Open Access News

ICOLC (the International Consortium of Library Consortia) is looking for US academic libraries and library consortia interested in joining CERN's SCOAP3 project.  From yesterday's announcement:

...SCOAP3, the Sponsoring Consortium for Open Access Publishing in Particle Physics, is an effort to convert to open access a core set of journals in high energy physics (HEP).  The initiative is based at CERN but is intended to be a worldwide effort.  SCOAP3 will operate as a funding consortium, aggregating financial contributions from individual libraries, library consortia, and other organizations to convert HEP content in 7 existing journals that publish most of the HEP research to open access by funding peer review and publication in those journals....

SCOAP3's current efforts are aimed at collecting formal expressions of interest from libraries and consortia around the world, in order to determine if there is a sufficient level of potential support for the initiative to succeed. 

These expressions of interest are not binding....

To date a significant number of European countries and consortia have signed formal letters of intent to contribute if sufficient critical mass can be achieved.  At least 30% of the required level of support has been tentatively offered so far, demonstrating a high level of interest from around the world. CERN will continue to work directly with libraries and consortia outside the U.S. to solicit their support.  However, SCOAP3 cannot succeed without a comparable level of support within the U.S.

ICOLC has agreed to serve as a collection point for expressions of interest from U.S. consortia....

U.S. Consortia willing to support SCOAP3 are asked to issue a formal expression of interest at...[this web form].

The form asks you to indicate whether you are willing to join SCOAP3 and to indicate the amount of funding you are tentatively willing to allocate to the initiative (so you will need to do your homework).  The expression of interest assumes that existing subscription and/or license fees for the affected journals will be re-directed to SCOAP3, without requiring any increase in overall expenditures....

World Intellectual Property Organization member states felt their way slowly this month in the first committee meeting on how to implement 45 agreed recommendations for transformation of the United Nations organisation toward a stronger development orientation. But the slow start may have been good for development, some supporters said.

The first meeting of the new Committee on Development and Intellectual Property was held from 3-7 March. It was agreed at the conclusion that the chair would hold informal consultations before the next scheduled meeting of the committee in July.

Participating officials asked about accomplishments during the meeting were hard-pressed for specifics as much of the week’s work was on procedure. But members from various levels of development appeared unsurprised that more substantive work was not done. ...

A number of regular followers of the Development Agenda process were on hand during the meeting and some made statements.

The Library Copyright Alliance, a coalition of several library groups, and Electronic Information For Libraries (eIFL), submitted a joint statement calling for a stronger emphasis on strategies for using intellectual property “for the benefit of general education, research, preservation and access to knowledge, and the social good that results from a true balance between intellectual property protections and the public interest.”

The groups encouraged recognition of copyright as subsidiary to social and cultural development. “Whatever considerations are put forth to advance the aims of copyright industries, an equally compelling rationale can be made for the benefits of a dynamic and free exchange of knowledge and information, which ultimately gives back to national economies by transforming the minds of individuals,” they wrote. The groups proposed additions to several recommendations, such as those related to the public domain and pro-competitive IP licensing practices, where they cited the growing “Open Access to Scholarly Communications” movement worldwide. ...

Knowledge Ecology International backed a recommendation by the Friends of Development for an open forum on access to knowledge, plus discussions in other WIPO committees. KEI suggested, for example, that this week’s meeting of the WIPO Standing Committee on Copyright and Related Rights consider global norms to facilitate access to orphaned copyrighted works, cross-border services for the visually impaired or for distance learning. It also welcomed a recommendation to exchange experiences on open collaborative projects such as the Human Genome Project ...

... I’m giving a talk with the following abstract in a few weeks and am still doing research for the talk. If you have written something on the topic, let me know so I can be sure to include you. If you know of something interesting in this area that you didn’t write, please let me know anyway!

(1) Open educational resources such as MIT OpenCourseWare demonstrate that educational materials are increasingly becoming a free, ubiquitous infrastructure for teaching and learning. Leveraging free and open access to a wide range of high quality educational resources can allow the faculty member to drastically change their role in supporting learning.

