Show me the data!
Header

Author Archives: rmounce

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 very probably are sending takedown notices to institutions and websites across the globe.
No-one is safe from these legal threats.

Not only that, but they seem to be encouraging universities to be pro-active and takedown more than just the specific articles identified in the DMCA notice they send! They are encouraging universities to limit access to their research works. This is simply disgraceful (even though I acknowledge they are technically, legally within their rights to do this because of the way in which their copyright transfer agreements are written, which incidentally many academics are effectively forced to sign in order to get published and make progress in their careers).

For background information read:

How one publisher is stopping academics from sharing their research. The Washington Post 19/12/2013

Elsevier steps up its War On Access SVPOW 17/12/2013

300px-Elsevier_poster_with_text

Librarians and university web admins: please publicly come out with more examples like this. Researchers, readers and taxpayers desperately need to know about this. Silence and subterfuge benefits no-one, these chilling effects must be publicly revealed.

This is the email I received with certain parts redacted:

*** Sent via Email – Inappropriate postings of Elsevier’s journal articles / DMCA Notice of Copyright Infringement ***

Dear Sir/Madam,

I write on behalf of Elsevier to bring to your attention the inappropriate posting of final published journal articles to your institutional website. I am President at Attributor (A Digimarc Company), which assists some of the world’s most prominent publishers, including Elsevier, with digital content protection (www.digimarc.com/guardian). Following the discussion below, a formal DMCA takedown request is included as Appendix A.

As you probably know, Elsevier journal article authors retain or are permitted a wide scope of scholarly use and posting on their own sites and for use within their own institutions. Those rights are more expansive when it comes to author preprints or accepted manuscripts than with respect to the final versions of published journal articles. Elsevier recognizes that in some cases authors or their institutions may not be fully aware of these rights and can by mistake post the final version of their articles to institutional websites or repositories. Unfortunately, it has come to our attention that copies of final published journal articles have, perhaps inadvertently, been posted for public access to one of your institutional websites.

I therefore request your cooperation to remove or disable access to these articles on your site, including but not limited to the articles identified in Appendix A. We have identified merely a sample in Appendix A, and as a publisher of close to 2,000 journals this might mean that more articles published by Elsevier could be found on your site. Please may I therefore draw your attention to Elsevier’s posting policy and ask for your attention to ensuring that your posting practices comply with this?
http://www.elsevier.com/about/open-access/open-access-policies/article-posting-policy#published-journal-article

In particular I note that Elsevier currently doesn’t permit posting of the final published journal article, and if there is a mandate or systematic posting mechanisms in place then Elsevier asks for a cost-free agreement with the institution before accepted author manuscripts are posted.
I would also recommend considering the use of DOI links as a way to access to the version of records of a published article. This would allow authors to list their work and to provide easy access to peers.

Finally, should you need any help in properly identifying a final published article to prevent any future improper posting, please do get in touch via the email address below.

I appreciate your anticipated cooperation and if you have any questions or feedback, or if you believe you have received this message in error (as you have received permission to post this article from Elsevier), please contact: UniversalAccess@Elsevier.com
Thank you.

Sincerely,
Eraj Siddiqui
Attributor (A Digimarc Company)

Appendix A

Copyright Infringement Notice

This notice is sent pursuant to the Digital Millennium Copyright Act (DMCA), the European Union’s Directive on the Harmonisation of Certain Aspects of Copyright and Related Rights in the Information Society (2001/29/EC), and/or other laws and regulations relevant in European Union member states or other jurisdictions.

Please remove or disable access to the infringing pages or materials identified below, as they infringe the copyright works identified below.

I certify under penalty of perjury, that I am an agent authorized to act on behalf of the owner of the intellectual property rights and that the information contained in this notice is accurate.

I have a good faith belief that use of the material listed below in the manner complained of is not authorized by the copyright owner, its agent, or the law.

My contact information is as follows:

Organization name: Attributor Corporation as agent for [Publisher Company]
Email: counter-notice@attributor.com
Phone: 650-340-9601
Mailing address:
400 South El Camino Real
Suite 650,
San Mateo, CA 94402

My electronic signature follows:
Sincerely,
/E Siddiqui/
E. Siddiqui
Attributor, Inc.

