Kaitlin Throgmorton's blog

Celebrating Open Access Week with New Workshops and More!

Ahead of Open Access (OA) Week, the Cushing/Whitney Medical Library is celebrating all things open! Whether you’re looking to make your next paper open access, lower (or eliminate!) your article processing charges (APCs), choose a dataset license, or learn more about fair use, we’ve got you covered with a curated bundle of open access trainings, events, and activities for the week of October 21-27, 2024. Attend a Workshop: October 22, 11:00 – 11:45 a.m.: Exploring PubMed Central: Finding Free Full-Text Literature, Advanced Search Strategies, and Recent Updates October 22, 3:00 – 4:00 p.m.: Open Access Office Hours October 23, 5:00 – 6:00 p.m.: Navigating Open Access Publishing: A Brief Overview for Scholars October 23, 6:00 – 8:00 p.m.: Open Access Office Hours October 24, 11:00 a.m. - 12:00 p.m.: Discovering Data in PubMed & PubMed Central: Strategies for Successful Searches October 25, 10:00 – 10:45 a.m.: Exploring PubMed Central: Finding Free Full-Text Literature, Advanced Search Strategies, and Recent Updates October 25, 11:30 a.m. - 12:00 p.m.: Unlock the Power of Sharing: Demystifying Data and Code Licensing Head to our training calendar for even more programming. Plus, find more open access events hosted by the larger Yale Library system. Explore Self-Guided Learning: Open Access Research Guide : Everything you want to know about the library’s philosophy of open access, how to get library support for open access publishing, and more. What is Scholarly Communication? This page includes information about open access, publishing considerations, journals with no APCs (more below!), and other FAQs. Make Your Research Open – Potentially for Free! Did you know? The library has negotiated agreements that allow Yale authors to publish without paying APCs (article processing charges) in more than 700 journals. Check out the list of 180 titles relevant to the medical campus. Learn about how these agreements have benefitted Yale researchers through the stories below: “Thanks to Yale's agreements, we have had the opportunity to publish open access at no cost in peer-reviewed journals and share our research with more people worldwide." – Courtney Choy, MPH, PhD, Postdoctoral Associate, who published 5 papers OA with Yale Library agreements "In global health, making sure our findings are accessible to the communities in which we work is paramount. These open access agreements are transformative for community engagement and transparency." – Nicola Hawley, PhD, Associate Professor of Epidemiology, who published 7 papers OA with Yale Library agreements "As an early-career researcher, publishing open access in PLOS Global Public Health through Yale's transformative agreement was invaluable. It removed financial barriers, made my work accessible to the research community, and encouraged me to further dig into my study field. This agreement is truly helpful for junior researchers to build their confidence and contribute more to science." – Bohao Wu, PhD, MBBS, Postdoctoral Research Scientist, who published “Global prevalence of preterm birth among Pacific Islanders” OA with Yale Library agreements "Our lab has benefitted much from the agreement between Yale and PLOS that allows Yale researchers to publish Open Access articles for free. Through nine papers published in PLOS Genetics and PLOS Computational Biology since 2020, not only have we been able to get our work disseminated at these leading statistical genetics and computational biology journals, the open access has made our work available to a much larger audience without imposing fiscal burden on us, unlike other open access publications." – Hongyu Zhao, PhD, Ira V. Hiscock Professor of Biostatistics, Professor of Genetics and Professor of Statistics and Data Science, who published 9 papers OA with Yale Library agreements Come back to this page throughout the rest of October as more opportunities and resources are added.

Access to American Hospital Association (AHA) Data

Access to American Hospital Association (AHA) Data After years of requests for American Hospital Association (AHA) data, the Medical and Marx libraries at Yale have made access to this important U.S. hospital data available for all Yale affiliates. Containing multiple decades of annual survey and supplemental datasets, this data resource provides information about U.S. hospitals' organizational structure, service lines, utilization, finances, insurance and payment models, and staffing, enabling peer comparisons, market analysis, and health services research. To access AHA data, create an account on the platform, Wharton Research Data Services (WRDS), with your yale.edu email address. To learn more about how to get started, consult this research guide. If you already have a WRDS account, access AHA data now. Quick facts about AHA Data: 40+ years annual hospital survey data, dating back to 1980 1,000+ data points about U.S. hospitals for each survey year In addition to survey results, additional hospital data has been curated by AHA, including data and information from government sources, hospital accrediting bodies, and other organizations as well as AHA's financial database Beyond the data itself, WRDS features include a query builder, manuals, data dictionaries, documentation, and more to facilitate data use

Poison Yesterday and Today – New Exhibition and PSA for National Poison Prevention Week