(2) The increasing connectivity of teachers and learners via email, SMS, instant messenger, Twitter, and other tools allows us to move beyond “groups” in our thinking of multi-person assignments to a broader, more loosely knit notion of networks. Large-scale, collaborative social networks challenge our ideas of academic honesty but are a simple fact of life that instructors can either fight against or leverage to better support learning.

(3) Open educational resources and social networks point toward a future for higher education in which services traditionally consolidated within a single institution (e.g., providing content, providing learning support, providing assessments, providing degrees) are disaggregated and provided by a number of institutions that compete on quality of service and price for learner business. ...

DSpace version 1.5, Release Candidate 1, is now available for downloading.

Update.  The final release of version 1.5 is now available.  See the March 25 announcement for a list of its new features.

Yan Han and Atifa Rawan, Afghanistan Digital Library Initiative: Revitalizing an Integrated Library System, Information Technology and Libraries, 26, 4 (2007) pp. 44-46.  Self-archived March 21, 2008. 

Abstract:   This paper describes an Afghanistan digital library initiative of building an Integrated Library System (ILS) for Afghanistan universities and colleges based on open source software. As one of the goals of the Afghan eQuality Digital Libraries Alliance, the authors applied systems analysis approach, evaluated different open source ILS, and customized the selected software to accommodate users' needs. Improvements include Arabic/Persian language support, user interface changes, call number label printing and new ISBN-13 support. To our knowledge, the ILS is the first big academic libraries in the the world running on open source software.

From the body of the paper:

...Based on the availability of existing funding, experiences with commercial vendors, and consideration of vendor supports and future directions, the authors decided to build the Digital Library infrastructure with the "open" concept (open access, open source, and open standards). The decision is widely influenced by globalization, open access, open source, open standards, and increasing users expectations....

PS:  For background, see my January 2008 post on the ADL and my other past posts on OA in Afghanistan.

It can be used to harvest metadata from OAI-PMH compliant repositories. It can also be used to create new OAI-ORE Resource Maps from scratch, to parse existing ones and to serialize them to xml.

Background: Sharing data is a tenet of science, yet commonplace in only a few subdisciplines. Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers. The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing.

Methods: We investigated these relationships with respect to gene expression microarray data in the journals that most often publish studies about this type of data. We measured data sharing prevalence as the proportion of papers with submission links from NCBI’s Gene Expression Omnibus (GEO) database. We conducted univariate and linear multivariate regressions to understand the relationship between the strength of data sharing policy and journal impact factor, journal subdiscipline, journal publisher (academic societies vs. commercial), and publishing model (open vs. closed access).

Results: Of the 70 journal policies, 18 (26%) made no mention of sharing publication-related data within their Instruction to Author statements. Of the <42 (60%) policies with a data sharing policy applicable to microarrays we classified 18 (26% of 70) as moderately strong and 24 (34% of 70) as strong.

Existence of a data sharing policy was associated with the type of journal publisher: half of all commercial publishers had a policy compared to 82% of journals published by academic society. All four of the open-access journals had a data sharing policy. Policy strength was associated with impact factor: the journals with no data sharing policy, a weak policy, and a strong policy had respective median impact factors of 3.6, 4.5, and 6.0. Policy strength was positively associated with measured data sharing submission into the GEO database: the journals with no data sharing policy, a weak policy, and a strong policy had median data sharing prevalence of 11%, 19%, and 29% respectively.

Conclusion: This review and analysis begins to quantify the relationship between journal policies and data sharing outcomes and thereby contributes to assessing the incentives and initiatives designed to facilitate widespread, responsible, effective data sharing.

After more than a decade in print, the François-Xavier Bagnoud Center's Health and Human Rights journal will begin its next chapter as an on-line, open-access publication starting with Volume 10, Issue Number 1, in the Spring of 2008. [Partners in Health] co-founder Paul Farmer assumed editorship of the journal in 2007.

... The journal will endeavor to increase access to human rights knowledge in the health field by linking an expanded community of readers and contributors. Following the lead of a growing number of open-access publications, the full text of Health and Human Rights will be freely available to anyone with internet access. This priority will be addressed directly in the first on-line issue in an article entitled "Excluding the poor from accessing biomedical literature: a rights violation that impedes global health," by Gavin Yamey. Yamey is a Senior Editor at PLoS Medicine and an incoming member of the Health and Human Rights Editorial Board. ...