***List of Works and Location of Infringing Page or Material ***

Infringing page/material that I demand be disabled or removed in consideration of the above:

*** INFRINGING PAGE OR MATERIAL ***

Infringing page/material that I demand be disabled or removed in consideration of the above:

Rights Holder: Reed Elsevier

Original Work: [redacted]
Infringing URL: [redacted]

UPDATE:

Dutch Universities too are receiving DMCA’s from Elsevier:

2013-12-20-113623_939x846_scrot

@Wowter via Twitter

I’d just like to point out to anyone who asks, particularly CRC Press (part of Taylor&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.

Upon receiving a copyright transfer agreement as a PDF from them via email – I edited the PDF to reword the agreement to terms that were more agreeable to me (e.g. I did NOT want to transfer my copyright to them for my work).

The bit of wording I changed is as follows:

As such, copyrights in the Work will not inure to the benefit of the Publisher, the Publisher will not own the publication, its title and component parts, and all publication rights. This does not permit the Publisher, in its name, to copyright in the Contribution, make applications to register its copyright claim, and to renew its copyright certificate.

I signed this reworded form as PDF (displayed below, signature removed) and returned it to them. I have now kindly received a free ‘author copy’ of the printed book and my chapter has clearly been included so it’s too late for CRC press to exclude my chapter. I can only assume they agreed to the reworded terms of the contract I signed and sent them.

I doubt CRC press would even be bothered by my actions to be honest. They are allowing another of their books to be completely posted online for free, so in comparison to that, my action here is puny – but it certainly emboldens me for the next time I may have to sign a CTA form…

CRC Press are welcome to non-exclusively publish my book chapter. Thank you CRC Press for agreeing to my terms and conditions.

Contract

Lessons one might learn from this exercise:

DO NOT GIVE AWAY THE COPYRIGHT TO YOUR WORK!
PUBLISHERS DO NOT ‘NEED’ ALL YOUR COPYRIGHT TRANSFERRED TO THEM TO PUBLISH.
ALL THAT IS NEEDED IS FOR YOU TO GRANT THEM A NON-EXCLUSIVE LICENSE TO PUBLISH.

A word of warning though… I wouldn’t recommend relying on this method of editing CTA’s to get what you want. I was just lucky this time. Choosing an open access publication venue from the start is always the best option (if possible).

See also:

Mike Taylor 2010. Who Owns My Sauropod History Paper?
http://svpow.com/2010/10/13/who-owns-my-sauropod-history-paper/

Acknowledgements

October 21st, 2013 | Posted by rmounce in Open Access - (3 Comments)

I handed in my thesis not long ago, on Thursday 3rd October 2013. No idea when my viva is yet. I can’t blog many of the chapters because I haven’t convinced my manuscript co-authors of the value of preprints, yet. I’m also a bit unsure as to how some of the other chapters will be received and thus I’ll wait until after the viva before I decide what to do next with it.


Given it’s open access week this week, there is one bit of my thesis I should definitely share: the acknowledgements!

I can’t possibly thank everyone enough for the help I’ve received over the past 4 years – my knowledge, skills, and connections have been vastly extended. Note in particular the bit I’ve highlighted in bold just for this blog post – I want everyone to know how absolutely reliant I’ve been on ‘alternate’ forms of literature access during my research – this is the new ‘normal’ for many early career researchers I fear, until open access is more prevalent we’ll have to continue to hunt, scavenge, beg, steal, and borrow for every PDF. My generation of researchers grew-up using Napster, Isohunt, Library.nu. Copyright infringement is an everyday activity for many of us – WE DONT CARE. Have you been to a conference? How many of the pictures on the speakers slides weren’t technically infringing someone else’s copyright? WE DONT CARE. One can shut down or block specific portals, but doing so doesn’t really solve the basic problem: from what I’ve seen, time and time again, copyright’s only role in science is to obstruct it. My biggest hope for Open Access Week 2013 is that someone will torrent Elsevier’s back catalogue – journal/publisher torrents have been done before and will be done again!  It probably won’t happen, but I can dream…