As we launch the Medical Library's exhibition "Killer or Cure? Poison through the Centuries" on March 23rd, we'd like to remind you that while poison has often captured the public imagination through the ages, today it can cause real harm, and even death. Unfortunately, as of 2021, poison is the leading cause of injury death in the United States, and three-quarters of poison deaths are unintentional. Nearly half (41%) of cases occur in children under age 5. Nearly all (93%) poison cases these days occur at home, and most implicated poisons are regular household items – such as common drugs (analgesics and antidepressants), cleaning substances, and cosmetics – that become fatally toxic when not used as intended1. In Connecticut during 2018-2021*, most accidental poisoning deaths occurred due to exposure to drugs**. This data and the figure below are produced from data on underlying causes of death extracted from the Centers for Disease Control (CDC) WONDER Database2. This figure on accidental poisoning deaths in Connecticut was created by data librarian for the health sciences, Kaitlin Throgmorton, using Python 3, pandas, matplotlib, seaborn, and Jupyter Notebook – view the code. *CDC Wonder Underlying Cause of Death Files do not include data on infants. These files may not include all data, as data are suppressed when the data meet the criteria for confidentiality constraints. **Drugs combines several categories, including: other and unspecified drugs, medicaments and biological substances; narcotics and psychodysleptics [hallucinogens], not elsewhere classified; antiepileptic, sedative-hypnotic, antiparkinsonism and psychotropic drugs, not elsewhere classified. In addition to the launch of the poison exhibition this week, this week is also National Poison Prevention Week. You can help prevent unintentional poisoning with a few simple tips3: Keep cleaning supplies, medicines, and other household items well out of reach of children. Make sure you know what medicines and supplies you have, and that they're correctly labeled. Call the Poison Help Line at 1-800-222-1222 (or visit www.poisonhelp.org) if you need assistance. References: America’s Poison Centers. National Poison Data System (NPDS) Interactive Dashboard. https://public.tableau.com/app/profile/aapcc/viz/APC_2021-NPDS-Public-Dashboard_PUBLISHED_2023-01-16/AnnualSummary. Accessed at https://poisoncenters.org/national-poison-data-system on Mar 16, 2023. Centers for Disease Control and Prevention, National Center for Health Statistics. National Vital Statistics System, Mortality 2018-2021 on CDC WONDER Online Database, released in 2021. Data are from the Multiple Cause of Death Files, 2018-2021, as compiled from data provided by the 57 vital statistics jurisdictions through the Vital Statistics Cooperative Program. Accessed at http://wonder.cdc.gov/ucd-icd10-expanded.html on Mar 16, 2023. America’s Poison Centers. National Poison Prevention Week 2023. https://poisoncenters.org/nppw-2023. Accessed on Mar 20, 2023.

Love Data Week 2023 Recap

This past February, the Cushing/Whitney Medical Library, together with the Digital Humanities Lab and other campus partners, celebrated Love Data Week, an international event dedicated to data enthusiasm and education. With more than two hundred attendees across seven events (including many community attendees at the keynote, which was open, virtually, to the public), the week was a resounding success. At Dr. Yanni Alexander Loukissas' keynote, participants heard about the importance of data settings and of grounding data in the real communities they represent. At various training events, participants learned about working with data in Python and R, as well as about the many data management tools available to them at Yale, alongside real-world researcher data management use cases (view a recording of this session). To round out the week, attendees also had the opportunity to attend a documentary film screening on data technology advances and a wellness event focused on managing motivation and increasing mindfulness in data work. We'd like to extend our gratitude to the following campus partners who presented or assisted with event organization for Love Data Week: Digital Humanities Lab, REDCap @ Yale, Yale Film Archive, Yale School of Medicine Student Mental Health and Wellness Program, Yale ITS Enterprise Storage Team, and Yale Center for Research Computing. We'd also like to thank the following individuals: Sana Ali, Sundari Birdsall, Hannah Clark, Steve DeGroat, Sofia Fertuzinhos, Mary Geda, Dana Haugh, Lisa Ho, Michael Kerbel, Kaylea Nelson, John Onofrey, Vermetha Polite, Kayla Shipp, Sui Tsang, Chris Zollo. Download the Love Data Week 2023 event flyer for more information about the week's activities. And the Love Data Week celebrations aren't quite over! On the afternoon of March 30th, Dr. Lauren Klein will be giving an in-person talk at Yale titled, "The Line Graph and the Slave Ship: Rethinking the Origins of Data Visualization." Register now!