The Health and Human Rights website will include content in addition to the articles published in the journal’s semi-annual print edition. A regularly-updated “perspectives” section will provide space for contributors to share information and express their views on a broad range of topics, including but not limited to the themes of the journal’s print issues. Additionally, a blog feature on the site will allow authors to provide additional insight and background into their articles and readers to post their comments. ...

Andrea Gawrylewski, Publishers ask NIH to delay open access, The Scientist, March 21, 2008.  Excerpt:

At the National Institutes of Health open meeting on the new public access mandate yesterday (March 20), publishers continued to criticize the plan and called for the agency to delay implementing it....

NIH director Elias Zerhouni said the agency was "all ears" to recommendations of how to best move forward with implementing the policy....

Jack Ochs, from the American Chemical Society, gave the first five-minute comment. He started out by saying that a brief meeting was no substitute for the formal comments on rulemaking process like the one the NIH held when they were implementing the voluntary submission program in 2005. He was the first of several to call a halt to implementing the mandate so the details could be worked out.

Several publishers said that the NIH's plan for PubMed Central to be a massive, searchable database for research papers duplicates what publishers have been investing in for years....Martin Frank from the American Physiological Society said that the NIH is using taxpayer dollars to become another publisher. "Scientific literature is available only due to the money already spent by publishers," he said....

Even some of the public access supporters who gave a comment had concerns regarding the new policy. They wanted to know how the NIH will ensure compliance to the mandate, who will have access to the manuscripts submitted to PubMed Central, and how authors are to know publication dates of their papers so far ahead of time.

At the end of the meeting [NIH Director of extramural research, Norka Ruiz Bravo] reiterated that the NIH will be taking all comments into consideration and that the NIH has issued a request for information open from March 31 to May 31, where the public can submit further comment. The agency will be issuing its report on these comments no later than September 30....

Comments

• "Several publishers said that the NIH's plan for PubMed Central to be a massive, searchable database for research papers duplicates what publishers have been investing in for years."  One huge difference:  NIH will make the contents freely available to everyone within 12 months of publication.  If free online access were routinely provided by publishers, the NIH policy would probably never have been adopted. 
• "Martin Frank from the American Physiological Society said that the NIH is using taxpayer dollars to become another publisher."  One huge difference:  The NIH will not perform peer review or tell journals how to conduct peer review.  It's not replacing publishers but improving access to peer-reviewed literature --because publishers haven't done so themselves.
• Martin Frank said, "Scientific literature is available only due to the money already spent by publishers."  True, but then there's the money already spent by taxpayers on the underlying research (not to mention the taxpayer money already spent by public universities on researcher salaries and journal subscriptions).  The public funds spent on an NIH research project can be hundreds of times greater than the cost of publishing the resulting papers in peer-reviewed journals.  Publishers who want to repeal the OA mandate have a one-sided view of added value and no view at all of the public interest.  Publishers who want a compromise fail to recognize that the current policy is already a compromise.  It only applies to the final version of the author's peer-reviewed manuscripts, not to the published version, and it permits an embargo period of up to 12 months. 

Update (3/25/08).  Also see the article in Library Journal Academic Newswire.

Michael Cross, In sight of victory, The Guardian, March 20, 2008.  Excerpt:

Two years ago, we launched our Free Our Data campaign on an act of faith. We knew that making the government's information available freely - and for free - for re-use by individuals, charities, academics and entrepreneurs was the right thing to do. What we did not know was precisely how much richer Britain could be as a result.

Last week, an authoritative independent economic study, commissioned by the government and published along with the Budget, answered that question. Looking at the arms of government most dependent on selling data and taking conservative and pessimistic scenarios throughout, the study - Models of Public Sector Information via Trading Funds - concludes that the benefits of giving government data away outweigh the loss of income from licence fees from the current practice of "cost recovery" by more than £160m for the largest six "trading funds" alone....

TGE Adonis is launching a study to evaluate French publishing in the social sciences and humanities.  (Thanks to the INIST Libre Accès blog.)

