Publisher Data Requirements Revisited

In May and September of 2017, the Library wrote posts (read them here and here) about a number of publisher research data policies. Over the last year, publishers have engaged in conversations with institutions, funders, and not-for-profit organizations to examine how they can better shape and influence the sharing of research data.

Image from Unsplash by Franki Chamaki

To accompany their data sharing policies and recommendations, publishers like Springer Nature and Elsevier recently developed their own research data services to better assist researchers who are preparing their data to be published alongside a manuscript. They now provide individual guidance (for a fee) and repositories in which to deposit and share data. Please talk to a consultant at UC Berkeley’s Research Data Management program about the guidance we can provide along with University of California supported data sharing options.

Elsevier continues to communicate about research data through a series of principles (data should be made available free of charge wherever possible with minimal reuse restrictions; by enabling effective reuse of data we’re finding efficiencies and preventing duplication of effort). These principles map to a series of policies. The policies speak to how Elsevier will support and encourage researchers when sharing data. Elsevier’s research data guidelines, which remain largely unchanged since last year, prescribe how and when researchers will share their data. Elsevier’s journals are assigned to one of five research data guidelines, which have slight variations in language and range from “encouraged to deposit research data” to “required to deposit research data.”

When submitting to an Elsevier journal, be sure to check the individual journal’s Guide for Authors, which is located on the journal homepage. Elsevier does not maintain a master list of journals mapped to the five research data guidelines. Your subject librarian can provide guidance if you need more information about the data publishing policies from a specific Elsevier title. If you don’t know where you will submit your research, it’s best to prepare for the most rigorous data policy by adhering to a data management plan throughout the course of your work.

Springer Nature’s data publishing policies follows the same, four tiered structure they developed in 2017; however, they’ve added more nuanced requirements within each tier for the life sciences and non life sciences. Check here to see the publisher’s list of journals and their assigned data publishing policy.

Wiley applies one of three data sharing policies to their journals: encourages data sharing; expects data sharing; and mandates data sharing. The publisher has created an author compliance tool, which enables researchers who are submitting papers to one of the publisher’s journals to check what they need to do with their data to be in compliance with their funder, institution, and journal. For example, if your research is funded by the NIH, you work at a University of California institution, and would like to publish in Bioengineering and Translational Medicine, you’ll learn that the journal encourages you to share your data, the NIH requires you to share your data, and the university does not have a policy. In cases like this, you need to default to the entity that requires the most sharing. In this case, you would share your data as stipulated by the NIH.

Wiley’s author compliance tool points out the gaps in policy that exist for researchers, especially in the United States. Data sharing policies differ widely between institutions, publishers, and funders which leads to confusion for the researcher. In general, when planning research and communicating your results, take the Open Science approach, which advocates for showing your work and sharing your work in the name of advancing science. By thoroughly documenting your data and research process, others are better able to understand your work and potentially utilize the data for another research purpose. The Open Science approach supports transparency and reuse, which results in better science and more rapid advances. If you would like more information about preparing your data to be shared with others, please contact the Research Data Management Program.

 


2018 Winners of the Ig® Nobel Prize Announced!!

…For achievements that first make people LAUGH then make them THINK

MEDICINE PRIZE [USA] — Marc Mitchell and David Wartinger, for using roller coaster rides to try to hasten the passage of kidney stones.
REFERENCE: “Validation of a Functional Pyelocalyceal Renal Model for the Evaluation of Renal Calculi Passage While Riding a Roller Coaster,” Marc A. Mitchell, David D. Wartinger, The Journal of the American Osteopathic Association, vol. 116, October 2016, pp. 647-652.

ANTHROPOLOGY PRIZE [SWEDEN, ROMANIA, DENMARK, THE NETHERLANDS, GERMANY, UK, INDONESIA, ITALY] — Tomas Persson, Gabriela-Alina Sauciuc, and Elainie Madsen, for collecting evidence, in a zoo, that chimpanzees imitate humans about as often, and about as well, as humans imitate chimpanzees.
REFERENCE: “Spontaneous Cross-Species Imitation in Interaction Between Chimpanzees and Zoo Visitors,” Tomas Persson, Gabriela-Alina Sauciuc, and Elainie Madsen, Primates, vol. 59, no. 1, January 2018, pp 19–29.

