The National Library of Medicine (NLM) is working closely with publishers and scholarly societies to expand the quantity of coronavirus-related articles in PubMed Central (PMC), including supporting data when available. For more information, please see “The National Library of Medicine Expands Access to Coronavirus Literature through PubMed Central” (National Institutes of Health News Release, March 25, 2020).
Streamline Your Workflow with LabArchives
What is LabArchives? It is ERN software licensed by Pitt since 2016 for the organization, communication, instruction, sharing, and management of scientific research and data.
What is an ERN? An Electronic Research Notebook is a secure, cloud-based platform to organize and manage your research and lab data safely.
Why use LabArchives? Digital notebooks offer features that are not possible with traditional paper lab notebooks. Continue reading
Open Access COVID Datasets and Software
“Sharing vital information across scientific and medical communities is key to accelerating our ability to respond to the coronavirus pandemic,” said Dr. Cori Bargmann, Head of Science at the Chan Zuckerberg Initiative, regarding a call to action to develop new text and data mining techniques that can help the science community answer high-priority scientific questions related to COVID-19.
Over the past few weeks, two notable resources have been made available, providing open access to COVID datasets and related software:
Filtering by Article Type in PubMed
If you’re a frequent user of PubMed, you may be familiar with the Article Types filter available on the Search Results page. This filter limits search results by attaching an additional search term to your search string. So, for example, if you enter the search terms “therapeutic hypothermia cardiac arrest” in PubMed, applying the Clinical Trial filter adds “AND Clinical Trial[pytyp]” to the end of the PubMed search string. That will limit your search to records tagged with Medical Subject Headings such as Clinical Trial, Controlled Clinical Trial, or Randomized Controlled Trial.
While the Article Types filter is one option for limiting to a particular study type, it can severely reduce the number of records you see and, more importantly, miss the records of very recently published articles. If that is a concern for you, check out another set of PubMed filters available through PubMed Clinical Queries. Also found as link on the PubMed home page, this set of filters is more “sensitive” than the Article Types filter, meaning they are more likely to find relevant records, including records for recently published studies. Continue reading
Tutorials for the New PubMed Now Available
The new version of PubMed will soon be live. Now is a good time to familiarize yourself with the new format. The National Library of Medicine has developed a number of short, to-the-point tutorials on how to search the new PubMed by topic, subject, author, and more. To view the list of tutorials, visit “PubMed Essentials: New Quick Tours and On-Demand Class on the New PubMed” in the March-April 2020 issue of the NLM Technical Bulletin.
Going forward, the bi-weekly HSLS Painless PubMed class will focus on the new PubMed.
Treasures from the Rare Book Room: Humphrey Ridley Remembered
Humphrey Ridley (1653-1708) was a little-known English neuroanatomist who studied medicine at Merton College in Oxford, and received his medical degree from Leyden University in 1679. Upon his return to England, he was a physician at Cambridge University and a member of Royal College of Physicians. There is not much known of his personal life, and he left only three published works: first on the topic of venereal diseases (1679), next on anatomy of the brain (1695), and the third on asthma (1703).
His book, Anatomy of the Brain Containing Its Mechanism and Physiology, followed two earlier and more commonly cited works in neurology, one by Thomas Willis and the other by Raymond Vieussens, but Ridley’s was the first neuroanatomy treatise in the English language. He acknowledged the brilliance of his predecessors, but also corrected some of their mistakes and omissions. He was the first to describe the ophthalmic artery and the ganglion of the fifth cranial nerve. According to Thakur, et al., Ridley was also the first to describe arachnoid cisterns and the arachnoid membrane, but because his contributions were not previously mentioned, Bichat and Ruysch held this claim even though their works were published later. Thakur and his colleagues speculated that Ridley’s stationary life and lack of clinical legacy might have contributed to the sad fact that his mastery in cadaveric injections and his novel contributions have gone unnoticed and uncited for so long.
HSLS Staff News
The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.
Names in bold are HSLS-affiliated
News
Carrie Iwema, Coordinator of Basic Science Services, has become a Certified Carpentries Instructor. The Carpentries project includes Software Carpentry, Data Carpentry, and Library Carpentry with the shared mission to teach foundational computational and data science skills to researchers.
Welcome
Holly Hill joined the HSLS staff as the new Program Manager and will be supporting HSLS’s partnership with UPMC for providing digital library resources and services. Holly previously held administrative positions at UPMC and in the business sector. Continue reading
Classes for April 2020
Due to recent University of Pittsburgh restrictions, HSLS will be offering all classes online until further notice.
Painless PubMed, Wednesday, April 1, 8:30–9:30 a.m.
Basic Python through Jupyter, Friday, April 3, 1–4 p.m.
Basic EndNote, Tuesday, April 7, 11 a.m.–12 p.m.
Genetic Variation, Wednesday, April 8, 10 a.m.–3 p.m.
Share Data with the Pitt Data Catalog, Thursday, April 9, 10:30–11 a.m.
Beyond Beginner Workshop: Getting Going with Pandas in Python, Friday, April 10, 1–4 p.m.
Visual Abstracts, Monday, April 13, 10:30 a.m.–12 p.m.
Painless PubMed, Monday, April 13, 12–1 p.m.
Bulk RNA-Seq., Wednesday, April 15, 10 a.m.–3 p.m.