The goal is to identify indicators to measure the impact of OA policies, especially for publicly-funded research.  Read yesterday's announcement in French or in Google's English.

If you recall, Austria's Förderung der wissenschaftlichen Forschung (Fund to Promote Scientific Research, or FWF) strengthened its OA policy earlier this month.  FWF has now released the policy in English.  Excerpt:

a) The FWF expects the results of the research it supports to be made public and when possible published also in digital form and made available free of charge on the Internet (open access). Contributions should be submitted to subject-specific or institutional electronic archives (repositories) in addition to being sent to scientific publishers or they should be published directly in peer reviewed journals that are freely available (e.g. in open access journals or in hybrid journals).

b) In their contracts with publishing houses, scientists participating in projects supported by the FWF should as far as possible attempt to secure lasting and non-exclusive rights for the electronic publication of their research results for the purpose of non profit-oriented utilization....If there is a restricted period during which the submission of published research results to subject-specific or institutional electronic archives is not permitted, this should generally not last for longer than 6 months for journal articles and for 12 months in the case of books.

c) Applications for reimbursement of costs associated with the submission of scientific articles to refereed open access journals or with making articles in conventional journals freely available (hybrid journals) within three years of the end of the project may be sent to the FWF....

d) Open access activities must be indicated in all reports submitted to the FWF. If there are legal reasons why the FWF's policy on open access may not be followed, these must be justified....

The Canadian House of Commons Standing Committee on Industry, Science and Technology has announced hearings Canadian on science and technology policy.  (Thanks to Heather Morrison.)  The committee will take oral testimony from key stakeholder groups and accept written testimony from anyone else.  Written briefs should be sent to INDU@parl.gc.ca by April 18, 2008. 

According to Michael Geist:

The hearings represent an exceptionally important opportunity to advance issues such as open access, crown copyright, access to public data, and the need for greater flexibility in intellectual property rules....

New Zealand's Otago Polytechnic has a progressive IP policy with implications for OA.  (Thanks to Sarah Stewart.)

With a couple of exceptions, it authorizes "free and open access" under a CC-BY license to all the intellectual property the institution "owns or co-owns". 

Two more excerpts:

Unless specifically contracted to do so, nothing in this policy is to be interpreted as the Polytechnic claiming any form of ownership over research outputs....

[However,] the Polytechnic encourages staff and students to support free and open access to IP and also to apply the Creative Commons Attribution framework to work created.

Intellectual property rights are affecting human rights in several areas such as public health, access to knowledge and agriculture, and human rights advocates have a decisive role to play to reverse the trend, according to members of a recent panel discussion on the negative impacts of intellectual property systems.

The event organised on 13 March by the International Environmental Law Research Centre (IELRC) and 3D -> Trade - Human Rights - Equitable Economy in cooperation with the United Nations Office of the High Commissioner for Human Rights, brought together speakers whose primary aim was to provide entry points and opportunities for human rights advocates to challenge the current trend in intellectual property policy-making. ...

For Eddan Katz of the Electronic Frontier Foundation, the intellectual property system has failed to preserve access to education, the right to free expression and the right to cultural participation. ...

The need for effective advocacy also was put forward by Katz, who is in favour of open access and encouraged the lobbying of education ministers and the raising of awareness about the tensions between intellectual property rights and human rights.

An event at the World Intellectual Property Organisation (WIPO) last week brought some key actors in copyright and related rights to discuss the value of limitations and exceptions and to present a recently released study describing an international instrument on limitations and exceptions. ...

The 11 March side event to the weeklong [Standing Committee on Copyright and Related Rights] meeting was organised by the Electronic Information for Libraries, the International Federation of Library Associations and Institutions, Knowledge Ecology International, and the Library Copyright Alliance. ...

The Purdue University Senate endorsed the CIC author addendum.  (Thanks to Charles Bailey.)  From Tuesday's announcement:

...Last year, the leadership of the Senate attended a CIC Conference on Faculty Governance at which the CIC Statement on Publishing Agreements was discussed. As of June, 2007, faculty governance from six of the CIC campuses formally endorsed this statement and Addendum to Publication Agreements for CIC Authors. This fall, we asked the Faculty Affairs Committee to consider endorsing this agreement for use at Purdue University....[T]he Faculty Affairs Committee has recommended that the Senate endorse this agreement....