BIOLOGY PRIZE [SWEDEN, COLOMBIA, GERMANY, FRANCE, SWITZERLAND] — Paul Becher, Sebastien Lebreton, Erika Wallin, Erik Hedenstrom, Felipe Borrero-Echeverry, Marie Bengtsson, Volker Jorger, and Peter Witzgall, for demonstrating that wine experts can reliably identify, by smell, the presence of a single fly in a glass of wine.
REFERENCE: “The Scent of the Fly,” Paul G. Becher, Sebastien Lebreton, Erika A. Wallin, Erik Hedenstrom, Felipe Borrero-Echeverry, Marie Bengtsson, Volker Jorger, and Peter Witzgall, bioRxiv, no. 20637, 2017.

CHEMISTRY PRIZE [PORTUGAL] — Paula Romão, Adília Alarcão and the late César Viana, for measuring the degree to which human saliva is a good cleaning agent for dirty surfaces.
REFERENCE: “Human Saliva as a Cleaning Agent for Dirty Surfaces,” by Paula M. S. Romão, Adília M. Alarcão and César A.N. Viana, Studies in Conservation, vol. 35, 1990, pp. 153-155.

MEDICAL EDUCATION PRIZE [JAPAN] — Akira Horiuchi, for the medical report “Colonoscopy in the Sitting Position: Lessons Learned From Self-Colonoscopy.”
REFERENCE: “Colonoscopy in the Sitting Position: Lessons Learned From Self-Colonoscopy by Using a Small-Caliber, Variable-Stiffness Colonoscope,” Akira Horiuchi and Yoshiko Nakayama, Gastrointestinal Endoscopy, vol. 63, No. 1, 2006, pp. 119-20.

LITERATURE PRIZE [AUSTRALIA, EL SALVADOR, UK] — Thea Blackler, Rafael Gomez, Vesna Popovic and M. Helen Thompson, for documenting that most people who use complicated products do not read the instruction manual.
REFERENCE: “Life Is Too Short to RTFM: How Users Relate to Documentation and Excess Features in Consumer Products,” Alethea L. Blackler, Rafael Gomez, Vesna Popovic and M. Helen Thompson, Interacting With Computers, vol. 28, no. 1, 2014, pp. 27-46.

NUTRITION PRIZE [ZIMBABWE, TANZANIA, UK] — James Cole, for calculating that the caloric intake from a human-cannibalism diet is significantly lower than the caloric intake from most other traditional meat diets.
REFERENCE: “Assessing the Calorific Significance of Episodes of Human Cannibalism in the Paleolithic,” James Cole, Scientific Reports, vol. 7, no. 44707, April 7, 2017.

PEACE PRIZE [SPAIN, COLOMBIA] — Francisco Alonso, Cristina Esteban, Andrea Serge, Maria-Luisa Ballestar, Jaime Sanmartín, Constanza Calatayud, and Beatriz Alamar, for measuring the frequency, motivation, and effects of shouting and cursing while driving an automobile.
REFERENCE: “Shouting and Cursing While Driving: Frequency, Reasons, Perceived Risk and Punishment,” Francisco Alonso, Cristina Esteban, Andrea Serge and Maria-Luisa Ballestar, Journal of Sociology and Anthropology, vol. 1, no. 12017, pp. 1-7.
REFERENCE: “La Justicia en el Tráfico: Conocimiento y Valoración de la Población Española” [“Justice in Traffic: Knowledge and Valuation of the Spanish Population”)], F. Alonso, J. Sanmartín, C. Calatayud, C. Esteban, B. Alamar, and M. L. Ballestar, Cuadernos de Reflexión Attitudes, 2005.

