May 2018 Library News Round-up: PubMed Data Filters, Data Management Webinars, and Staying Up-to-Date with MLA 2018

After a few exciting weeks of profiling incredible librarians from around the world, I’m relieved to return to familiar territory with a good ol’ fashioned news round-up.  For May 2018, I want to highlight a few interesting new data resources for librarians from National Library of Medicine (NLM) and the National Network of Libraries of Medicine (NNLM), including new data filters on PubMed and PubMed Central and an upcoming webinar series about research data management.  Also, there’s the equivalent of the Super Bowl for medical librarians coming up next week, the annual Medical Library Association (MLA) conference, this year in Atlanta, GA.  I unfortunately won’t be there in person this year, but I’ll follow along through Twitter and blogs.

PubMed Data Filters

On April 24, 2018, the NLM Technical Bulletin announced the ability to filter PubMed and PubMed Central search results to view articles that have associated data sets.  The NLM Technical Bulletin article describes the following data-related filtering options:

  • PubMed
    • Use  data[filter] to find citations with related data links in either the Secondary Source ID field or the LinkOut – Other Literature Resources field.
Data filter on PubMed.

Availability of related data sets is an important step towards improving reproducibility and transparency for research articles.  Hopefully these data-related filters will eventually be more prominently featured in the PubMed filter options (such as in the side-column list of filter options beside search results).

NNLM Research Data Management Webinar Series

The NNLM Research Data Management (RDM) webinar series is kicking off June 14, 2018, 2-3pm ET, with the free webinar Research Data Management Services: Beyond Analysis and Coding.  The presentation by Margaret Henderson, a Health Sciences Librarian at San Diego State University Library, will “show you how to start RDM services, even if you don’t feel confident about your statistical skills or knowledge of R.”

The NNLM RDM webinar series will be an ongoing bimonthly webinar series, with the aim to “support RDM within the library to better serve librarians and their institutional communities.”  I’m personally very excited about this series, since I’ve recently become interested in finding free online training resources related to research data management that are more geared towards information professionals (and less heavily focused on programming skills).  Once again, NNLM delivers with incredibly useful (and FREE!) online professional development resources.

MLA 2018 Resources

I won’t be at the annual MLA conference this year unfortunately (it was an incredible experience last year), but I can avoid fear of missing out (FOMO) thanks to a few helpful resources:

  • Twitter: I’ll definitely be following the #mlanet18 hashtag to learn some of the great insights other medical librarians are taking away from MLA speakers, sessions, and posters (especially the official MLA ’18 Tweeters).
  • Blogs: I’ll check the blog post summaries from the MLA’18 Blog Correspondents.

Have a great time if you’re going to MLA 2018, and remember to Tweet!


3 Places to Find Pre-Recorded Webinars for Librarians

I prefer to do most of my continuing education through online methods, like self-paced online courses and webinars.  Live webinars are a great opportunity to interact with other professionals interested in a common topic and ask instructors questions, but some days I may be too busy to take an hour at a specific time to attend a live webinar.  In those circumstances, I always appreciate when the organization hosting the webinar later offers a recorded version of the training that they post online.  Many organizations (including national networks of libraries like NNLM and FDLP) offer recorded archives of their webinars, and these webinar archives can be a fantastic source of on-demand training.

Here are three library organizations that offer webinar archives featuring a wide range of training topics, from marketing and data visualization to finding government and health information resources:

Watch a recording of Midday at the Oasis: Good Design for Data Visualization at the NNLM YouTube channel.
    • Federal Depository Library Program (FDLP) Academy: Choose the “View past webinars” option on the FDLP website to view a list of past Depository Library Community Webinars, Federal Agency Webinars, FDLP and C&I Webinars (related to cataloging and indexing), and GPO’s Federal Digital System (FDsys) and govinfo Webinars.  You can choose to download the slides and completion certificates for webinars and watch a recording of the WebEx presentation.  Example: View another webinar related to data visualization and infographics, with the 35-minute presentation Telling your Story with Data.
    • WebJunction: The WebJunction site from OCLC offers recorded webinars that can be accessed for free by all library workers and volunteers.  Users need to register to access the recorded webinars and self-paced trainings that cover topics ranging from social media, marketing, and outreach to collections development and organizational management. Users can also download slides, handouts, and chat transcripts from the webinars and find links to related resources. Example: Watch yet another webinar related to data visualization: Data Visualization for the Rest of Us: A Beginner’s Guide (1 hour).

Even if you just have thirty minutes to spare during the workday, you can use these webinar archives to find interesting learning topics and watch high quality trainings anytime.

Testing Free Diagramming Software…(by creating decision flowcharts for my cats)

Librarians can use diagramming tools to create professional flowcharts for use in presentations, to illustrate steps for anything from electronic journal management to IT troubleshooting, or to chart the complex inner decision making processes of their pet cats.  I decided to take on this Herculean challenge of charting the rich inner lives of my cats Chloe (the dumb one) and Vlad (the twitchy one) while also trying to identify a quick and easy free diagramming tool.  I’ve usually just used the SmartArt features in Microsoft Word or PowerPoint to create any flowcharts I needed for papers or presentations, but the chart formatting options in Word/PowerPoint are very limited and clunky.  I’ve never used Microsoft Visio, which seems to be the most popular subscription-based diagramming tool.

