Biology Library News

Selected open access and public access news

Now available: written and public comments from the two meetings on Public Access to Federally-Supported Research and Development Data and Publications. You may wish to browse written comments for statements from your scholarly societies or favorite publishers, etc.

NIH Public Access Policy overviews are scheduled twice this summer on the medical campus, Farrell Learning and Teaching Center, Room 214
Wednesday 12 June 2013, Noon-1:00 pm OR
Wednesday 17 July 2013, Noon-1:00 pm
Intended Audience: NIH-funded investigators/scholars, grant managers or administrative assistants.
TO REGISTER: There is no fee for this presentation. Please register via online form or email Cathy Sarli (sarlic@wustl.edu) to reserve a seat. While Cathy Sarli is the campus expert, Ruth is happy to help with questions or present overviews for groups or individuals on request.

Funding mandate for open access books and book chapters? While I do not think Wellcome Trust funds any WU researchers, this is interesting news which may forecast a trend that NIH and other funders could follow: Wellcome Trust extends open access policy to include scholarly monographs and book chapters "...a significant amount of scholarly work is published in monographs and book chapters and we want to ensure that these, too, reach as wide an audience as possible. ... The new policy does not apply to textbooks, 'trade' books, general reference works or works of fiction, or to collections edited but not authored by Trust grantholders. It would not affect, for example, a non-fiction work written by a medical historian aimed at a general audience and published by a commercial publisher." | Comments from Peter Suber. (Peter Suber is the new director of the Office for Scholarly Communication at Harvard University and author of the book Open Access, which will become entirely open access in June 2013.)

Interesting reading:
    -- Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. (2013) The Case for Open Preprints in Biology. PLoS Biol 11(5): e1001563. doi:10.1371/journal.pbio.1001563
    -- Why is science behind a paywall - blog post summarizing issues with many comments.
    -- Nature Web Focus: Do Open Access journals have impact? - reports on a small study from Thomson ISI - Web of Science
    -- Another study which adds discussions about article quality to the analysis, that is that high quality articles benefit more from being open access than lower quality articles: McCabe, Mark J. and Snyder, Christopher M., The Rich Get Richer and the Poor Get Poorer: The Effect of Open Access on Cites to Science Journals Across the Quality Spectrum (May 23, 2013). Available at SSRN: http://ssrn.com/abstract=2269040 or http://dx.doi.org/10.2139/ssrn.2269040

Assessment of research and criticism of Journal Impact Factor in the news

On May 17, 2013, the San Francisco Declaration on Research Assessment (DORA) launched, with support from journals, publishers, individuals and scientific organisations. On the DORA site there are links to several editorials in Science, Journal of Cell Biology, eLife and others, as well as a growing number of blog posts. Please do look at the full declaration, but here is a piece:
"General Recommendation: Do not use journal-based metrics, such as Journal Impact Factors, as a surrogate measure of the quality of individual research articles, to assess an individual scientist's contributions, or in hiring, promotion, or funding decisions."

This is a much-needed initiative. Thomson Reuters Journal Impact Factors (available to WU users in the Journal Citation Reports/JCRweb database) have long been criticized, particularly when they are mis-used as measures of article and researcher quality by tenure-review committees, funding agencies, etc. But the Impact Factor has been around a long time and is relatively easy to obtain and understand. There are many other research assessment possibilities but none as easy to implement institutionally. I look forward to progress in this area. This Research Impact and Evaluation guide includes links to many related resources.

I don't see this blog post on the DORA site so I'll share it also: Impact Factors: A Broken System; there will probably be a lot written in the coming weeks about this.

Although not specifically related to DORA, the June 2013 issue of Elsevier's newsletter Research Trends is devoted to Research Assessment. I found these two articles interesting: The use of assessment reports to generate and measure societal impact of research and The Challenges of Measuring Social Impact Using Altmetrics.