REPRODUCTIVE MEDICINE PRIZE [USA, JAPAN, SAUDI ARABIA, EGYPT, INDIA, BANGLADESH] — John Barry, Bruce Blank, and Michel Boileau, for using postage stamps to test whether the male sexual organ is functioning properly—as described in their study “Nocturnal Penile Tumescence Monitoring With Stamps.”
REFERENCE: “Nocturnal Penile Tumescence Monitoring With Stamps,” John M. Barry, Bruce Blank, Michael Boileau, Urology, vol. 15, 1980, pp. 171-172.

ECONOMICS PRIZE [CANADA, CHINA, SINGAPORE, USA] — Lindie Hanyu Liang, Douglas Brown, Huiwen Lian, Samuel Hanig, D. Lance Ferris, and Lisa Keeping, for investigating whether it is effective for employees to use Voodoo dolls to retaliate against abusive bosses.
REFERENCE: “Righting a Wrong: Retaliation on a Voodoo Doll Symbolizing an Abusive Supervisor Restores Justice,” Lindie Hanyu Liang, Douglas J. Brown, Huiwen Lian, Samuel Hanig, D. Lance Ferris, and Lisa M. Keeping, The Leadership Quarterly, February 2018.

As always, winners from previous years, as well as all kinds of stuff, may be found on the Improbable Research website.


New Resource: ACS Reagent Chemicals

The ACS Committee on Analytical Reagents sets purity specifications for almost 500 reagent chemicals and over 500 standard-grade reference materials. ACS Reagent Chemicals provides general physical properties and analytical uses for all reagent chemicals as well as guidelines for standard analytical methods.

The new online version has integrated supplements and updates to provide the most up-to-date content and includes new benefits such as:

  • Mobile-friendly operation
  • Live links between reagents and methods
  • HTML or printable PDF formats
  • Fresh, user-friendly interface

You can search ACS Reagent Chemicals in OskiCat or access it through the Chemistry and Chemical Engineering Library Guide under Properties and Data. Contact the Chemical Information Librarian, Kortney Rupp with any issues or questions.

 


NEW DMPTool Launched!

A shiny new version of the DMPTool was launched at the end of February. The big change, beyond the new color scheme and layout, is that it is now a single source platform for all DMPs. It now incorporates the codebase from other instances of  the program from all over the world, including: DMPTuuli (Finland), DMP Melbourne (Australia), DMP Assistant (Canada), DMPOnline (Europe), and many more! The move was made to combine all platforms into one in order to focus on best practices at an international level. Please learn more about the new instance by visiting the DMPTool Blog.

DMPTool Logo


Cambridge Structural Database 2018 Available

The 2018 Cambridge Structural Database System (including ConQuest and Mercury) is available for downloading from the UC distribution site. The Cambridge Structural Database is crystal structure database, with over 900,000 entries for organic and organometallic compounds.

Downloading CSD:

  • You must be on the campus network or wifi or using VPN to access the files on that page.
  • Don’t forget the site and confirmation codes, which you can get by clicking Berkeley (UCB) link. You’ll need those codes during the CSDS installation.
  • CSDS is available for Windows, OSX, and Linux/Unix. It is recommended that you uninstall CSDS 2017 before you start this installation.
    • There’s an additional Windows application that can be downloaded separately. CrossMiner is a “novel tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries.”
  • You can also search the CSD structures through WebCSD, without installing any software.

CSDS Documentation:

Please contact Kortney Rupp if you have questions about CSD.


Love Data Week 2018!