Acknowledgements

I would like to thank my supervisor, Matthew Wills for putting up with me all this time. I
have been lucky to have such accommodating and understanding support. I also must
thank my lab mates Martin Hughes, Anne O’Connor, Sylvain Gerber, Katie Davis, Rob
Sansom and everyone else in the Biodiversity Lab at the University of Bath – we had some
great times and some brilliant times together. Sincere thanks also to the University of Oslo
Bioportal computing cluster for providing me free cloud computation for my work.
Many people have helped spur my imagination along the way with ideas for different
chapters of this thesis. For this I would like to thank Ward Wheeler, Pablo Goloboff, Mark
Siddall, Dan Janies, Steve Farris and the generous financial support of the Willi Hennig
Society. I want to thank all those in the palaeontology community who have shared their
published data with me, particularly Graeme Lloyd for his stirling work in making
dinosaurian data available – I hope I have done something interesting with the data I have
used and opened eyes to new possibilities. I also want to thank all those in the open
science community – Peter Murray-Rust, Todd Vision, Heather Piwowar, Mark Hahnel,
Martin Fenner, Geoffrey Boulton, Jenny Molloy and so many more I’ve had the pleasure of
meeting in person. The energy and enthusiasm I drew from countless online discussions
on Facebook, Google+ and Twitter was truly inspirational.
For facilitating greater access to scientific literature I must heartily thank the Natural
History Museum, London library and archives, the #icanhazpdf community on Twitter,
Wikipaleo on Facebook, References Wanted on FriendFeed, Library.nu, and SciHub.
Without these additional literature access facilitators I would not have been able to read
half the sources I cite in this thesis.
I must thank my wife Avril for her patience with me especially during the write-up phase,
for allowing me to go away to all these amazing conferences abroad, and for tolerating all
those long nights into mid-morning when I was tapping away on my noisy keyboard.
Finally, I thank my family: Richard, Rosemary & Tara for repeatedly encouraging me to
finish my thesis – I got there in the end!

Setting-up AMI2 on Windows

October 6th, 2013 | Posted by rmounce in Content Mining - (1 Comments)

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!

So yeah, I really didn’t have time blog until now.

But now my PhD thesis is handed-in I can concentrate on the next step… Matthew Wills, myself, and Peter Murray-Rust have an approved BBSRC grant to work on further developing AMI2 to extract phylogenetic trees from the literature (born-digital PDFs).

At the moment it is in alpha stage so it doesn’t extract trees perfectly – it needs work. But in case you might want to try it out I thought I’d use this post to explain how to get a test development of it running on Windows (I don’t usually use Windows myself, I much prefer linux). These notes are thus as much an open notebook science ‘aide memoire’ for myself as they are instructions for others!

Dependencies and IDE:

1.) You’ll need Java JDK, Eclipse, Mercurial and Maven for starters.

If you haven’t got this setup already you may need to set your environment variables e.g. JAVA_HOME

2.) Within Eclipse you need to install the m2e (maven integration) plugin

(from within the Eclipse GUI) click ‘Help’ -> Install New Software -> All available sites (from the dropdown) -> select m2e

 

3.) Using mercurial, clone the AMI2 suite to a clean workspace folder. The suite includes:

 

[euclid-dev itself has many dependencies which are indicated in its POM file which you shouldn’t need to worry about – they should be pulled-in automatically. These include:  commons-io, log4j, xom, joda and junit.]

4.) From within the Eclipse GUI import your workspace of AMI2 tools:

click ‘File’ -> Import -> Maven -> select ‘Existing Maven Projects’ -> Next -> select your workspace

 

5.) Test if it works. In the package explorer side-pane window you should now see folders corresponding to the six AMI2 tools listed above.

Right-click on svg2xml-dev -> select ‘Run-as’ -> JUnit Test

and sit back and watch the test run in the console at the bottom of the Eclipse GUI.

