagically transfer this post from my blog to their site at the click of a button.]  There’s a 1,000-word limit for this competition, so forgive my brevity. I could easily write ten thousand! These are merely a couple of vignettes.

Anecdata On Sharing Science

Today (2015-09-01), marks the public announcement of Research Ideas &amp; Outcomes (RIO for short), a new open access journal for all disciplines that seeks to open-up the entire research cycle with some truly novel features  I know what you might be thinking: *Another open access journal? Really? *  Myself, nor Daniel Mietchen simply wouldn’t be involved with this project if it was just another boring open access journal.

I am supporting RIO Journal. I think you should too

I’ve just given an email interview for Abby Clobridge, for a forthcoming short column in Online Searcher. I give many of these interviews and often very little material from it gets used, so I asked Abby if it was okay if I reposted what I wrote. Her response: “go for it” – thanks Abby! So here’s my thoughts on Generation Open, for a readership of librarians and information professionals:


My thoughts on Generation Open

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.

Deep indexing supplementary data files

[Update 5.30PM 2015-03-26: Wiley have now ‘freed’ the wrongly-paywalled articles in response to this. It doesn’t change the fact that these articles were wrongly on sale for 2 months and 26 days.

Wiley are charging for access to thousands of articles that should be free

you weren’t much loved in your short existence you weren’t much use to readers or text-miners because we often couldn’t find where you were – hiding amongst shadows. you were significantly more expensive than your ‘full’ open access cousins  In March, 2015 ‘hybrid OA’ died after a short-life of neglect.

A Eulogy for Hybrid OA

On Monday 29th June 2020, I learned from Retraction Watch that Clarivate, the for-profit proprietor of

 Journal Impact Factor

™ has newly “suppressed” 33 journals from their indexing service.

Suppression as a form of liberation?

Part inspired by the ‘Bugs!’ blogging contest, part inspired by Morgan Jackson’s post I thought I’d write some thoughts and observations on the recent FlyToL paper (Wiegmann

 et al.

, PNAS, 2011). [

 IMPORTANT UPDATE


 Since I wrote this blogpost, the authors have made the data publicly available.

A FlyTree in the Ointment of Falsifiability

UPDATE

01/06/11

 I’ve now submitted a modified version of this abstract. Many thanks to all who commented.

One of the many conferences I’m going to this year is a fairly big event. The abstract deadline also happens to be very soon too. So I thought I’d post a draft of my abstract here and see what peeps think. Is my Latin correctly formed? What do you think?

A Conference Abstract #OpenDraft

I handed in my thesis not long ago, on Thursday 3rd October 2013. No idea when my viva is yet.


Acknowledgements

I need a space to layout my thoughts in a longer form than Twitter or Facebook.  So I thought: “hey, why not start a blog?”  -&gt;  TA-DA!  *Posts will be infrequent and sporadic both in tempo and topic   Many thanks to http://twitter.com/jezcope for the quick hands-on WordPress tutorial, and Mark Hahnel for suggesting I blog here.


First Post

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.


Beware when using Thompson Reuters Web of Knowledge

It’s the Olympics now so this work update is a) late and b) short  Nevermind…  As ever progress has been exciting – look what we can extract from some PDFs: 			 				 			 			 				 			 		  (click to enlarge each) Attribution: The left panel is from Cánovas et al. BMC Evolutionary Biology 2011 11:371 doi:10.1186/1471-2148-11-371  On the left is the original figure, and on the right we have an SVG representation of the data we can extract


Panton Fellowship updates: July (month 4)

I said I would make an update on Tuesday (today), so if I get this posted before midnight I will (

 just

) have met that  goal… In this (minor) update I have:

 added:

Ubiquity Press (great low cost option!), SPIE (scored for 1-column per page), SAGE Open, Frontiers, WileyOpenAccess, OxfordOpen (OUP hybrid option), GigaScience, Open Biology (Royal Society)

 added the label for:

Pensoft (sincerest

The Gold OA plot v0.2

In the last 2 weeks I’ve given talks in Brussels &amp; Amsterdam. The first one was given during a European Commission (Brussels) working group meeting on Text &amp; Data Mining. There were perhaps only ~30 people in the room for that. The second presentation was given just a few days ago at Beyond The PDF 2 (#btpdf2) in Amsterdam.


Worldwide Dissemination

This is a quick post to announce what I’ll be doing next after my postdoc at the Department of Plant Sciences, University of Cambridge. From June 2017 onwards, I’m delighted to say I’ll be the new Open Access Grants Manager for Arcadia Fund.