Open access and public access news, April 2013

• Two planning meetings in May about Public Access to Federally-Supported Research and Development Data and Publications :
  Publications: May 14 (9-5 edt)-15(9-noon edt), 2013
  Data : May 16 (9-5 edt)-17 (9-noon edt) , 2013
  I don't really expect any of us to spent 3 days monitoring this discussion but these meetings will be webcast and archived if you want to sample the events. The webcast will be accessible from this site on the day of the meeting and thereafter. Also 2-page written statements are accepted through the registration sites. The deadline for registration and/or submitting written comments in May 7th.
• PeerJ in the news:
  • Interview With PeerJ Editor Keith Crandall - many biofolk will remember that Keith was a graduate student here.
  • PeerJ Supports Undergraduate Authors Pilot through 2013: "authors who were undergraduates when the research was conducted will be able to publish in PeerJ for free (with the caveats that the submission should also have senior author(s) who have a normal Membership status and assuming the submission passes peer review as normal)"
  • PeerJ accepted for indexing by PubMed Central, PubMed and Scopus
  • PeerJ Preprints is now distributing preprints, Literature Review Articles, Commentaries, Opinion Pieces, Case Studies, and Case Reports in the biological, medical and health sciences
• Scientific articles accepted (personal checks, too) New York Times article , April 7, 2013, by Gina Kolata, has been getting a lot of discussion on the NYT site and various blogs. Don't miss Michael Eisen's post: Door-to-door subscription scams: the dark side of The New York Times
• The problem of fraud in publishing is not new and not limited to open access, but the internet and open access publishing make way for a whole new wave of scams, sham journals and conferences, etc. We have a new library guide on the subject: Author Beware.
• Links from UK: Open access: four ways it could enhance academic freedom (April 22) | Nature's publishers to launch open-access platform for data sets (April 7).
• Preprints in biology? : Who Killed the PrePrint, and Could It Make a Return?By Jason Hoyt and Peter Binfield, Scientific American blog,April 3, 2013 | The case for open preprints in biology, available for download on Figshare | Haldane’s Sieve, an entire blog for discussing preprints in population and evolutionary genetics.
• Interview with Mark Patterson, Executive Director of eLife

Publishing, open access, public access - links from March, 2013

-- Nature special issue, v.495 (no. 7442) March 28, 2013 "This special issue of Nature looks at the transformation taking place in scientific publishing. A News Feature weighs claims that online, author-pays publishing can drastically cut costs, and several authors discuss how they make open-access publishing work for them. The special also looks at broader aspects of publishing, including the idea that the concepts of journal and article are being superseded by real-time filtering algorithms and what the future holds for libraries or their virtual successors."

-- The PeerJ Blog has had a series of interviews with authors: Jeremy Bruenn, Jennifer Wagner, James Meadow. I think it is interesting to see why scholars choose to publish in this new venture.

-- Alternatively, this is also interesting, from an ecologist: Why I published in PLoS ONE. And why I probably won’t again for awhile, by Andrew Tredennick

-- For NIH-funded authors, there are two new help documents from Becker Medical Library: Compliance Management Using the My Bibliography Tool in My NCBI and The Big Picture: NCBI, My Bibliography, PMC, PubMed, NIHMS, eRA Commons, NIH RePORTER, RPPR and the NIH Public Access Policy, a chart that shows this increasingly linked network, where one system updates information in other systems. I welcome your questions and concerns; I recommend this page as a nice overview and place to begin if this is new to you: http://scholarlycommunications.wustl.edu/issues/nih/index.html.

Data Management Education

What are you teaching students (especially graduate students) about data management and organization practices? These two blog posts describe a survey of instructors of ecology courses. "The gist is this: ecology undergraduates aren’t learning about data management. Although the professors find data management topics to be important for their own work, they are not inclined to find time in their curriculum to teach their students these topics." Data management education? and Data management education pt. 2.

Open Access/Public Access News

February 2013 has been a big month for this!

