A new law that introduces major changes in the way many U.S. scientific papers are published and redistributed is about to go into effect. Late last year, President Bush signed into law H.R. 2764 (now Public Law 110-161), part of which gives a broad new mandate to the NIH to intervene in the scientific publication system:

SEC. 218. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

A new NIH Public Access Website describes how the agency intends to implement the law. Recipients of NIH funds have two options for complying:

1. If you choose to publish your article in certain journals, you need do nothing further to comply with the submission requirement of the Policy. See http://publicaccess.nih.gov/submit_process_journals.htm for a list of these journals.

2. For any journal other than one of those in this list, the author must:

   a. Inform the journal that the article is subject to the Public Access Policy when submitting it for publication.

   b. Make sure that any copyright transfer or other publication agreement allows the article to be submitted to NIH in accordance with the Policy. For more information, see the FAQ Whose approval do I need to submit my article to PubMed Central? and consult with your Institution.

   c. Submit the article to NIH, upon acceptance for publication. See the Submission Process for more information.

The new policy becomes effective April 7, 2008.

In other words, all recipients of NIH funds will soon have an obligation under Federal Law to disclose to journals not on the NIH's list that their work is subject to PL 110-161.

The question is: what will the journals, some of which represent the most prestigious in their field, do with this information?

What Will the ACS Do?

For an organization making a lot of noise recently about its new Web site and focus on communication with its members, the ACS has been very quiet on what what position, if any, it will take regarding the new law.

In fact, from the ACS Homepage, one might get the impression nothing has changed. Looking at the home pages for flagship journals with a large amount of NIH-funded content provided no insights, either; J. Med. Chem, J. Org. Chem., and Org. Lett. have nothing to say on PL 110-161 that I could find.

The ACS author copyright release form doesn't appear to have changed. In other words, when you agree to publish your article in an ACS journal, you're still handing over copyright in your work to the ACS, who has the right under Copyright Law (and presumably PL 110-161) to prevent NIH grant recipients from depositing their manuscript into PubMed Central.

Even the ACS Office of Policy and Legislative & Government Affairs has zero guidance, as of this writing, to offer prospective authors who may have questions about complying with PL 110-161.

Misplaced Burden of Compliance

One of the many problems with PL 110-161 Section 218 is that it places the burden of compliance on authors themselves, not publishers. The law states very clearly that implementations must be "consistent with copyright law." As I wrote previously, this provision gives all the latitude needed to continue business as usual, which is exactly what we're seeing so far.

Two critical questions remain unanswered:

• What obligation, if any, does the ACS have to reject manuscripts from NIH-funded authors, given that it remains ACS policy to take copyright from its authors and with it the right to deposit the accepted manuscript into PubMed Central?

• What obligation, if any, do NIH-funded authors have to avoid publication in journals that strip copyright from them and thereby prevent their ability to comply with PL 110-161?

In partial answer to the second question, the NIH offers this FAQ:

Whose approval do I need to submit my article to PubMed Central?

Authors own the original copyrights to materials they write. Consistent with individual arrangements with authors' employing institutions, authors often transfer some or all of these rights to the publisher when the journal agrees to publish their article. Some publishers may ask authors to transfer copyrights for a manuscript when it is first submitted to a journal for review.

Authors should work with the publisher before any rights are transferred to ensure that all conditions of the NIH Public Access Policy can be met. Authors should avoid signing any agreements with publishers that do not allow the author to comply with the NIH Public Access Policy.

Federal employees always may submit their final peer-reviewed manuscript to PubMed Central, because government works are not subject to copyright protection in the United States.

But even here the language is garbled. Saying that an author "should avoid signing any agreements with publishers that do not allow the author to comply with the NIH Public Access Policy" is not the same as saying authors "shall not sign any agreements with publishers that do not allow the author to comply with the NIH Public Access Policy."

The former describes a suggestion; the latter describes a punishable offense.

Regardless of whether or not PL 110-161 is good public policy, far greater clarity will be needed from both the NIH and scientific publishers if the new law is to be enforced effectively.

Image Credit: wili_hybrid

Disclaimer: I am not a lawyer.

Searching the primary literature on the Internet leaves a lot to be desired. For example, nothing puts the brakes on a search faster than finding a reference to a key paper, but being unable to download it due to the access policies of the hosting journal.

Enter ChemRefer. The site works very simply: type in a keyword and get a list of papers matching it somewhere in the article. Click on one of the search results links, and you'll get the entire article as a PDF file.