 About Arcadia Fund

If you haven’t heard of it before here’s what you need to know: Arcadia is a charitable fund, set up by Peter Baldwin and Lisbet Rausing in 2002.

New Career, Same Me

This morning, a PhD student asked me if I could get access to copy of: “Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses” by Jeremy M Brown and Robert C Thomson which was first published online (ahead of print) on 20th December 2016.

Oxford University Press have failed to preserve access to the scholarly record

An interesting move from Nature Publishing Group today…  In a press release dated 7 November 2012 they’ve announced they’re allowing the Creative Commons Attribution (CC BY) license to be applied to articles in some (but not all) of their journals, specifically citing Wellcome Trust and RCUK policies that now require their funded authors to publish Gold OA with a CC BY license (or alternatively to use the Green OA route), recognizing that more


Gold OA Pricewatch

Anyone who knows me, knows I’m very passionate on the subject of data sharing in science, and after all the relevant conferences I’ve been to and research I’ve done – I don’t mind saying I’m fairly knowledgeable on the subject too.  It’s part of the reason I got this Panton Fellowship that has helped me develop my work and do what I want to do in pursuit of Open Data goals.  So when I saw this article come up on my RSS feeds – I thought great!


From card catalogs to computers: databases in vertebrate paleontology

A few months ago I gave a short talk about the Open Knowledge Foundation and its activities as relevant to academics at a small (but good!) palaeontology conference in Cambridge (which I blogged about previously). I didn’t

 need

to give this talk. Neither the OKF nor my academic progression required me to give this talk.

Opportunity Knocks

I am highly curious as to why Elsevier do not seem to be responding to emails at the moment:  Four days ago, continuing an existing thread on the public GOAL mailing list, I wrote to Dr Alicia Wise (Director of Access and Policy at Elsevier), about how Elsevier’s paywall systems are wrongly defrauding readers across the world by charging them to access content that has been paid-for to be open access.

Seeking Justice for Readers

How many learned societies publish Diamond Open Access journals? To seek an answer to the question posed in the title, I sought out reliable data on open access journals.

To seek an answer to the question posed in the title, I sought out reliable data on open access journals. My first port of call was the Directory of Open Access Journals (DOAJ). Although DOAJ certainly isn’t a complete listing of open access journals, as is well documented in ‘The OA Diamond Journals Study’ (2021), it will at least help provide a minimum bound answer to the question.

How many learned societies publish Diamond Open Access journals?

As you may have seen in the news, the British Library has been affected by a significant cyberattack. Many of the digital services it provides have gone down and stayed down for many weeks now, whilst investigations take place. I have a lot of sympathy for the BL staff. As has been observed, public services can be a relatively easy target.

Resilience: another advantage of openly-licensed content

Sometimes you just have to laugh… The year is 2012, we have the internet, we have blogs, and a huge variety of other tools to enable free, efficient and rapid communication of information and yet the Society of Vertebrate Paleontology annual meeting rules still

 insist

that all information within this year’s abstract booklet remain a big secret until the day of the event. Many others have justly written to complain about this before.

The ridiculous SVP embargo is back again

I have previously commented elsewhere on other blogs, that uniquely, with BOAI-compliant Open Access literature, one is able to re-distribute research however one wishes (provided proper attribution is given). I believe this to be hugely beneficial and perhaps a rather under-appreciated facet of the plurality of benefits offered by Open Access publishing.


Libre redistribution &#8211; a key facet of Open Access

Doing some information research ahead of my imminent OKCon 2011, Berlin talk, it’s come to my attention that the Open Access journal PLoS ONE is actually an excellent journal to publish in, with respect to Impact Factor. In the Digital Age, journals are merely vessels in which we can publish our research.


If PLoS ONE Paleontology was a journal…

On the 26

 th

October 2021, Springer Nature published version 1 of a (not peer-reviewed) “white paper” titled “Going for gold: exploring the reach and impact of Gold open access articles in hybrid journals” by Christina Emery, Mithu Lucraft, Jessica Monaghan, David Stuart, and Susie Winter.

Pricing, Citation Impact, and Springer Nature (Part 1)

The TL;DR summary: In February 2017, when Elsevier were accused of selling one paid-for hybrid open access article, at first they sowed doubt about it, then three days later admitted it to be true. In their admission they state that it is the only wrongly paywalled open access article “affected” at their websites.

