The links below refer to the notable data changes made to MEDLINE during the annual National Library of Medicine (NLM) maintenance known as Year-End Processing (YEP) for 2018:
MeSH Vocabulary Updated for 2018
Updated MeSH in MEDLINE Citations
Changes to MeSH Headings
New MeSH Headings and Concepts
MeSH Publication Types
MeSH Qualifier (Subheading) Changes
MeSH Tree Changes
Do Not Confuse
One MeSH Concept Split into Two
Entry Combination Revisions
New Databank Sources
Data Distribution Notes
Policy Updates and PubMed Notes
What is the 21st century equivalent of a worksheet? Consider the hyperdoc.
I discovered hyperdocs through a recent MLA News article (subscription required). Hyperdocs are a “transformative, interactive Google Doc replacing the worksheet method of delivering instruction,“, according to the Hyperdoc Girls, a group of three teachers who coined the term after their schools adopted Google Apps for Education.
Hyperdocs take components of a worksheet, such as directions and links to more information, and add collaboration and reflection, creating a digital space for blended learning and interaction. “A HyperDoc is a digital document where all components of a learning cycle have been pulled together into one central hub,” writes Jennifer Gonzalez of the blog Cult of Pedagogy. She provides a good example of a how hyperdocs work using a ‘digital roadtrip’ geography lesson.
Hyperdocs are gaining popularity in K-12 settings, including school libraries. School Library Journal covered the trend in April 2017, while Our Lovely Library presents a “before” and “after” perspective on using hyperdocs for a research project lesson.
What other uses could hyperdocs have in libraries? A couple ideas: a student-built resource guide, a hub for flipped classroom materials, or a self-paced guided tutorial for primary source documents.
Personally, I think hyperdocs have potential as a tool for teaching information literacy skills. There’s a seems to be a congruence between the hyperdoc learning experience and the ACRL Framework for Information Literacy. Perhaps this is a tool to help cross the threshold? If you’re interested in learning more, try starting with this pre-built Hyperdoc template in Google Drive or browse this directory of K-12 hyperdocs for inspiration.
Happy hyperdoc-ing! (I couldn’t resist.)
We’ve heard from our community that you wish you could get CE credit for watching recorded sessions of our series PubMed for Librarians. Now you can! Just follow these steps:
1. Watch a recording of PubMed for Librarians and complete the handout for the class.
2. Handout is provided in the video’s YouTube description and on our PML class page under Course Materials.
3. Email your completed handout to firstname.lastname@example.org.
4. We will send you a link to the class evaluation, which includes a code to use for 1.5 hours of CE credit from the Medical Library Association.
We are so excited to bring you another way to keep up to date with PubMed, on your own terms! Happy watching!
TOXNET is a suite of toxicology databases from the NLM. We’re prepping for some upcoming instruction on TOXNET ourselves, and wanted to share something we found today. This article is indexed in PubMed and the full text is freely available. What’s more, it’s written by project scientists at the Specialized Information Services division of NLM. The TOXNET experts!
On to the reading!
Health effects of toxicants: Online knowledge support.
Wexler P, Judson R, de Marcellus S, de Knecht J, Leinala E.
Life Sci. 2016 Jan 15;145:284-93. doi: 10.1016/j.lfs.2015.10.002. Epub 2015 Oct 24.
- Outlines all of the databases in TOXNET
- Discusses National Library of Medicine (NLM) and its Toxicology and Environmental Health Information Program, the United States Environmental Protection Agency (EPA), and the Organisation for Economic Co-operation and Development (OECD)
- Includes reading list of related publications about toxicology databases
Want to know more, but hate to read?
Health science librarians are invited to participate in a rigorous online biomedical and health research data management training course, sponsored by the National Library of Medicine (NLM) and the National Network of Libraries of Medicine Training Office (NTO). The course provides basic knowledge and skills for librarians interested in helping patrons manage their research data. Attending this course will improve your ability to initiate or extend research data management services at your institution. Familiarity with the research lifecycle is recommended but not required.
The major goal of this course is to provide an introduction to data issues and policies in support of developing and implementing or enhancing research data management training and services at your institution. This material is essential for decision-making and implementation of these programs, particularly instructional and reference services. The course topics include an overview of data management, choosing appropriate metadata descriptors or taxonomies for a dataset, addressing privacy and security issues with data, and creating data management plans.Course Components
The online asynchronous component of the program is 8 weeks from January 8 – March 2, 2018. The format includes video lectures, readings, case studies, hands-on exercises, and peer discussions. Expect to spend up to 4 hours each week on coursework. Participants will be assigned a mentor, who will be available to guide and advise throughout the course and in the completion of a Capstone Project.