Advanced OpenRefine Functions, Thursday, April 16, 3–4 p.m.
Data Journals: Standalone Publication for Replication, Negative, Intermediate, or Simply Noteworthy Data
As the scholarly community continues to recognize the importance of open data sharing for increasing the reproducibility of research, researchers are faced with a growing menu of options through which to make their data available. For example, is it better to deposit data in a digital repository, which often grants depositors a Digital Object Identifier (DOI), or to formally describe a dataset in a data journal article, or to share it through a metadata registry like the Pitt Data Catalog? A recent video call for papers from the journal Data in Brief argues that data journals offer a unique opportunity for standalone publication of genres that are often critically underserved by the scholarly publishing ecosystem: datasets containing replication data, negative results, and intermediate data for research in progress. Continue reading
CANCELED- “Lab Girl” Book Discussion for the NEA Big Read
HSLS is hosting a discussion of the book Lab Girl by Hope Jahren on Tuesday, March 24. This memoir explores Hope Jahren’s upbringing and training as a geobiologist, her experiences in the lab, her musings on nature and the environment, and the peaks and valleys of being a scientist.
Free copies of Lab Girl are available thanks to an NEA Big Read grant awarded to Duquesne University. NEA Big Read is a program of the National Endowment for the Arts in partnership with Arts Midwest.
Abigail Rothrauff, Department of Immunology, will lead the book discussion. Join us from 12:30-2 p.m. in Falk Library for conversation and pizza. Please bring your own drink.
Space is limited, so register soon to reserve your spot (and to have time to read the FREE BOOK)! Continue reading
JAWS® Screen Reader Now at Falk Library
Job Access With Speech
, or JAWS®, is software that reads text on a computer screen to enable easier computer access for people who are blind or have low vision. Listening to JAWS® with headphones, you can use a mouse and keyboard to read a website, edit a document, and send an e-mail. One of the most popular screen reader programs, JAWS® features two multilingual synthesizers and can easily be paired with Braille keyboard input. With licensing support from Pitt Information Technology, JAWS® is now available on Falk Library computers running Windows OS, including classroom computers and laptops. Continue reading
Accessing Full Text at HSLS
Do you ever find yourself stuck when trying to access the full text of an article? One of the benefits of your University of Pittsburgh affiliation is the ability to access the full range of electronic resources that the library offers. A quick video, Locating Full Text Using HSLS Resources, was created to help you. This video walks you through the three ways to access full text at HSLS: using Links@Pitt, searching PITTCat, and using Document Delivery.
HSLS Staff News
The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.
Names in bold are HSLS-affiliated
Welcome
HSLS welcomes three new research and instruction librarians. Stephen Gabrielson previously worked as the pharmacy librarian at the M.B. Ketchum Memorial Library at Marshall B. Ketchum University in Fullerton, CA. He earned his MS in library and information science at Simmons University in Boston, MA, and a BA in art history from Humboldt State University in Arcata, CA, where he also earned a Certificate in Museum and Gallery Practices. Rachel Suppok was a graduate teaching assistant at the Waidner-Spahr Library at Dickinson College in Carlisle, PA. She received an MLIS from the University of Wisconsin-Milwaukee and a BS in neuroscience from Dickinson College in Carlisle, PA. She also studied at the Danish Institute for Study Abroad. Francesca Yates was the health sciences librarian at the Geisinger Commonwealth School of Medicine in Scranton, PA. She received an MLIS from Pitt and a BA in Spanish at the State University of New York at New Paltz, where she doubled minored in linguistics and psychology. Continue reading
Classes for March 2020
EndNote for Research Teams, Monday, March 2, 11 a.m.–12 p.m.
Basic EndNote for Macs, Tuesday, March 3, 10–11 a.m.
Painless PubMed, Tuesday, March 3, 1–2 p.m.
Gene Expression Visualization, Wednesday, March 4, 10 a.m.–3 p.m.
Basic EndNote, Thursday, March 5, 10:30–11:30 a.m.
Introduction to Data Management, Tuesday, March 10, 1–2 p.m.
File Naming Best Practices, Thursday, March 12, 10:30–11 a.m.
Advanced EndNote, Tuesday, March 17, 10–11 a.m.
Pathway Enrichment Analysis–IPA & MetaCore, Wednesday, March 18, 10 a.m.–3 p.m.
Painless PubMed, Thursday, March 19, 10–11 a.m.
Crafting a Data Management Plan, Thursday, March 19, 12–1 p.m.
“3R” Literature Searching for Animal Research Protocols Presentation, Friday, March 20, 2–3 p.m.
Introduction to Image Editing: Adobe Photoshop and Illustrator, Tuesday, March 24, 10–11:30 a.m.
NEA Big Read @ Pitt HSLS, Tuesday, March 24, 12:30–2 p.m.
Single Cell RNA-Seq, Wednesday, March 25, 10 a.m.–3 p.m.
Exploring and Cleaning Data with OpenRefine, Thursday, March 26, 2:30–4 p.m.
Introduction to Adobe Photoshop, Friday, March 27, 10–11:30 a.m.
“3R” Literature Searching for Animal Research Protocols Drop-In Session, Friday, March 27, 2–3 p.m.
Introduction to Adobe Illustrator for Diagrams, Tuesday, March 31, 10–11:30 a.m.