The TL;DR summary:
 

* In February 2017, when Elsevier were accused of selling one paid-for hybrid open access article, at first they sowed doubt about it, then three days later admitted it to be true. In their admission they state that it is the only wrongly paywalled open access article “affected” at their websites.

Hybrid open access is unreliable

TL;DR Elsevier are selling access to open access articles again

I saw this humorous tweet today: This tweet references the fact that Elsevier have been caught selling access to paid-for “open access” articles in 2014, 2015, and 2016.

Elsevier selling access to open access again

OpenCon 2015 Brussels was an amazing event. I’ll save a summary of it for the weekend but in the mean time, I urgently need to discuss something that came up at the conference. At OpenCon, it emerged that Elsevier have apparently been blocking Chris Hartgerink’s attempts to access relevant psychological research papers for content mining. No one can doubt that Chris’s research intent is legitimate – he’s not fooling around here.

Traditional Publishers: please stop blocking research

TL;DR summary: ESA data papers should be free to read but Wiley (ESA’s new publishing ‘partner’) just charged me $45.60 yesterday to access one of them. They have done this kind of ‘accidental’ profit-generation before, as have other big publishers. John Wiley &amp;

TL;DR summary:
 
 ESA data papers should be free to read but Wiley (ESA’s new publishing ‘partner’) just charged me $45.60 yesterday to access one of them. They have done this kind of ‘accidental’ profit-generation before, as have other big publishers.

John Wiley &amp; Sons (whom I will refer to as ‘Wiley’ from now on) is not a very competent company when it comes to providing free or open access to research.

ESA moves to Wiley and predictably there are problems already

This has done the rounds on Twitter a lot recently, and justifiably-so but just in case you haven’t seen it yet…  I thought I’d quickly blog about this excellent graph published on a FrontiersIn blog late last year (source/credit: http://blog.frontiersin.org/2015/12/21/4782/ )  With data from 570 different journals, it appears to demonstrate that rejection rate (the percentage of papers submitted, but NOT accepted for publication at a

Why do we rejoice in rejecting perfectly valid research?

[Update 2015-09-19: since writing this, I notice my open access article has now been unpaywalled at Wiley’s site. No-one from Wiley has reached out to me to explain how, why, or when this happened. No compensation has been offered, nor any apology. I note that all the other articles in the special section, which should also be open access (CC BY) are still on sale, behind a paywall.

I’m saying NO to Wiley

Last Friday, I genuinely thought Elsevier had illegally sold me an article that should have been open access. This post is to update you all on what we’ve found out since:

 The Scale of the Problem

No one really knows how many articles are wrongly paywalled at all of Elsevier’s various different sales websites.

Wrongly paywalled articles: a recap of what we now know

For those that know me as a biologist it might perhaps surprise you to know that my most cited publication so far is on Open Access and Altmetrics (published in April 2013, 25 cites and counting…) — nothing to do with biology per se!  So I took great interest in this new publication:  Wang, X., Liu, C., Mao, W., and Fang, Z. 2015. The open access advantage considering citation, article usage and social media attention.

Page View Spikes on Research Articles

My full comments on the PLOS ONE manuscript submission modelling paper:

On 27 January 2015 at 23:05, Chris Woolston &lt;REDACTED&gt; wrote: Yep I remember. Sure why not? Thanks for the compliment :) Salinas S, Munch SB (2015) Where Should I Send It? Optimizing the Submission Decision Process. PLoS ONE 10(1): e0115451. doi: 10.1371/journal.pone.0115451 A worthy choice.

Manuscript submission modelling – my comments in full

Now I’m at the Natural History Museum, London I’ve started a new and ambitious text-mining project: to find, extract, publish, and link-up all mentions of NHM, London specimens published in the recent research literature (born digital, published post-2000).  Rod Page is already blazing a trail in this area with older BHL literature.

Text mining for museum specimen identifiers

Yesterday, I tried to read a piece of research, relevant to my interests that was published in 1949. Sadly as is usual, I hit a paywall asking me for £30 + tax to read it (I didn’t pay). Hincks, W. D. 1949. IV.—systematic and synonymic notes on passalidae (col.).  Annals and Magazine of Natural History 2:56-64.

Who actually has access to paywalled research?

A quick blog from Meise, Belgium at the Pro-iBiosphere wrap-up event. Yesterday I gave a talk about my progress liberating, and making searchable, OA figures from academic literature:

 Liberating OA figures from PDF to Flickr (a Pro-iBiosphere talk)

from

 Ross Mounce

I’ve had a lot of great feedback and interest in what I’m doing with this.

Progress Update from Meise, Belgium

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.