Between the end of the online component and the Capstone Summit, participants will complete a Capstone project, demonstrating improved skills, knowledge, and ability to support data management services at their institution. The experience will culminate with a Capstone Summit, to be held on April 10-11, 2018 at NIH in Bethesda, Maryland. Each participant will receive up to $900 to support travel to the Capstone Summit. At the Summit, participants will have the opportunity to share their Capstone projects, network with experts and each other, meet with NLM leaders in data science, and learn about cutting edge NIH data initiatives.CE Credits
Participants who complete all modules, the Capstone Summit, and the course evaluation will receive MLA CE credit (exact number of hours to be determined). No partial CE credit is granted.Instructors
The primary instructor is Shirley Zhao, MSLIS, MS, Data Science Librarian from the Spencer S. Eccles Health Sciences Library, University of Utah.
Each module will be co-taught by a practicing data librarian.Who can apply?
- Applications are open to health science librarians in the United States.
- Applicants will be accepted from libraries currently looking to develop or enhance research data management training and services.
- A letter of institutional support is required. See application instructions below.
- Enrollment is limited to 40 participants.
There is no charge for participating in the program. Participants will receive a stipend of up to $900 to cover travel costs to the Capstone Summit. Additional travel costs must be covered by the individual or their institution.Important Dates
- Application deadline: November 8, 2017
- Notifications: Week of December 4, 2017
- Online Course: January 8 – March 2, 2018
- Capstone Summit: April 10-11, 2018
- Name and Contact Information
- Current Role/Title
- Place of Employment
- Briefly describe your current experience or interest in research data management and why you would like to participate in this training.
- Briefly describe the current status of research data management services at your library, including any barriers to implementation.
- This training will have been worthwhile to you and your institution if…
Please fill out the online Application Form, and upload a PDF of your current CV and your letter of institutional support. The letter of institutional support must be from your supervisor and address the following:
- time for participation in online course and Capstone Summit;
- the library’s commitment to or plans for adding or enhancing research data management services.
Please submit your application via the online form by November 8, 2017:
Contact NTO at email@example.com
Join the NNLM Training Office (NTO) for a free, online class to discover TOXNET and other National Library of Medicine environmental health databases through videos, guided tutorials, and discovery exercises.
The class is taught online, over a 6 week period, in 13 independent units. Complete only the units that interest you; there is only one required unit.
What are the dates of the class?
November 6, 2017 – December 18, 2017
Visit this URL to register:
What is TOXNET?
TOXNET is a freely available suite of databases from the National Library of Medicine covering hazardous chemicals, environmental health, toxic releases, chemical nomenclature, poisoning, risk assessment and regulations, and occupational safety and health.
What do we mean by Independent Units?
There is only one required unit, Introduction to TOXNET, all the other units are optional to complete.
Which databases are covered?
TOXLINE, ChemIDplus, TRI, TOXMAP, Hazardous Substances Data Bank (HSDB), IRIS, Haz-Map, Household Products Database, LactMed, WISER, CHEMM, REMM and the Drug Information Portal.
Who should take the class?
Health sciences librarians, public health and environmental science professionals.
How much time will the class take?
You will work on your own time over a period of 6 weeks to complete the units that are of interest to you. There is one required unit; the remaining units are optional. This class is offered for variable MLA Continuing Education credit. Each unit carries anywhere from 0.5 to 2.0 credit hours, for a total of up to 12 hours. Credit will not be awarded for partial completion of a module. Total credit awarded will be based on completed units.
What happens during the class?
This course is offered asynchronously through Moodle; you will work at your own pace. Each unit consists of guided interactive tutorials AND/OR tutorial videos, and discovery exercises. Instructors will be available to answer questions and provide assistance throughout the course.
Visit this URL to register:
Are you an information professional experienced in research data management? Are you eager to share your knowledge with others and help expand the community of data librarians? The National Network of Libraries of Medicine Training Office has several opportunities for you to contribute to shaping a new training experience specifically for librarians.