What makes this remarkable is that most of ChemRefer's holdings appear to come from copyrighted, subscription-only journals. For example, searching for "taxol" produces links to the full PDFs for papers published in Tetrahedron Letters., Org. Letters, and J. Med. Chem., among others.

It's not clear whether ChemRefer is legally or illegally redistributing these articles. The results are not comprehensive, indicating some form of pre-selection. The journals in question are known for their tough copyright stance and high prices, so there may be a problem regardless of how the material was originally obtained. ChemRefer's founder, William James Griffiths was interviewed on Reactive Reports about his service.

Regardless of the legal status of its holdings, ChemRefer offers an intriguing window into another world. What wonders might result if independent Internet services could mash-up the primary literature at will?

The appearance of chemical blogspace is just one indication that the amount of new content created by scientists but appearing outside of scientific journals is set to increase in coming years. This new content will likely take the form of written work, images, movies, and digital audio. With this situation comes a new problem for authors - managing all of their new content.

By way of Web 2.0 Magazine's Top 100 Web 2.0 Sites, I found a service called Numly that may offer a solution to this problem. Numly enables individual authors to assign unique identifiers that can be used to establish copyright on a work, make licensing to a work known (for example, Creative Commons), provide a way to aggregate all of an author's copyrighted work, and create a permanent URL through which a work can always be accessed.

Numly works by associating a copyrighted work with a Numly Number, which is a unique numerical identifier not unlike a DOI or ISBN. The number can, apparently, be assigned to any work - perhaps even blog comments. Numly may also offer a solution to the problem of self-archiving Open Access articles. As an experiment, I'll be assigning a Numly number to this article.

As with any new service, it's difficult to predict how Numly will ultimately be used. All that can be said for sure is that the future of scientific communication is open. With this move will come new, unforeseen problems that services like Numly may be able to solve.

74817-070104-665306-45



This work is licensed under a Creative Commons Attribution 2.5 License.

Selecting an open-source license is a minefield for which few are prepared when they need to be. There are a plethora of licenses under which open-source software can be released. Selecting a license at the initiation of a FOSS [Free and Open Source Software] project is likely to be a low priority, as there is no initial value to the project. Without a line of source code written, wading through the legalese and nuances of distribution licenses seems unimportant. In reality, the irrevocable nature of the license makes this the most critical time if authors wish to eventually exercise control over derivative works. ... Unfortunately, even the most carefully selected and restrictive license may not afford complete protection from unanticipated and undesired uses.

-Matthew T. Stahl, Drug Discovery Today

Few subjects cause as much confusion and as many heated debates as Open Source licensing. The Open Source Initiative has approved over 50 licenses compatible with their ten-point definition of "Open Source". Whenever that many solutions to a problem exist, it's a sure sign that one size does not fit all. In this article, I'll introduce some of the key concepts in Open Source licensing.

Disclaimer

There is a phrase used so often in discussing the legal aspects of Open Source software that it has its own acronym: I Am Not A Lawyer (IANAL). Clearly IANAL, and chances are that you are not one either. Yet the very acts of writing and using Open Source software require basic familiarity with licensing terms and concepts. My aim in this article is not to provide legal advice, but rather to relate what I've found useful in trying to understand Open Source licensing for my own work. When in doubt, hire a lawyer.

One Good Book

The best writing on the subject of Open Source licensing I've read can be found in the book Open Source Licensing by Lawrence Rosen. An intellectual property attorney, Rosen also served as general counsel and secretary of the Open Source Initiative. His book is remarkably clear and easy to read. If you'd rather not pay for a hardcopy, it can be viewed in its entirety online.

The Good News

Fortunately, all Open Source licenses share some common features, if you know what to look for. For example, most licenses can be divided into one of two major categories:

• Academic Licenses These licenses, named for their original use in universities, allow unlimited freedom to distribute binaries based on altered source code without making these changes public. Examples of widely-used academic licenses include the Apache License, the BSD License, and the MIT License.

• Reciprocal Licenses These licenses require, to varying degrees, the developer of a derivative work to release his or her modifications to the public if their work is distributed. The question of what constitutes a "derivative work" varies from license to license, but most generally involves the modification of the files of a software package. Examples of widely-used reciprocal licenses include the GNU General Public License (GPL), the GNU Lesser General Public License (LGPL), the Mozilla Public License (MPL), and the Common Public License (CPL).

The Importance of Copyright

A frequently-encountered misconception equates Open Source licensing with release into the "public domain." Nothing could be further from the truth. The difference is in the ownership of copyright.