Content mining for phylogenetic data

[A monthly update on my Panton Fellowship related activities]  Last month I was slightly late with my monthly report, so this month I’m going to get things back on track and write my post now, on this leisurely sunny Sunday afternoon…  It’s been a good month:  First of all, I had the chance to speak about my Fellowship work for the Ede &amp; Ravenscroft Prize final.


Panton Fellowship updates: May (month 2)

To try and publicize the variety of Gold Open Access article publication options on offer, I’ve decided to create a visualization of the journal data that has previously been collected as part of my survey of ‘Open Access’ publisher licenses’ spreadsheet. Here is version 0.1 of the ‘Mounce plot’ (much more data still to be added!


A visualization of Gold Open Access options

Here’s my submission for the House of Lords inquiry. I rather ran out of steam writing it so you’ll see it tails off towards the end. There’s probably loads of things I should mention too. But alas, I have lots of other work to be getting on with right now. Ironically, I highlight the excellent journal Impact Factor‘s of some OA journals. Please forgive me for those sins! So here it is:


My submission for the House of Lords inquiry

[UPDATE: 2015-01-07 It appears the full text of this article is now freely available from the publishers website. A moving wall system? This still doesn’t change the fact that this article was not publically available for 12 months. The maximum embargo allowed by MRC funding is just 6 months from publication.]

I note with interest that article publication charge data from the University of Edinburgh has been released on Figshare today.

Do &#8216;green&#8217; access strategies actually achieve public access?

So, apparently Elsevier are launching a new open access mega-journal some time this year, joining the bandwagon of similar efforts from almost every other major publisher. A lovely acknowledgement of the roaring success of PLOS ONE, who did it first a long time ago. They’re only ~8 years behind, but they’re learning. I for one am pleased they are asking the research community what they want from this new journal.


Elsevier wants our feedback. Here&#8217;s mine

Last week, on Monday 19th January, I co-organised the first ever Open Research London event at Imperial College London, with the help of local organisers; Jon Tennant &amp; Torsten Reimer. We invited two speakers for our first meeting: Chris Banks (Director of Library Services at Imperial, and an elected Board Member of Research Libraries UK) &amp;


Open Research London launch event

This post was originally posted over at the LSE Impact blog where I was kindly invited to write on this theme by the Managing Editor. It’s a widely read platform and I hope it inspires some academics to upload more of their work for everyone to read and use

Recently I tried to explain on twitter in a few tweets how everyone can take easy steps towards open scholarship with their own work.

Easy steps towards open scholarship

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


Research data should be appropriately licensed with re-use in mind

[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 &amp; excessive profiteering*** causes.

Journal mega-bundles &#038; TheCostOfKnowledge

It’s that time again… time to write my monthly Panton Fellowship update. The trouble is, as I start writing this it’s 6am (London, UK). I arrived back from the Hennig XXXI meeting (University of California Riverside) after a long flight yesterday and am

 supremely

jetlagged. I still can’t decide whether this is awesome (I can get more work done, by waking up earlier), or terrible as I can’t keep my eyes open past 9pm at night!

Panton Fellowship updates: June (month 3)

Why is it so difficult to identify academic publisher PDFs?

With published MP3 files of

 audio

you get rather good metadata. Take for example an MP3 file I downloaded from Hacker Public Radio available at the bottom of this post.

PDF metadata &#8211; why so poor?

Last Saturday I went to Hack4Ac – a hackday in London bringing together many sections of the academic community in pursuit of two goals: To demonstrate the value of the CC-BY licence within academia. We are interested in supporting innovations around and on top of the literature. To reach out to academics who are keen to learn or improve their programming skills to better their research.


Hack4ac recap

Having just written a lengthy blog post / rant about publishing data for another blog (I’ll link to it later if/when it gets published). I thought I’d post a technical demonstration of my issues here. I want need to extract simple matrices of numbers from research papers for my PhD research. Theoretically, I shouldn’t even need to do this.


Using off-the-shelf OCR to re-extract data

After more than 6 months of waiting, my long overdue first paper has

 finally

been published in Nature Why do I say ‘long overdue’? Doesn’t it usually take a long time for academic papers to get published?

My 1st peer-review published paper

I’ve just read a paper published in

 Systematic Biology

called ‘A Falsification of the Citation Impediment in the Taxonomic Literature’. Having read the full paper many times, including the 64-page PDF supplementary materials file. I’m amazed the paper was published in its current form.

What is Journal Visibility?