By passing Senate Document 07-9, Purdue joined other CIC institutions such as the University of Illinois (both the UI-C and UIUC campuses), Indiana University, the University of Minnesota, Northwestern University, and the University of Wisconsin-Madison as endorsing faculty rights to retain use of their intellectual property. The Addendum to Publication Agreements for CIC Authors is now available for use by Purdue faculty, if they chose to do so.

Comment.  The Committee on Institutional Cooperation (CIC) is a consortium of 12 research universities:  University of Chicago, University of Illinois, Indiana University, University of Iowa, University of Michigan, Michigan State University, University of Minnesota, Northwestern University, Ohio State University, Pennsylvania State University, Purdue University and the University of Wisconsin-Madison.  As a consortium, CIC has organized provost support for FRPAA (July 2006), joined the Google Library project (June 2007), and written an author addendum (May 2007).  While more than half the CIC institutions now endorse the addendum, none requires its use, not even with an opt-out e.g. as Harvard now does.

eIFL-OA Program seeks to enhance access to, and greater use of research findings, increase the efficiency of research and developments, accelerate use and innovation, stimulate economy. To achieve this, we apply the developing practices of Open Access as defined by the Budapest Open Access Initiative.

eIFL-OA Program:

1. builds networks of Open Access repositories, Open Access journals, Open Access education materials;
2. provides training and advice on Open Access policies and practices;
3. empowers library professionals, scientists and scholars, educators and students to become open access advocates.

We invite libraries, Universities or any other research and development organisation from eIFL.net countries that are interested in Open Access projects, plan activities listed above, and ready to organise local and national events to make themselves known to the eIFL-OA Program Manager, Iryna Kuchma, iryna.kuchma[at]eifl.net.

• Priscilla Markwood, The NIH mandate - we're not in Kansas any more, editorial
• Tarja Koskinen-Olsson, Access to knowledge in the digital era
• Irene Perciali and Aaron Edlin, Journals at bepress: new twists on an old model
• Weihong Cheng and Shengli Ren, Evolution of open access publishing in Chinese scientific journals
• Greg Tananbaum, Adventures in open data

The INIST Libre Accès blog has posted some notes on the round-table discussion of OA publishing at Le Salon du Livre (Paris, March 14-19, 2008).  Read the notes in the original French or Google's English.  Also listen to the French podcast of the discussion.

Cliff Morgan, The Latest OA Landscape, Wiley-Blackwell Journal News, March 2008.  (Thanks to Robin Peek.)  A short summary of recent developments, including the NIH mandate, the ERC mandate, the Harvard mandate, the Berkeley OA journal fund, and the EU Council Conclusions.  Here's the only part that may be new to OAN readers:

...In general, the European Commission favours an evidence-based approach to policy in this area, and with that in mind it will fund a project known as PEER (Publishing and Ecology of European Research) in which a number of STM publishers (including Wiley-Blackwell) will participate together with the European research community (funders and institutions). The project (which will run for at least 3 years as part of the EC’s eContent Plus program) will develop an Observatory to monitor the impact of large-scale archiving in repositories of journal articles that have been accepted for publication on journal viability, researcher access and productivity, and systemic costs.

Comments 

• Morgan makes it appear that the EC isn't in a position to adopt an evidence-based OA policy without running a new, three-year study.  This is untrue.  The EC commissioned a study in 2006 which drew upon many previous studies, and it has the January 2007 report from the European Research Advisory Board (EURAB).  EURAB was established specifically to offer independent advice on EU research policy.  Apart from these, it has heard from more than 1,300 European research institutions and more than 25,000 individual researchers in support of an OA mandate.  The EC's own Research Directorate-General supported OA in its February 2007 Communication (p. 7):  "Initiatives leading to wider access to and dissemination of scientific information are necessary, especially with regard to journal articles and research data produced on the basis of public funding." 
• The EC has enough evidence, today, to adopt the OA recommendations of its own commissioned study, its own research advisory board, its own research directorate, and the 1,300+ research institutions throughout the continent.  Similarly, cautious governments or public funding agencies in 10 countries (including the EU, through the European Research Council) have adopted OA mandates on existing evidence.
• The new PEER study will turn up relevant evidence, but the EC should use that evidence to fine-tune its policy.  It should not use the study to delay the policy itself as if there were insufficient evidence today.  If the PEER question is whether high-volume OA archiving will cause journal cancellations, then the EC can also benefit from the publishers' own study that high-journal prices are a significant cause of cancellations and that "availability via delayed OA...[is] relatively unimportant."
• I made a related point in an article last September:

