Archive for the 'ecology' Category

Why Doesn’t the Ecological Society of America Allow Their Open Access Content to be Text Mined?

A recent tweet from Todd Vision and blog post by Jonathan Eisen’s have alerted me to the shameful defense of the status quo in scientific publishing advanced by the the Ecological Society of America concerning the Office of Science and Technology Policy’s recent request for information on Open Access. This particular thread caught my eye because I still have fresh bruises from being denied access to Open Access ESA journal content for text-mining research. Denied access to Open content – how is this possible, you say?

Over the last two years I have been targetting scientific society’s whose journal’s are not in the tiny fraction of the scientific literature in the PubMed Central Open Access subset, hoping to encourage them to release their content for text-mining research projects in my group (e.g. My attitude has been that Society’s are the ones to go after, since they often hold the copyrights and are typically run by colleagues who I can directly appeal to. After productive (yet rather protracted) communication with The Genetics Society of America, the UK Genetics Society and the Society for Molecular Biology and Evolution, we’ve been able to obtain back-content for Genetics, Heredity and Molecular Biology and Evolution for our projects.* Heredity has gone far enough to announce that their content is now open for text-mining research on their home page (victory!)

In stark contrast, a similar line of inquiry with the Ecological Society of America has led to a very sour and unproductive experience which I will summarize here to demonstrate the the ESA’s recent response letter to the OSTP is consistent with a general attitude of protecting their journal content. This narrative echoes Peter Murray-Rust’s painful story of his years negotiating with Elsevier for access to content, which likewise has no positive conclusion.

While Katherine McCarter is true in saying that the ESA publishes a subset of their content under OA licenses, it is not true that this content in is in any meaningful way “open” in a 21st-century, linked-data, remix-and-reuse context. Why? Because like virtually all of the ecological, agricultural and environmental literature, ESA OA content is not deposited in a public archive like PubMed Central, and can only be accessed via the ESA journal website.  However, this content is not accessible to text-mining since the ESA journal permissions clearly state:

Altering, recompiling, systematic or programmatic copying, or reselling of text or other information from ESA Journals in any form or medium is prohibited. Systematic or programmatic downloading, service bureau redistribution services, printing for fee-for-service purposes and/or the systematic making of print or electronic copies for transmission to non-subscribing institutions are prohibited.

Since I have been burned in the past by aggressive closed-access publishers shutting down my office IP for naively downloading content that my univeristy has a site license for, I dutifully went down the proper channel of requesting permissions to automatically download ESA content from the Permissions Editor, Dr. Cliff Duke. For the record, I can say that Dr. Duke has been faultlessly professional throughout the process and was positive about my initial request, an excerpt of which follows:

From: Cliff Duke <>
Date: 28 June 2011 14:19:18 GMT+01:00
To: Casey Bergman <>
Subject: RE: request for permission to use ESA content in text-mining research


In answer to your question — not that I recall, but I also don’t recall any previous similar requests, and I’ve been the permissions editor for about seven years. However, I doubt your request will be the last such, given the increasing interest in this kind of research.


—–Original Message—–
From: Casey Bergman []
Sent: Tuesday, June 28, 2011 9:14 AM
To: Cliff Duke
Subject: Re: request for permission to use ESA content in text-mining research

Dear Dr. Duke -

Many thanks for the very quick reply.  I appreciate your efforts in bringing this to the attention of the ESA leadership and I fully understand that this may take some time to sort out (it took several months with GSA).

One quick question at this stage: is there any precedent at ESA for permitting bulk access for text mining research?

Best regards,

—–Original Message—–
On 28 Jun 2011, at 13:48, Cliff Duke wrote:

Dr. Bergman,

I will discuss your request with our executive director and editors and get back to you as soon as I can. Our director is on travel this week, and I am on vacation next week, so it may be a couple of weeks before you hear back from us. Let me know if you have any questions meanwhile.