Biomedical and Health Research Data Management Training for Librarians is an 8-week online class with engaging lessons and practical activities, starting in January 2018. Students will complete a capstone project at the end of the course and the experience will culminate in a Capstone Summit at NIH on April 10-11, 2018. A short description of the whole program can be downloaded here.
Modules for the course may include, but are not limited to the following core research data management (RDM) areas:
- Data Lifecycle and RDM Overview
- Data Documentation
- Data Wrangling
- Data Standards, Taxonomies, and Ontologies
- Data Security, Storage, and Preservation
- Data Sharing and Publishing
- Data Management Plans
- RDM at Your Institution
We are looking for experienced data librarians to participate in this project as module reviewers, co-teachers, and/or mentors. You may (and are encouraged to) apply for more than one role, and for more than one module.
Reviewers: Critique module content, test exercises, make suggestions, add resources.
Deliverable: written report of findings (due November 30, 2017).
Co-Teachers: Assigned to one or more modules. Work with course facilitator to create a case study related to module topic (due November 15). Provide feedback on student assignments and answer questions for your module(s) in a timely manner during the course (January – March 2018).
Deliverables: Case study by deadline, written report of suggestions for class improvement (due April 2, 2018).
Mentors: Participate in class discussions, sharing expertise as needed, during the course (January – March 2018). Provide at least 2 mentoring sessions to each assigned student (4-5) for completing the Capstone project, attend and participate in the Capstone Summit.
Deliverables: written report of experience as mentor, suggestions for program improvement and sustainability of project.
Paid $1250, and travel support to Capstone Summit up to $1250.
All reviewers, co-teachers, and mentors will be required to submit a W-9. Those receiving $1000 or more will also be required to complete a contract with the University of Utah.Applications
Please submit your application via the online form by October 20, 2017:
- Current Role/Title
- Place of Employment
- Please briefly describe your area(s) of interest, research, or primary expertise in data management.
- Please summarize your qualifications to serve as a content reviewer, co-teacher, and/or mentor for this research data management class.
- Indicate which modules you would like to serve as a content reviewer and/or co-teacher.
- Would you like to serve as a mentor for 4-5 students in completing the Capstone Project?
- Curriculum vitae (attachment)
Please contact Shirley Zhao, Training Development Specialist.
The NTO is hiring an instructional technologist. The position is based in Salt Lake City, Utah. It is a three-year appointment. More information, salary and application info below.
The faculty and staff of the Spencer S. Eccles Health Sciences Library (EHSL) at the University of Utah invite applications for an Instructional Technologist for the National Network of Libraries of Medicine Training Office (NTO). The NTO supports the training and educational missions of the National Network of Libraries of Medicine (NNLM) by delivering high-quality, innovative training to diverse audiences nationwide in support of the effective use of NLM information products and services.
The NNLM has embarked on a 3-year pilot program with the NIH All of Us Research Program to stimulate and facilitate community engagement and participant support through the NNLM, including developing community based participatory programming for geographic areas. The Instructional Technologist promotes the use of technology-based resources in learning and teaching and provides consultation, instruction, and assistance to a national network of educators and librarians in the editing, design, and production of learning objects, classes and curricula in support the All of Us Community Engagement program. Salary: $31,600 – $52,000 /yr
PubMed Health provides information for consumers and clinicians on prevention and treatment of diseases and conditions. Can you find answers to these questions?
Can you find:
a. The source of this month’s featured review?
b. A book about understanding health statistics?
c. The amount of clinical effectiveness information added/updated in the last week? Last month?
d. Information for clinicians about using mushrooms to treat cancer?
HINT: you’re on your own for this one! (Just kidding.)
PubMed Health specializes in reviews of clinical effectiveness research, with easy-to-read summaries for consumers as well as full-text technical reports. Clinical effectiveness research finds answers to the question “What works?” in medical and health care. Try PubMed Health for information on the prevention and treatment of diseases and conditions, for clinicians and patients.
The National Library of Medicine recently awarded NTO an administrative supplement for Biomedical and Health Research Data Management Training for Librarians. The aim of this project is to improve the competency of information professionals in the area of biomedical and health sciences data management through a rigorous educational experience. In addition to supporting researchers who need to meet the data management plan requirements of funding agencies, these information professionals will be able to support reproducible research, drive discoveries through reusing data or identifying linkages between disparate data sources, and derive new roles as the field progresses. Participants will also be ready to take next steps to support data science, which includes data analysis and data visualization.Why do we need this?