Note to the EU, US, and other jurisdictions considering an OA mandate:  there are at least nine [now 10] national-level, multi-disciplinary OA mandates and even more softer OA policies that encourage OA without requiring it.  These constitute a large, ongoing natural experiment.  By all means look at the evidence, but don't fall for the argument that we must delay the adoption of new OA policies in order to launch another, later, smaller study of the effect of OA archiving on journal subscriptions.

There are important roles for vendors of aggregated databases, such as EBSCO and ProQuest, in transitioning to open access, and in a fully open access environment.

One role is increasing access to the journal's contents through indexing.

Another, related role is supporting the Directory of Open Access Journals (DOAJ). EBSCO is listed on the DOAJ's Sponsors page; CSA ProQuest and Swets are DOAJ members.

Another role for aggregators is to contribute to the economics of open access publishing; if a journal is open access, there is no reason why it cannot also be included in an aggregated database, for a reasonable fee to help support the journal.

This is a win-win-win situation. For the aggregator, this is added content at extremely reasonable fees; for the publisher, economic support and additional impact; for the library subscribers, more content accessible through one familiar, well-developed tool with lots of support such as online help guides and training.

Kevin Haggerty from the Canadian Journal of Sociology recently mentioned that EBSCO is continuing to provide support for the journal after its transition to open access, including continuing to provide electronic access to back issues, and economic support for including current content. Kudos to EBSCO for a sensible move here! ...

...A pioneer in using computer technology to advance scholarship in the humanities, Ross is perhaps best known as the founding editor of the Stoa Consortium for Electronic Publication in the Humanities. The Stoa, established in 1997, set the standard for Open Access publication of digital humanities work in the classics, serving as an umbrella project for many diverse projects that provide functionality, and have requirements, not supported by traditional (print) publishers. In addition to providing Open Access publication for the work of other scholars, Ross strived to make his own work (and the raw materials behind that work) available freely to others. He was the co-creator of Diotima: Materials for the Study of Women and Gender in the Ancient World and of the Neo-Latin Colloquia collection, both of which are published on The Stoa.

According to his principled belief in Open Access, Ross was always a stern critic of models of scholarship that were needlessly exclusionary in their presentation or implementation. He firmly believed in the potential afforded by technology to bring the highest levels of scholarship to the widest possible audience, and in the obligation of learned societies to make their work freely available to all interested readers. ...

1. Welcome & Opening Address - Tom Leonard (University Librarian, University of California, Berkeley); George Breslauer (Executive Vice Chancellor and Provost, University of California, Berkeley)
2. What is Open Access, Anyhow? - Rick Luce (Emory University)
3. The SCOAP3 Model - Salvatore Mele (CERN)
4. Fund-raising in Europe - Jens Vigen (CERN)
5. Expectations of a Large Research Institution - Ralf Schimmer (Max Planck Digital Library)
6. US Consortia in SCOAP3 - Ivy Anderson (California Digital Library)
7. Individual US Libraries and SCOAP3 - Part 1 - Miriam Blake (Los Alamos National Laboratory)
8. Individual US Libraries and SCOAP3 - Part 2 - Kimberly Douglas (Caltech)
9. OA Synergies: Repositories for High Energy Physics - Travis Brooks (Stanford Linear Accelerator Center)

Noel M. O'Boyle, Chris Morley, and Geoffrey R. Hutchison, Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit, Chemistry Central Journal, March 9, 2008.  Abstract:

Background.  Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit.

Results.  Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel.

Conclusion.  Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

PS:  Also see OBRuby, the Ruby interface to Open Babel.