I’ve been rather preoccupied in the last few months hence the lack of blog posts. (Apologies!) Here’s a quick recap of some things I’ve done since July: Got married in China (in September) Successfully proposed that the Systematics Association (of which I’m a council member) should sign DORA Gave an invited talk on open science at an INNGE workshop at INTECOL 2013 Completed and

 handed-in my PhD thesis

last Thursday!

Setting-up AMI2 on Windows

I just sent this email to Darin Croft (of SVP). I chose to contact him because he recently answered questions about the embargo for EmbargoWatch and it was rather unclear who else I should approach. I did

 not

want to blanket email the whole council.

Some further questions for SVP about their talk abstract embargo

Yesterday, I made a journal scraper for the International Journal of Systematic and Evolutionary Microbiology (IJSEM).  Fortunately, Richard Smith-Unna and the ContentMine team have done most of the hard work in creating the general framework with quickscrape (open-source and available on github), I just had to modify the available journal-scrapers to work with IJSEM.

Making a journal scraper

I’d just like to point out to anyone who asks, particularly CRC Press (part of Taylor&amp;Francis Group, who are in turn part of Informa PLC) that by posting the full text of my book chapter to Academia.edu I am *not* breaching the copyright transfer agreement I signed.


Edit Your Copyright Transfer Agreement Contract

I’ve been quoted in a Nature News story about Open Access journal licencing. I’m a staunch defender of the use of the Creative Commons Attribution licence, as it’s a good licence for academic research. Here’s just some of what I sent Richard Van Noorden (Nature News) by email. I don’t blame him for only using select quotes.


Further info about the licences that free/open access journals use

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.


FUBAR’d ScienceDirect RSS feeds

Today, the author of a paid-for, ‘hybrid’ open access article published in 2009, found that it was wrongly on sale at a Springer website:  https://twitter.com/zentree/status/592547039474421760  FWIW it’s still freely available at the original publisher website here.

Springer caught red-handed selling access to an Open Access article

Updated 2017-02-01: Mathematical equation rendering failures spotted at the journal ‘Molecular Biology &amp; Evolution’ (MBE). Added to the lengthy list.

In this post I shall try and summarise the different types of error that are occurring across Oxford University Press (OUP) journals at the moment.

Documenting the many failures across OUP journals

This week I chose the papers for the Brockington Lab ‘journal club’ here at the Department of Plant Sciences, University of Cambridge (I prefer to call it the ‘weekly research round-up’ though, because good content has nothing-to-do with

 journals

per se!). We rotate the choice of papers between each lab member every week.

Brockington Lab Weekly Research Round-Up

Just a quick update to let you know how the new Research Ideas and Outcomes (RIO) journal is going. You may remember I wrote a blog post here explaining my enthusiasm for this new journal. I’m delighted to say it is exceeding my expectations.

RIO Journal Blossoms: an overview of RIO so far

Anyone care to remember how awful and unusable the web interface for accessing the NHM’s specimen records used to be? Behold the horror below as it was in 2013, or visit the Web Archive to see just how bad it was. It’s not even the ‘look’ of it that was the major problem – it was more that it simply wouldn’t return results for many searches. No one I know actually used that web interface because of these issues.

Using the NHM Data Portal API

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.

Advice for journal-publishing academic societies

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.

Command-line access to research: getpapers

Roughly ten days after I first blogged about this (see: Springer caught red-handed selling access to an Open Access article), Springer have now made a curious public statement acknowledging this debacle: Statement on Annals of Forest Science article   Berlin, 6 May 2015  A number of tweets posted by Prof.

Springer admits wrongdoing in selling open access article

“In statistics, a central tendency (or measure of central tendency) is a central or typical value for a probability distribution. Colloquially, measures of central tendency are often called averages. The most common measures of central tendency are the arithmetic mean, the median, and the mode.” — Wikipedia.  In the UK, we teach school kids how to calculate the mean, median, and mode in Year 6 (kids aged 10-11), it’s simple stuff.

Central Tendency, Citation Distributions, and Springer Nature (Part 2)

In late 2016, Martin Eve, Stuart Lawson and Jon Tennant referred Elsevier/RELX to the Competition and Markets Authority. Inspired by this, I thought I would try referring a complaint to the UK Advertising Standards Authority (ASA) about some blatant fibbing I saw Elsevier engage-in with their marketing spiel at a recent conference.

Referring Elsevier/RELX to the Advertising Standards Authority

In 2017, we have a vast toolbox of informative methods to help us analyse large volumes of text. Sentiment analysis, topic modelling, and named entity recognition are to name but a few of these exciting approaches. Computational power and storage capacity are not the limiting factors on what we could do with the 100 million or so journal articles that comprise the ever-growing research literature so far.