Software in the public domain has no owner. All enjoy unrestricted freedom to copy and otherwise use public domain software. A well-known example is David Megginson's SAX XML toolkit. Megginson, by placing his software in the public domain has forfeited all rights to control how his work is used. Sun Microsystems incorporated SAX into their Java Development Kit without any obligation to Megginson whatsoever. SAX is not Open Source software; it is public domain software.

In contrast, software distributed under an Open Source license remains the intellectual property of the copyright owner. The license is simply a mechanism for the software's creator to give some (or all) of their rights to a licensee, usually in exchange for conditions that must be met. Ownership remains with the creator, who is free do distribute his or her work simultaneously under commercial and Open Source licenses if they so desire.

As you can see, copyright gives a license its legal legitimacy. Far from placing software in the public domain, Open Source licenses use copyright law in the same ways as commercial licenses. This is why understanding Open Source licenses is so important for developers and users alike.

Reciprocity: Share and Share Alike?

Critics of the GPL frequently cite its "viral" nature. The debate essentially boils down to the following paragraph:

You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.

-GNU General Public License Section 2a

Like a virus that spreads through replication, the GPL spreads by forcing licensees to release their modifications under the GPL. There are at least two other terms that describe this concept. The Free Software Foundation (FSF) uses the term "copyleft." Lawrence Rosen prefers the term "reciprocity" because of its neutral tone and greater descriptive ability. It's the term I'll also use. Reciprocity is such a fundamental concept in the GPL and other licenses that Rosen's book dedicates an entire chapter to the subject.

Developers distribute their software under reciprocal licenses for a variety of reasons. Two of the most common are:

• To limit "freeloading", or the use of the software by those (typically companies) who contribute nothing back to the developer community.

• To prevent "forking", or the establishment of a competing software package based on the original package.

In reality, Open Source licenses are limited in their ability to prevent either freeloading or forking. For example, provided that a company distributes no modifications to a GPLed package, they are under no obligation to release any of their own source code. Forking happens whenever one or more developers feel strongly enough about a subject to go in a different direction; an Open Source license does nothing to change this.

Given the limitations (and complexities) of reciprocity provisions, one might ask "why bother?". This is an excellent question, the answer to which will depend on your specific goals for your software. And as Stahl points out, the time to make this choice is before a line of code has been written.

Conclusions

Although Open Source licensing may appear to be a minefield, there is nothing mysterious about it. A lot of good writing is available on the subject, with Lawrence Rosen's book being a prime example. If you plan on creating or using Open Source software, learning the basic ideas behind Open Source licensing is a wise investment.

What happens to an article in an Open Access journal that shuts down? Recently, this question was raised on the Blue Obelisk mailing list about an article published in the Internet Journal of Chemistry (IJC). Because the lights now appear to be out for good at IJC, are its articles lost forever?

The good news is that by retaining copyright, authors of Open Access articles have the right to copy or reprocess their work in any form they see fit. If a traditional subscription-based journal shuts down, the fate of its entire article collection is up to the publisher, who is in nearly all cases the sole copyright holder. It's remarkable that self-respecting scientists would knowingly allow the fruits of their hard work to meet with such a fate. With Open Access, the author is in control of keeping their article publicly visible.

The bad news is that keeping an article publicly visible is the last thing most scientists want to spend valuable time and energy on. After all, that's what the journal was there for, wasn't it? Given the technical barriers to self-archiving Open Access content, who could blame them? First, an author needs to find a server willing to host their content. After that comes learning the software to get the article onto the server. Then comes the need to decide on the archival format, being ever-mindful of the hamburger effect. Of course, authors would probably want some assurance that the location of this article won't change and will be "permanently" available. Does a DOI need to be re-assigned? And let's not forget about how the poor reader is supposed to find these articles (some would say that Google is the answer, but I would disagree). Expecting each author to solve these problems on his or her own simply won't work. There must be a better way.

To my knowledge, there is no solution to the Open Access archiving problem. But if history is any guide, this is a huge opportunity that will soon disappear. Maybe a SourceForge-like repository for Open Access content would work. Perhaps something less structured would be enough. The profit motive would certainly come into play, as the successful solution to this problem would easily have thousands, if not tens of thousands, of regular users. Whatever form the solution might take, it would most likely be a simple system built by a small organization using off-the-shelf components. I would expect nothing less from a disruptive technology like Open Access.

As one or more solutions to the Open Access archival problem begin to gain traction, other opportunities may arise and be exploited by enterprising individuals and small organizations. And so on, until a thriving ecosystem becomes established.

Proponents have been debating the "how" of Open Access for some time now. Maybe it's time to start thinking about what comes after the Open Access transition.