• Feb. 13: Fair Access to Science and Technology Research Act (FASTR) Introduced in U.S. House and Senate: FASTR is the "successor to the Federal Research Public Access Act (FRPAA). FRPAA had been introduced in three earlier sessions of Congress (May 2006, April 2009, and February 2012) but had not come up for a vote. In the 113th Congress, Congressional supporters of OA decided to introduced a modified bill. The result is FASTR, a new and strengthened version of FRPAA. Both bills would require open access (OA) to peer-reviewed manuscripts of articles reporting the results of federally-funded research." [from Notes on the Fair Access to Science and Technology Research Act] Here are a few links for more information:
  Notes on the Fair Access to Science and Technology Research Act Berkman Center, Harvard Open Access Project
  SPARC FAQ for the Fair Access to Science and Technology Research Act (FASTR)
  Fourth time lucky for US open-access bill? Nature News
• Feb. 22: White House Office of Science and Technology Policy (OSTP) Policy Memorandum on Expanding Public Access to the Results of Federally Funded Research directs Federal agencies with more than $100 million in research and development spending to develop plans to make the published results of federally funded research freely available to the public within one year of publication, and requiring researchers to better account for and manage the digital data resulting from federally funded scientific research. Here is a small sampling of this growing discussion:
  White House Delivers New Open-Access Policy That Has Activists Cheering [Chronicle of Higher Education]
  AAP [Association of American Publishers] Supports OSTP Policy Urging Collaboration in Public Access
  NSF responds: National Science Foundation Collaborates with Federal Partners to Plan for Comprehensive Public Access to Research Results | NSF Anticipates Pushing Boundaries on Open-Access Plan [Chronicle of Higher Education]
  No celebrations here: Why the White House public-access policy sucks Michael Eisen's responds because it's not enough; he sees a "huge missed opportunity that will ultimately be viewed as a major setback for open access"
  US science to be open to all Nature News
  and much more: Public Access in the Media [Alliance for Taxpayer Access]
• Ecological Society of America struggles with how to have open access and maintain needed income: Scott L Collins. 2013. Opening access to ESA journals. Frontiers in Ecology and the Environment 11: 3–3. http://dx.doi.org/10.1890/1540-9295-11.1.3
• A new tool to help with NIH Public Access Policy compliance: How to Confirm Journal Policies for NIH-Funded Authors Based on Submission Methods
• PeerJ, which has an unusual author-pays model for open access, has published its first articles. Unrelated to OA really, but I found this PeerJ blog post interesting, The thinking behind the design of PeerJ’s PDFs. There does seem to be growing discontent with the PDF format and I've been noting several examples of experiments with alternatives.

News about Open Access issues this month

Paying to Publish: For 2013, WU Libraries is no longer paying Hindawi open access Author Processing Charges for WU authors; also we are no longer institutional PLOS members, which gave WU authors a discount on publication fees in 2012. A few discounts to OA publishing fees remain, for 2013 at least. We continue to struggle with whether and how libraries should use their limited budgets to support open access publishing. I am always interested to hear your feedback about library resources and services! (rlewis@wustl.edu or 935-4819).

Publishers are struggling with these issues also. This month Sage Open (which is a multidisciplinary open access social sciences and humanities journal) reduced their author fees from $395/article to $99/article. Comments have compared this with the possibly unsustainable $99/life fee from Peer J and new OA journals with no fees (at least initially) such as ELife.

Cost Effectiveness for Open Access: The Cost Effectiveness for Open Access site has been in the news this month. This graph may occasionally be useful in choosing the best value open access publishing options. More info: Cheap Impact? "A new online tool allows researchers to compare open-access journal publication fees with article influence, and reveals that you don’t necessarily get what you pay for." {The Scientist, Jan. 23, 2013) | Price doesn't always buy prestige in open access "Online comparison tool reveals which journals provide the biggest bang for the buck." (Nature News Jan. 22, 2013).

The Ecological Society of America weighs society economics, publishng costs and open access trends. See this recent article and call for comments: ESA and Scientific Publishing—Past, Present, and Pathways to the Future Bulletin of the Ecological Society of America 94:4–11.

Open Education Week will be during WU spring break, March 11-15, 2013.

Managing your data; finding data

Online Data Management Planning Tool (DMPTool) Now Available! Washington University now has institutional access to a flexible online tool to help researchers generate data management plans. Developed by the California Digital Library and a group of major research institutions, the DMPTool is designed to help researchers:
* Create ready-to-use data management plans for specific funding agencies
* Meet requirements for data management plans
* Get step-by-step instructions and guidance for a data management plan
To access the DMPTool, visit: https://dmp.cdlib.org/institutional_login and select "Washington University in St. Louis" from the drop down menu. After signing in with your WUSTL Key, this tool will step you through the process of writing a data management plan. WUSTL's University Libraries and Office of Sponsored Research Services have partnered to provide support for data management. For more information about grant requirements, contact: Laura Langton, PhD, Research Development Manager, Office of Sponsored Research Services, langton@wustl.edu. For more information about data management and storage, contact: Cynthia Hudson, MALIS, Digital Data Outreach Librarian, WUSTL Libraries, chudson@wustl.edu. Library guide: Managing your Data

Another nice guide from the Libraries at University of Colorado Boulder: Writing a Data Management Plan

Comment in Nature about an NSF policy change; "...a scientist's worth is not dependent solely on publications. Data sets, software and other non-traditional research products will count too." Piwowar H. (2013). Altmetrics: Value all research products, Nature, 493 (7431) 159-159. DOI: 10.1038/493159aValue of all research products. [In order to include such products, they need to be citeable. The Libraries are working with others at the university to be able to provide DOI's [digital object identifiers] as needed by groups at the university. This NSF change contribute some urgency to that initiative.] I found this blog post about the Process behind a Nature Comment interesting also.