Cliff Duke

Clifford S. Duke, Ph.D.
Permissions Editor

Ecological Society of America
1990 M Street NW, Suite 700
Washington, DC 20036
Phone: (202) 833-8773
Fax: (202) 833-8775
E-mail: csduke [at]

—–Original Message—–
From: Casey Bergman []
Sent: Tuesday, June 28, 2011 8:34 AM
To: Cliff Duke
Subject: request for permission to use ESA content in text-mining research

Dear Dr. Duke -

Greetings, I am a researcher at the University of Manchester, with an interest in application of text and data mining to biological problems at the interface of computational and evolutionary biology. I am writing to request permission to use ESA journal content in text-mining research project that I am developing to submit as proposal to the UK Natural Environment Research Council. Specifically, I would like to request permission to automate download of the entire/the open-access subset of all ESA titles, which I understand is not permitted under the standard ESA policy (


Dr Duke then put me in touch with the Managing Editor of the ESA journals, David Baldwin who promptly ignored my request for several months, despite repeated emails and phone calls on e.g. 6 September 2011, 27 September 2011, 13 October 2011.  I finally received one email from David Baldwin on 20 October 2011, where he promised (but failed) to get back to me a few days later:

From: Casey Bergman <>
Date: 20 October 2011 12:42:01 GMT+01:00
To: J David Baldwin <>
Cc: Cliff Duke <>
Bcc: Casey Bergman <casey.bergman@xxx.xx>
Subject: Re: request for permission to use ESA content in text-mining research

Dear David -

Many thanks for replying. I fully understand that nonstandard requests can take some time. My previous interactions with Genetics and Heredity have also taken many months to lead to positive decisions on releasing content for text mining research.

All that is required in the short term is explicit permission to execute automated downloads on the site that abide by the limits of your systems (<50 sessions in 10 minutes).  No other technical issues need to be addressed on your side.

Also, I am happy in the first instance to restrict automated downloads to the Open Access subset of ESA publications, if a decision to permit access to the entirety of ESA content is more difficult.

Best regards,

On 20 Oct 2011, at 12:03, J David Baldwin wrote:

Dear Dr. Bergman–

I know you are keen to discuss this, but I’m afraid you have picked a particularly bad week for contacting me. Today (Thursday, 20 October) won’t be any better than the past two days, and tomorrow (Friday) I’ll be out of town. I’ll look over your request before Monday, 24 October, and will e-mail you again by then. I’m afraid I get handed off the nonstandard requests (“the buck stops here”), and yet I have my own priorities (i.e., working to keep the journal issues on schedule).


—–Original Message—–
From: Casey Bergman []
Sent: Thursday, October 13, 2011 9:01 AM
To: J David Baldwin
Cc: Cliff Duke
Subject: Re: request for permission to use ESA content in text-mining research

Dear David -

Would there be a convenient time for you sometime in the next week or so to discuss how we might be able to access ESA content programmatically?  I am +5 hrs to you, so late afternoon for me = morning for you is typically the best timeline to arrange a call.

Best regards,

Well I can report that as of 6 January 2012, the buck certain has stopped with David Baldwin on this issue, since he still refuses to respond to the most minimal request for permission to automatically download only the Open Access subset of the ESA content. Since no effort is required on his part other than to say “yes”, I take his inaction to speak for the ESA that they have no interest in supporting text and data mining research on their content — even their OA content — which is fully consistent with their specious arguments for protectionism of society subsidies through closed access publishing put forward in their response letter to the OSTP. Given the undeniable importance of data in the ecological literature for science and society, the ESA should be ashamed for locking away this precious resource from the world and being adamant in their position that this is in any way morally or ethically justified.

I look forward to David Baldwin’s response on this request, and hope the the ESA is more progressive in their outlook toward open access publishing and text/data mining in the coming years….

* Credits to Tracey DePellegrin Connelly, Scott Hawley and Lauren McIntrye for helping to free Genetics content;  Roger Butlin for helping free Heredity content; and Ken Wolfe, Soojin Yi and the SMBE council for helping to free MBE content.

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