While there are many resources available to learn about data management principles and services, there is a need for a comprehensive training program for information professionals that brings together the best of these resources and enhances them with meaningful, practical activities focused on biomedical and health research data. The training program will build on existing resources and transform the learning experience from a largely self-directed, isolated endeavor to an organized program supported by experienced peer mentors and culminating with a capstone project to demonstrate improved skills and knowledge.Who is working on this project?
Shirley Zhao, MSLIS, MS is the Data Science Librarian at Spencer S. Eccles Health Sciences Library and is the training development specialist for this program. Shirley brings deep experience in developing and teaching workshops to support data science researchers. She recently developed and taught a course in research reproducibility for a data science for health sciences summer school program at the University of Utah. Components of this course encompassed best practices in data management, storage, preservation and dissemination, which will inform the development of this program. Shirley was previously the Physical Sciences Librarian at Dartmouth College and holds a BA (mathematics major, chemistry minor) from Smith College, a MSLIS from Long Island University, and a MS (mathematics) from New York University. More information about Shirley can be found on her website: https://shirl0207.wordpress.com/. Follow her on Twitter @zhao_shirley or email her directly at firstname.lastname@example.org.
Stay tuned for more details and to find out how to apply for this new training experience.
This week I’m going to let Sarah Cooper, a writer and comedian, fill this space. She’s written a book called 100 Tricks to Appear Smart in Meetings. It’s funny! She’s posted 10 of her tricks here. She also has a website called the Cooper Review, which says it’s THE MOST IMPORTANT BUSINESS WEBSITE IN THE WORLD. I think that’s supposed to be funny too.
September is National Preparedness Month. Here is a list of recent disaster guides resources from around the National Library of Medicine.
DIMRC – Disaster Information Management Resource Center
The Disaster Information Management Resource Center is a portal to disaster health information. It includes fact sheets, full text governmental reports, mobile apps for emergency responders, the DISASTERLIT database, and community training programs for many major disasters. All DIMRC topics provide access to curated, reliable information from vetted federal, state, and local governments and organizations. Newly updated topics in September include: Hurricanes of 2017, Fires and Wildfires, and Coping with Disasters, Violence and Traumatic Events.
DISASTERLIT is a database of disaster-related grey literature that lives inside of DIMRC. It includes interviews, tools, guidelines, governmental reports and more, much of it full-text. Search DISASTERLIT in addition to PubMed for a current picture of disaster-related literature. A scan of their recent publications include an open data geospatial platform for Hurricane Irma, an Opioid Action Plan template, and a CDC guideline for treating tetanus in hurricane-affected areas.
Around the country, our Network of Regional Medical Libraries have gathered regional information and disaster support for libraries.
Southeastern / Atlantic Region (SEA)
Emergency Preparedness & Disaster Recovery Resources – disaster response plan consultations available for regional network members.
Disaster Information Resources for SEA Network Members
South Central Region (SCR)
Disaster Information Resources – Harvey Disaster Relief and funding
Harvey Has Passed, But Risks Still Remain – SCR Blogadilllo post:
Pacific Northwest Region (PNR) –
Disasters Don’t Plan Ahead. You Can – 4 week preparation program.
Greater Midwest Region (GMR)
Bringing Health Information to the Community (BHIC) Blog
BHIC blog posts on emergency preparedness
Most days you probably don’t think about it. I know I don’t think about it. But after Hurricane Harvey hit land in Texas, which lead to power outages and then several explosions at a chemical plant outside Houston, you may be asking yourself: What chemicals are in my back yard?
The Environmental Protection Agency (EPA) and the National Library of Medicine (NLM) have tools to answer your questions. Both the Toxics Release Inventory (TRI) and TOXMAP can help answer your questions. NLM’s TOXNET suite of databases includes TRI and TOXMAP. All the data behind these two tools comes from the EPA.
What is the Toxics Release Inventory?
TRI tracks the management of certain toxic chemicals that may pose a threat to human health and the environment.
U.S. facilities in different industry sectors must report annually how much of each chemical is released to the environment and/or managed through recycling, energy recovery and treatment (A “release” of a chemical means that it is emitted to the air or water, or placed in some type of land disposal). The information submitted by facilities is compiled and helps support informed decision-making by companies, government agencies, non-governmental organizations and the public.
There are currently over 650 chemicals covered by the TRI Program.
Why was the TRI Program created?