Data Portal(BETA), The Open Data Hub of the European Union, contains 5829 datasets (geographical data, statistics, meteorological data, data from publicly funded research projects, digitised books from libraries and more) that you can browse, search, learn about and download (along with applications when needed). I sometimes see students looking for datasets which they can download and analyze. This may be a fruitful source for that.

Improving Data Access at PLOS | Easier access to PLOS data

If you didn't see this article in Nature, check it out! Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Nature (2013) doi:10.1038/nature11875. Thanks for WU Chemistry/Engineering Librarian Rob McFarland for tipping me off about this.

NIH Public Access Policy Overviews

The NIH Public Access Policy requires investigators and scholars to submit final peer-reviewed journal manuscripts that arise from NIH funds to PMC upon acceptance of publication. All journal manuscripts applicable under the NIH Public Access Policy must demonstrate evidence of compliance in NIH applications and reports. As of Spring 2013, NIH will withhold grant money to enforce public-access policy [Nat Med. 2013 Jan;19(1):3. doi: 10.1038/nm0113-3]. Another change this spring is an enhancement to My NCBI to facilitate reporting of publications in paper progress reports; More info about My Bibliography Tool in My NCBI; Research News: TWO Important Upcoming Changes to NIH Grant Policies.

• Are you preparing a manuscript for publication?
• Are you familiar with journal policies for NIH-funded authors?
• Do you need a NIHMSID or a PMCID for an application or progress report?
• Do you know how to respond to a request from NIH asking for documentation of compliance with the NIH Public Access Policy for your publications cited in a progress report?

This presentation (offered twice) will provide an overview of the NIH Public Access Policy including the steps involved in complying with the policy and how to demonstrate compliance.
Option 1: Location:Holden Auditorium at the Farrell Learning and Teaching Center
Date and Time: Thursday February 14, 2013, Noon-1:00 pm
NO REGISTRATION required for Feb. 14th session.
Option 2: Location: Farrell Learning and Teaching Center, Room 214
Date and Time: Wednesday 20 March 2013, Noon-1:00 pm
TO REGISTER: There is no fee for this presentation. Please register via online form or email Cathy Sarli (sarlic@wustl.edu) to reserve a seat.
Presentations are open to all NIH-funded investigators/authors, grant managers or support staff from both WU campuses.
If you have questions or would like to arrange a customized presentation in the biology department, please contact Ruth Lewis.

Miscellaneous news and links for biofolk

- Please share with any recent postdocs who are without a position: http://www.elsevier.com/postdocfreeaccess

- Blackboard training sessions for faculty and staff are planned several times in December and January. Registration is required so check your calendars now if you'd like to begin or improve your use of Blackboard.

- John Dupuis' blog Confessions of a Science Librarian is beginning the annual review of "best science books" lists. There will be many more posts if this is like previous years. These are available at http://scienceblogs.com/confessions/category/best-science-books-2012/. These are a great source for gifts or books to add to your future reading list.

- Thanks in Advance For Sharing Your Data - this blog post includes a list of journals that currently require data sharing. Although this is a fairly short list, it surprised me that so many important biology journals are included.

- Videos, slides and handouts are now available from the NCBI Discovery Workshop held at Becker Library in October, 2012. You may find some of these useful for your own teaching and learning about Sequences, Genomes and Maps; Proteins, Domains and Structures; NCBI BLAST Services;Human Variation and Disease Genes.

- PeerJ will begin accepting manuscripts on Dec. 3rd. PeerJ has an unusual business model involving a $99 basic membership for lifetime open access publishing charges and peer review for scientific and technical soundness followed by post-publication open peer review to judge impact and importance. | Call for papers on PeerJ blog. | PeerJ: An Open-Access Experiment, by Peter Binfield in Educause Review.

- As Open Access Explodes, How to Tell the Good From the Bad and the Ugly?, by Martin Enserink. Science 23 November 2012: Vol. 338 no. 6110 p. 1018 DOI: 10.1126/science.338.6110.1018