Johns Hopkins University has expressed interest in joining CERN's SCOAP3 project.  From the SCOAP3 announcement:

...In 10 days, 16 U.S. institutes have signed an Expression of Interest in joining SCOAP3, pledging a total of more than 10% of the U.S. contribution to SCOAP3....

"With increasingly rapid changes in the forms of scholarly communication and access, it is critical for libraries at research intensive institutions like Johns Hopkins to be open to all sorts of publishing models that benefit authors and advance scientific knowledge," said Winston Tabb, Sheridan Dean of University Libraries at Johns Hopkins.

Stevan Harnad, Publisher Proxy Deposit Is A Potential Trojan Horse, Open Access Archivangelism, March 18, 2008.  Excerpt:

I suggest not colluding with publishers offering to "Let us do the [mandated] deposit for you".

The reason is simple, if we take the moment to think it through: ...

[PS:  Stevan argues that mandating deposit in institutional repositories is a better policy than mandating deposit in central or disciplinary repositories like PubMed Central.]

(11) It would hence systematically undermine the scaling and convergence of OA self-archiving mandates onto university IRs to transfer responsibility for compliance to an external party -- the publisher as their employees' proxy self-archiver -- depositing in arbitrary and divergent external repositories.

(12) Universities and funders should universally mandate self-archiving directly in each author's own university's IR; they should say "no, thank you" to offers of proxy self-archiving on behalf of their employees from publishers. External collections can then be harvested, as desired, from the IRs that will then cover 100% of OA output....

Comment.  It's one thing to argue that the NIH policy should mandate deposit in the author's institutional repository (when they have one).  But as long as the NIH is mandating deposit in PMC, and as long as a journal meets the NIH's criteria for depositing articles on behalf of authors, then I don't see any reason why authors shouldn't take advantage of the option.  I did object to journal deposit under the older, voluntary policy, because it gave publishers the decision on the length of the embargo.  Under the new policy, however, the length of the embargo is already set by the time the author signs the copyright transfer agreement.  Hence, journal deposit cannot change the terms of the deal.  Or if there's some subtle way in which it can, then I'll join Stevan's call on authors to make the deposits themselves.  I already agree with him that, if the policy were to mandate deposit in the author's IR, then author deposits would make much more sense than journal deposits.

Update (3/20/08).  Stevan just updated his post to make clear that he was talking about publishers who want to charge fees for depositing papers in PMC.  My response above was limited to publishers who do not charge fees, and I share Stevan's objections to those who would charge fees.  For example, see my April 2007 article, Paying for green open access.

Update (3/22/08).  Also see Stevan's three follow-up posts:  Publisher Proxy Deposit Is A Potential Trojan Horse: II, Publisher Proxy Deposit Is A Potential Trojan Horse: III, and One Small Step for NIH, One Giant Leap for Mankind.  The last is a response to my blog comments above.

A three-day workshop on 'Open Access Repositories and Greenstone Software' was inaugurated in the Library Science department of Kashmir University Monday. The inaugural function was presided over by the vice-chancellor KU, Prof Riyaz Punjabi. Prof Shabahat Hussain, a guest from Aligarh Muslim University who specially visited the valley to attend the seminar was chief guest on the occasion. ... He advised the management of the department to look for possibilities to help affiliated colleges of the University to benefit from the new concept. The VC showed an urge for the formation of a committee, which would carry forward this work. ... In his address Prof Shabahat said that repositories were being established world over as free access to knowledge. "Open access repositories are being developed in the world and it is high time that the concept be seriously taken up," he said. ...

... I’m a little worried that students in the humanities might feel a bit left out from the OA debate, which has been largely dominated up till now by the sciences. I want to emphasize how OA has enormous implications for us, too, in that it currently represents the simplest and most obvious solution to the crisis in monograph publishing that is causing an insidious contraction in our fields, and is hitting younger academics particularly hard.

The real question is why humanities academics are not taking to the opportunities represented by OA in the same way as academics in the sciences. From speaking with colleagues, my sense is that free online publishing continues to have some way to go before it is fully accepted by our peers as a credible, let alone a desirable and prestigious, medium for one’s work. There’s still a lot of FUD among us: fear, uncertainty and doubt about the changes represented by new technologies, including whether online publications will count towards job offers or tenure, or even if OA journals will still be around and available on the web after a few years. ...