Description of event
The University Library,  Research IT,  and Berkeley Institute for Data Science invite faculty, students, and staff to a series of events on February 12th-16th during Love Data Week 2018.  Love Data Week is a nationwide campaign designed to raise awareness about data visualization, management, sharing, and preservation.
Please join us to learn about multiple data services that the campus provides and discover options for managing and publishing your data. Graduate students, researchers, librarians and data specialists are invited to attend these events to gain hands on experience, learn about resources, and engage in discussion around researchers’ data needs at different stages of their research process.
To register for these events and find out more, please visit: http://guides.lib.berkeley.edu/ldw2018guide
Schedule:
 
Intro to Scopus APIs –  Learn about different types of APIs Scopus has to offer and how to get data from APIs. In the first hour, learn about the portal, what the API can do, and about different use cases. Following a short break, the instructor will take the group through live queries, show how to test code, provide tips and tricks, and will leave the group with sample code to work with. Attendees will be able to follow up with the instructor via webinar to troubleshoot and ask further questions about specific projects. Register from here.
01:00 – 03:00 p.m.Tuesday, February 13, Doe Library, Room 190 (BIDS)
Refreshments will be provided.
Data stories and Visualization Panel – Learn how data is being used in creative and compelling ways to tell stories. Researchers across disciplines will talk about their successes and failures in dealing with data.
1:00 – 02:45 p.m.Wednesday, February 14, Doe Library, Room 190 (BIDS)
Refreshments will be provided.
Planning for & Publishing your Research Data – Learn why and how to manage and publish your research data as well as how to prepare a data management plan for your research project.
01:00 – 02:00 p.m.Thursday, February 15, Doe Library, Room 190 (BIDS)
We hope to see you there!

For your consideration: Electronic Laboratory Notebooks

Paper notebook and tablet

As a previous research chemist, I spent a lot of time populating laboratory notebooks during my undergraduate and graduate research. I used to pride myself in keeping what I thought to be a notebook in which the experiments could all be reproduced at any time (naive, I know). When I joined a research group in graduate school, my advisor told me we were going to use Microsoft OneNote as our group notebook. At first, I was confused and hesitant about making the switch.  My natural my workflow and data organization had to dramatically change to adjust to the digital recordkeeping environment I now found myself in. I soon realized the transition would allow me to focus more on the science and less on the printing, pasting, and handwriting. As an atomic force microscopist, I found it quick and easy to import digital images, chemical structures and screenshots of methods directly from digital articles. Over time I developed new strategies for organization including color coding to tie together sample preparations with the corresponding AFM images. I also created file naming standards and table of content pages to allow my labmates and advisor to search my notebook easily. These strategies ultimately allowed me to conduct my work in a more efficient and easily reproducible way and I now cannot imagine a world in which I could conduct science using a paper notebook.

Adopting any new workflows into an already complicated, time-sensitive environment can seem overwhelming and possess a steep learning curve. Libraries and librarians at UC Berkeley are well positioned to help researchers improve their productivity, transparency, and reproducibility by adopting a digital recordkeeping system. To try and provide some insight into how to determine which ELN to use and a strategy to make the transition to ELNs, I have created a guide and am available to assist throughout the transition process.


Alice Fan, MD: New Cancer Therapies & Women in Science

The last Nanoscale Science and Engineering (NSE) seminar of the semester is scheduled for Friday, December 1st from 2:00 – 3:00 in 180 Tan Hall. Alice Fan, from the Stanford Medical School, will be speaking on new nanoimmunoassays that enable the isolation and analysis of tumor cells. Following her talk, the Graduate Women in Engineering (GradSWE) will host a coffee hour from 3:30-4:30 in 242 Sutardja Dai Hall.

Alice Fan photo


bioRxiv: a free open access archive for unpublished preprints in the life sciences

bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.
bioRxiv accepts preprints of articles covering all aspects of research in the life sciences. Categories include:
  • Bioengineering
  • Cancer biology
  • Cell biology
  • Ecology
  • Epidemiology
  • bioRxiv logoGenomics
  • Molecular biology
  • Neuroscience
  • Pharmacology and toxicology
  • Scientific Communication and Education
and more.
Readers may add public comments to articles on bioRxiv. Comments are moderated to ensure they conform to the standards of normal professional discourse.
Once an article is published in a journal, bioRxiv will automatically update the preprint with a link to the published version.