Open in order to unleash the power of text mining

Any good scientist knows that one must have an adequate experimental control when trying to determine the significance of effects. Therefore, in order to test the significance of the 106 broken DOIs I reported at OUP yesterday, I created a comparable stratified ‘control’ sample of 21 journals NOT published by OUP that are indexed in pubmed.

Comparing OUP to other publishers

Widening the circle of care: An arts-based, participatory dialogue with stakeholders on cancer care for First Nations, Inuit, and Métis peoples in Ontario, Canada

There are a lot of really interesting works being published over at Research Ideas and Outcomes (RIO).  If you aren’t already following the updates you can do so via RSS, Twitter, or via email (scroll to the bottom for sign-up).  In this post I’m going to discuss why Chad Hammond’s contribution is so remarkable and why it could represent an exciting model for a more transparent and more immediate future of scholarly communications.

Publishing grant proposals, presubmission

In this post I’ll go through an illustrated example of what I plan to do with my text mining project: linking-up biological specimens from the Natural History Museum, London (sometimes known as BMNH or NHMUK) to the published research literature with persistent identifiers. I’ve run some simple grep searches of the PMC open access subset already, and PLOS ONE make up a significant portion of the ‘hits’, unsurprisingly.

BMNH specimens used in PLOS ONE

April Clyburne-Sherin asked an interesting question on the OpenCon Discussion List recently:

 Comment:

Quite rightly, April does not

 trust

the publisher to make the published work fully open access in perpetuity, and wants to do more as an author, with the publishing agreement (a formal contract) to ensure that the publisher

 will

actually provide the exact services she wants.

Agreements between authors and publishers

Just a quick note that BMC journal APC’s have increased from what they were in 2012.   Luckily I had the 2012 data saved on my computer so I can compare prices directly. I’ve put the data for 97 journals (not all of them) here on figshare.

 The mean price increase is just over 5%

. Although to give it a fair statistical treatment – the median price increase is just 3.3% (to 1 d.p.). There is a lot of variance.

Gold OA Pricewatch #2 &#8211; BMC journal APCs increase

I’ve written about MOOCs last December but never actually enrolled in one myself… until now. Sure, I’ve done Codecademy courses and Codeschool courses which I’ve immensely enjoyed but they’re perhaps(?) not quite the same thing.


I&#8217;ve enrolled in some MOOCs

This is a
 
 re-post
 
 of something I was invited to write to sum-up my experiences at OKCon 2011. The original post can be viewed here on the official OKFN Open Science blog.

Open Palaeontology @OKCon2011 (Berlin)

So a week ago, I investigated publisher-produced Version of Record PDFs with

 pdfinfo

and the results were very disappointing. Lots of missing metadata was found and one could not reliably identify most of these PDFs from metadata alone, let alone extract particular fields of interest. But Rod Page kindly alerted to me the fact that I might be using the wrong tool for this investigation.

PDF metadata: different tool, same story

If you haven’t heard yet – I was successful in my Panton Fellowship proposal  I wasn’t the only successful applicant either – huge congratulations to Sophie Kershaw and her excellent proposal to train doctoral students how to do Open Science at Oxford University.


The Panton Fellowship &#8211; April (month 1)

This is a parody of a recent blog post over in Elsevier-land by David Tempest.

Copyright in an Open Access World – a parody

Wow! Where to begin… In this post I shall

 attempt

to summarise some of OKFestival 2012.

 Some Background:

I had been to the Open Knowledge Conference last year (in Berlin), where I gave an invited talk on Open Palaeontology and met lots of brilliant people in the Open Science community like Bjoern Brembs, Cameron Neylon &amp; Peter Murray-Rust.

The Open Knowledge Festival 2012, Helsinki: some notes

This article is cross-posted from the main Open Knowledge Foundation blog, where I occasionally post. I realise I haven’t had time to post here on my own blog for over a month now(!), so I may well copy across a few more posts I’ve written for OKF.

Here at the Open Knowledge Foundation, we know Open Science is tough, but ultimately rewarding. It requires courage &amp; leadership to take the open path in science.

A blog by Ross Mounce

ESA moves to Wiley and predictably there are problems already

When is an ‘extinct’ plant actually extinct?

I’m saying NO to Wiley

Advice for journal-publishing academic societies

The Ecological Society of America wants ‘input’ on Open Access