The TRI Program was created as part of a response to several events that raised public concern about local preparedness for chemical emergencies and the availability of information on hazardous substances.
On December 4, 1984, a cloud of extremely toxic methyl isocyanate gas escaped from a Union Carbide Chemical plant in Bhopal, India. Thousands of people died that night in what is widely considered to be the worst industrial disaster in history. Thousands more died later as a result of their exposure, and survivors continue to suffer with permanent disabilities. In 1985, a serious chemical release occurred at a similar plant in West Virginia.
In 1986, Congress passed the Emergency Planning and Community Right-to-Know Act (EPCRA) to support and promote emergency planning and to provide the public with information about releases of toxic chemicals in their community. Section 313 of EPCRA established the Toxics Release Inventory.
What types of industries are included in TRI?
Facilities that report to TRI are typically larger facilities involved in manufacturing, metal mining, electric power generation, chemical manufacturing and hazardous waste treatment. Not all industry sectors are covered by the TRI Program, and not all facilities in covered sectors are required to report to TRI. See the Basics of TRI Reporting for more information.
TRI Chemical list: https://www.epa.gov/toxics-release-inventory-tri-program/tri-listed-chemicals
What’s in your neighborhood? TOXMAP is the place to look.
When you arrive at TOXMAP, choose Zoom to Location and then enter your zip code or an address. A navigation tool will appear on the left and blue dots will show TRI sites in the zip code area on the map.
Why is 2015 the most recent data?
TRI is always behind 1-2 years. Businesses have approximately a year to report for the previous year and then all the TRI data is cleaned up and then finally released to the public. TOXMAP currently shows 2015 data, but EPA has preliminary data for 2016:
ClinVar, MedGen, GTR, what do these odd words have in common? They are all NCBI databases that connect genetics to human health effects. NTO will host a webinar with NCBI Scientists on Wednesday September 20 where we’ll discover how to use these databases. Register for the class to learn more, or browse them yourself using the links below.
ClinVar: aggregates information about genomic variation and its relationship to human health.
Try this: Search for sickle cell anemia to see which genes are involved
MedGen: Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution.
Try this: Search for sickle cell anemia to find out characteristics of this blood disorder
GTR: Centralizes genetic test information which is submitted by providers. Records include the test’s purpose, methodology, validity, evidence of the test’s usefulness, and laboratory contacts and credentials
Try this: Search for sickle cell anemia to discover tests, conditions, genes and laboratories studying this disorder
Every summer I look forward to attending the Summer Institute of Distance Learning and Teaching conference (SIDLIT: pronounced Side Light) at Johnson County Community College in Overland Park, KS*. “The conference is an exchange of information and expertise between faculty and staff involved or interested in instructional technology, online instruction, and distance education.” Most attendees are from the Kansas/Missouri area.
I always learn something and I’d like to share some of the freely-available tools that I learned about this year. I’ve tried all of the tools below. These tools will be added to our Teaching Resources & Tips page.
Wink: a screen-casting program that lets you record short screencasts.
Office Lens: This app trims, enhances and makes pictures of whiteboards and documents readable. Office Lens can convert images to editable Word and PowerPoint files too.
Bubbli: bubbli™ is an app for making dynamic spherical photos called bubbles. Honestly, I don’t have a use for this app, but it seems cool. Do you have a use for it? Let me know in the Comments.
What the font? When you see a font in use and want to know what it is, you can submit an image to What The Font to find the closest matches in their database.
appear.in: I really like this tool. It’s free and very easy to use for online meetings up to 8 people. Create a URL for the room and you’re ready to go. If you want to use the room again, register and you’ll be able to use the same URL. Screen sharing, web cam for 8 people at once and audio capabilities.
*Yes, I work for the University of Utah, but I live in Kansas.
Got 40 minutes? Our most recent PubMed for Librarians series just wrapped up, and we’ve just posted the most recent webinar on our YouTube account
This webinar covers creating a My NCBI account, managing and manipulating settings in your My NCBI account, identifying available filters in your My NCBI account, and how to create a custom filter.
Need a live version? The next round of live PubMed for Librarians begins September 5, 2017.
Do you use UMLS (Unified Medical Language System)? Are you looking for practice guidelines? Watch this short video to see how to use UMLS to search for practice guidelines in the National Guideline Clearinghouse (NGC).
If you’d like to learn more about UMLS, visit this website: UMLS