(The tests are a little slow, have patience, it may take a few minutes – it took me 175 seconds)

To view the results, in the package explorer pane, navigate inside the svg2xml-dev document tree into /target/output/multiple-1471-2148-11-312 and click ont TEXT.0 to see what the text-extraction looks like. You should see something like this below (note it successfully gets italics, bold, and superscripts)

—————————————————————————————————-

Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes

Tomohide Hiwatashi 1 , Akichika Mikami 2,8 , Takafumi Katsumura 1 , Bambang Suryobroto 3 , Dyah Perwitasari-Farajallah 3,4 , Suchinda Malaivijitnond 5 , Boripat Siriaroonrat 6 , Hiroki Oota 1,9 , Shunji Goto 7,10 and Shoji Kawamura 1*

 

Abstract Background: Routine trichromatic color vision is a characteristic feature of catarrhines (humans, apes and Old World monkeys). This is enabled by L and M opsin genes arrayed on the X chromosome and an autosomal S opsin gene. In non-human catarrhines, genetic variation affecting the color vision phenotype is reported to be absent or rare in both L and M opsin genes, despite the suggestion that gene conversion has homogenized the two genes. However, nucleotide variation of both introns and exons among catarrhines has only been examined in detail for the L opsin gene of humans and chimpanzees. In the present study, we examined the nucleotide variation of gibbon (Catarrhini, Hylobatidae) L and M opsin genes. Specifically, we focused on the 3.6~3.9-kb region that encompasses the centrally located exon 3 through exon 5, which encode the amino acid sites functional for the spectral tuning of the genes.

Results: Among 152 individuals representing three genera ( Hylobates ,  Nomascus and  Symphalangus ), all had both L and M opsin genes and no L/M hybrid genes. Among 94 individuals subjected to the detailed DNA sequencing, the nucleotide divergence between L and M opsin genes in the exons was significantly higher than the divergence in introns in each species. The ratio of the inter-LM divergence to the intra-L/M polymorphism was significantly lower in the introns than that in synonymous sites. When we reconstructed the phylogenetic tree using the exon sequences, the L/M gene duplication was placed in the common ancestor of catarrhines, whereas when intron sequences were used, the gene duplications appeared multiple times in different species. Using the GENECONV program, we also detected that tracts of gene conversions between L and M opsin genes occurred mostly within the intron regions.

Conclusions: These results indicate the historical accumulation of gene conversions between L and M opsin genes in the introns in gibbons. Our study provides further support for the homogenizing role of gene conversion between the L and M opsin genes and for the purifying selection against such homogenization in the central exons to maintain the spectral difference between L and M opsins in non-human catarrhines.

 

Background In catarrhine primates (humans, apes and Old World monkeys) the L and M opsin genes are closely juxta-posed on the X chromosome and, in combination with the autosomal S opsin gene, enable routinely trichro-matic color vision [1,2]. The L and M opsin genes have a close evolutionary relationship and are highly similar in nucleotide sequence (~96% identity). Among 15

* Correspondence: kawamura@k.u-tokyo.ac.jp 1 Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan Full list of author information is available at the end of the article

amino acid differences between the human L and M opsin genes, three account for the main shifts in spectral sensitivities and tuning [3-9]. The organization of the L and M opsin genes among humans is known to be variable and includes the absence of an L or M opsin gene or the presence of L/M hybrid genes with an intermediate spectral sensitivity. A high incidence (approximately 3-8%) of color vision   deficien-cies in males results as a consequence [10].
Hiwatashi et al . BMC Evolutionary Biology 2011, 11 :312 http://www.biomedcentral.com/1471-2148/11/312
—————————————————————————————————-

If you’d like to try your own PDFs with it you’ll need to do two things:

A.) place the PDF(s) to be tested within the folder:    svg2xml-dev/src/test/resources/pdfs

B.) edit the file:    svg2xml-dev/src/test/java/org/xmlcml/svg2xml/pdf/PDFAnalyzerTest.java

so that

new PDFAnalyzer().analyzePDFFile(new File(” …

points at your file(s).

 

You can then right-click ‘multipletest’ from within PDFAnalyzerTest.java and select Run As -> JUnit Test

 

We’re working with BMC journal content for the moment, and when we perfect it on this, we will expand our scope to include subscription access content too.