How to Write a Data Management Plan - Email Course

On January 25, 2023, the National Institutes of Health (NIH) will update its Data Management and Sharing Policy to further accelerate biomedical research discovery through scientific data sharing. The policy includes two main requirements: submission of a data management and sharing plan and agreement to comply with that plan, including sharing and preserving data for the long-term. The Medical Library welcomes this new policy and supports its emphasis on translating research results into accessible knowledge on human health. Get step-by-step guidance on how to compile a data management plan in our new email course, “How to Write a Data Management Plan.” In this six-part email course, you will explore the main components of a data management plan. By the end, and through a series of three action items, you’ll complete a draft data management plan, ready to submit to a funder or to put into use within your research team. This course unfolds over a period of several weeks, and you can expect your first email to arrive within a few days, after sign-up. For more information on research data management, visit our "Manage Data" page.

Upcoming NIH Data Sharing Policy Change

On January 25, 2023, the National Institutes of Health (NIH) will update its Data Management and Sharing Policy to further accelerate biomedical research discovery through scientific data sharing. The policy includes two main requirements: submission of a data management and sharing plan agreement to comply with that plan, including sharing and preserving data for the long-term Though the policy builds on the NIH’s initial 2003 policy, one significant change is that the new policy will apply to all funded research, not just projects with large awards. The Cushing/Whitney Medical Library welcomes this new policy and supports its emphasis on translating research results into accessible knowledge on human health. To receive assistance with research data management, specifically help in writing a data management plan, please contact Kaitlin Throgmorton, data librarian for the health sciences, at kaitlin.throgmorton@yale.edu QUICK FACTS: The policy goes into effect for applications received on or after January 25, 2023. Complying with the policy is required for all NIH-funded research, including awards under $500,000. Data management plans must be submitted with NIH applications. There are also additional components to be included. Researchers are expected to share their data when appropriate. The NIH has launched a new website to support the policy. ADDITIONAL RESOURCES: Manage Data from the Cushing/Whitney Medical Library Scientific Data Sharing from the NIH Research Data Management from Yale Library DMPTool – a free tool for generating data management plans based on funder templates, including the new NIH policy (for writing DMS plans) re3data – a free tool for looking up research data repositories (for sharing data) FAIRsharing – a free tool for looking up data standards, databases, and policies (for writing DMS plans) Gonzales S, Carson MB, Holmes K (2022) Ten simple rules for maximizing the recommendations of the NIH data management and sharing plan. PLOS Computational Biology 18(8): e1010397. Michener WK. (2015). Ten simple rules for creating a good data management plan. PLOS Computational Biology, 11(10): e1004525.

Announcing: Love Data Week 2022 at the Medical Library

Love Data Week will be February 14-18, 2022. This event marks the importance of data in our lives, science, medicine, and countless other areas. This year’s theme — “data is for everyone” — reminds us both that data should be accessible and equitable. Everyone should be able to feel confident in accessing and using data, and everyone should see parts of themselves, and their communities, in the data we collect, analyze, and share. In the spirit of the idea that “data is for everyone” during Love Data Week, we’ll be offering data workshops for users at all levels, and we hope you’ll learn something new whether you’ve just started working with data, or you’ve been doing so for a while. Join Yale’s Cushing/Whitney Medical Library in observing Love Data Week with the following events: Where in the World is the Data You Need? How to Find and Reuse Data — Learn how to find, evaluate, and use data, especially publicly available data, in this session on Tuesday, February 15. You’re encouraged to BYOD (bring your own dataset) for an exploratory class where we’ll look for and discover data in the wild! Excel for Research Data Management — This session will cover tips and tricks for managing data in Excel, from text and data manipulation, to filters, functions, and formulas, and more. Join the Marx and Cushing/Whitney data librarians for this session on Friday, February 18. Data Librarian Office Hours — Starting Monday, February 14, the data librarian for the health sciences will be hosting office hours every other Monday afternoon. The first session during Love Data Week will focus on ‘adopting a dataset,’ but all topics are welcome. Managing Your Research with Electronic Notebooks: How to Use LabArchives — Get a jump start on Love Data Week with this session the week prior on managing data and research in electronic notebooks, happening on February 10th. Want more Love Data Week fun? Check out ICPSR's Adopt a Dataset initiative! (ICSPR, a data repository, is the international host for Love Data Week.) This is a great opportunity to explore and interact with a public dataset, and learn more about it. Plus, explore more Love Data Week sessions across the Yale University Library and at the National Library of Medicine. (And, here on campus, if you're into big data, don't miss Yale Center for Research Computing's Python for Big Data Analysis class on Friday, February 18.) We look forward to seeing you for Love Data Week, and beyond!