Open Students is a clear demonstration that students already “get” the way OA enables us to do more rigorous research when we have access to all the relevant materials, not just those which our library and interlibrary loan budgets can afford to purchase. What’s been interesting to discover is that some of the strongest OA advocates in the humanities are leading senior figures like J. Hillis Miller, Jonathan Culler and Stephen Greenblatt (all of whom are generously sharing their expertise on OHP’s advisory board). It suggests that what we really need now is to make overtures towards mid-career academics, many of whom have yet to fully understand what Open Access means. As OA journal editors, we are working to raise awareness and trust in OA publishing among these scholars but we would also love to hear ideas from students about how we can work together. As with many of the cultural shifts in recent history, it is students who are on the front-lines of this transformative change too. ...

... But do embargoes serve the public's interest? Various audience members highlighted the problem of "churnalism" whereby increasing numbers of news stories consist of little more than recycled copy from press releases and the news wires (see also David Bauder’s Associated Press story on this subject yesterday); these stories are then read by thousands or even millions of people. This means that a lot of power lies in the hands of the press officer to shape news coverage. The panel agreed that, on balance, embargoes are in the best interests of the public because, as [The Independent's Steve] Connor pointed out, they give journalists the time to prepare a more measured, thoughtful and analytical article on a complex topic. They also allow press officers to ensure that the busy authors of the papers are available for interview during a certain block of time prior to publication. ...

Of course, when it comes to public interest and the dissemination of scientific research, the ability to immediately read – without charge – the original study behind the news coverage is of great importance. It's easy to tempt lazy journalists, in need of a story, right now, to simply tweak a press release slightly to turn it into a news article. The availability of the research article, free and online, puts the power back in the hands of the readers so that they can see for themselves what the research actually involved and what conclusions can and can't be drawn from it. Papers published in PLoS's open-access journals are embargoed until 5 p.m. Pacific Time on the day before the paper is published – the approximate time the article is available online – for this reason. ...

The U.S. National Institutes of Health is holding a public meeting on the implementation of its recently-adopted OA mandate, on March 20 at the NIH offices outside Washington, D.C. The agency had solicited online comments in advance of the meeting for those unable to attend; that comment period closed yesterday. The comments received are now available online.

It doesn't appear to be possible to link to individual comments, but the page includes comments by SPARC, the Alliance for Taxpayer Access, ARL, Medical Library Association, Association of Academic Health Sciences Libraries, ACRL, Genetic Alliance, Wiley, AAP, STM, PLoS, and a number of other libraries, universities, societies, publishers, advocacy organizations, businesses, and individuals: 433 in total.

See also this earlier OAN post about the meeting and comment period.

Update. The Alliance for Taxpayer Access has posted its comment on its own Web site.

Update. Also see the short article on publisher responses in Library Journal Academic Newswire. The AAP/PSP still wants a formal hearing, still complains about "copyright concerns", and still hints at the possibility of a lawsuit.

Update. NIH has also posted 18 comments received via email.

Update.  The Professional/Scholarly Publishing (PSP) Division of the Association of American Publishers (AAP) has released a March 17 letter to NIH Director Elias Zerhouni, elaborating its objections to the NIH policy, and a March 20 call for more publisher consultation on the policy.

Update.  The NIH has released a 2 hour, 41 minute video of the meeting, and three slide presentations:

• Overview and Context (PDF, 1.1 MB)
• Policy Issues and Public Input (PDF, 65 KB)
• Preliminary Analysis of March 20 Comments (PDF, 52 KB)

... a metric boatload of early federal case law (1880-1923), known as the First Series of the Federal Reporter. The Second and Third series were released earlier this year, as well as the "Federal Cases" which are the precursor the Federal Reporter. We're about 89% of the way towards a complete release of the Courts of Appeals archive.

... to undertake a project to identify successful models for embedding repositories in research management systems and processes within higher education institutions.

A total of £50,000 is available for this project ... The work will be for six months beginning in April 2008.

The deadline for submission of proposals is no later than 12:00 noon on Friday 11th April 2008. ...