I first started by finding a few helpful articles reviewing free and low-cost diagramming tools:

I ultimately settled on testing, since it is completely free (at least for the average user), fully web-based (so I didn’t need to download any apps), and easily integrated with Google Drive (so I could save my diagrams easily to my Google account).  The interface for was easy and intuitive, and I was able to make two simple but fully customized flowcharts in about 45 minutes.

A few of the features on that I particularly liked:

  • Diagrams are automatically sized to US-letter paper size (8.5 by 11 inches) for easy printing.
  • You can export the diagrams in a variety of formats, including JPEG, PNG, PDF and more.
  • You can easily insert images or even add an image as the background for the diagram.
  • The gridlines in the work area are helpful for keeping the connector arrows straight.
  • You can easily choose a direction arrow beside a text box in the flowchart to automatically create a new clone text box and connector arrow to quickly expand your chart.

With, I carefully charted the complicated variables of my cats’ daily choices:

Chloe decision tree
Chloe (the dumb one)
Vlad's Decision Treejpg
Vlad (the twitchy one)

New Database Linking Research Articles to Grants, Patents, and Clinical Trials: Exploring New Dimensions

While browsing Twitter last week, I came across an article in Nature describing an interesting new database called Dimensions.  The article “Science search engine links papers to grants and patents” by Richard Van Noorden explains how “Dimensions not only indexes papers and their citations, but also — uniquely among scholarly databases — connects publications to their related grants, funding agencies, patents and clinical trials.”  The database, launched January 15th by Digital Science, offers both free and subscription versions.  I wanted to explore in a bit more detail the different versions of Dimensions, learn about the data coverage, and try a few test searches in the free version of the database.

Dimensions Versions

The Dimensions website offers a comparison chart of the features for the different versions of the database (Dimensions, Dimensions Plus, and Dimensions Analytics).

  • Dimensions: The free version of the database offers access to more than 89 million publications, with information on linked grants, patents, and clinical trials.  This version of the database also includes 20 million researcher profiles (currently in beta) and includes citation based metrics and article-level Altmetric data.
  • Dimensions Plus: This subscription version of the database includes “fully interlinked database with publications, grants, patents, clinical trials with more than 124m records”, access to additional search, filter, and data aggregation options, and access to the Dimensions Search API.
  • Dimensions Analytics: This subscription version includes all features of Dimensions Plus, as well as a reviewer identification tool, portfolio reporting functionalities, additional research classification systems, and private instance or custom integration of the database with client systems.

Dimensions Coverage

Dimensions provides documentation on its data sources and an overview of how the data is cleaned, organized and linked.  Here are a few highlights from the document:

  • Dimensions uses full-text indexing, research categories based on New Zealand Standard Research Classification (ANZSRC) system (and applied at an article level using AI/machine learning), institution disambiguation using the GRID database, and author disambiguation (using ORCID data) to improve retrieval.
  • Publication metadata comes from “openly-available databases together with those with permissive content licenses, such as PubMed, PubMed Central, ArXiv and CrossRef. “
  • Grant data was originally collected by “ÜberResearch (one of the six businesses in the Digital Science portfolio creating Dimensions)” in an effort to create a grant database, and the grant data has now been integrated into the broader Dimensions database.  The documentation also states:

    Grant data should not be taken as a complete view on all research related funding, as we pointed out in a recent report. It covers project-based funding from different types of funders (government, multinational, charities etc.)

  • Dimensions includes Altmetric data for each article, displayed on the article details page.
  • Clinical trials data comes from eight registries, including
  • Patent data is provided by “the Digital Science portfolio company IFI Claims” and currently covers about nine patent authorities.

Testing the Free Version of Dimensions

I did a quick test search on the free version of the Dimensions database, where you can search across about 89 million publications. Users can conduct a keyword search across full data or title/abstract only, or the user can paste in a document abstract to find similar articles. No advanced search fields seem to be available in this free version, although the help center does describe how basic Boolean operators, parentheses and quotes can be used in the keyword search form.

Search results list on the free version of Dimensions.

The results list includes filtering options like publication year, researcher name, field of research, publication type, source title, journal list, and open access.  Results can be sorted by relevance, publication date, RCR, citations, or Altmetric Attention Score.

An “Analytical Views” tab on the right side of the results list displays top fields of research, a graph of publications by year, and top source titles.

Analytical Views beside Dimensions search results.

After selecting a publication title from the results list you can view:

  • Citation and abstract data.
  • Publication references.
  • Supporting grants (no links to grant records provided in free version of database).
  • Publication citations.
  • Patent citations (no links to patent records provided in the free version of the database).
  • Linked clinical trials (no links to clinical trial records provided in the free version of the database).
  • Publication metrics (total citations, recent citations, field citation ratio, relevant citation ratio, Altmetric score).
  • Assigned research categories.
  • Links to external sources, such as publisher sites and PubMed.
Publication metrics, research categories, and external source links for an article on Dimensions.

Options to view the PDF (if open access) and to add the article to your library (if logged into a ReadCube account) are also available on the article details page.

Final Thoughts

I’m always excited to see linked research objects, and Dimensions takes a large step forward with linking a variety of research output, ranging from publications to patents and clinical trials. I hope government-funded databases like PubMed and PubMed Central can take a pointer from Dimensions and eventually include more linked content, such as links to related USPTO patents and applications, clinical trials from ClinicalTrials,gov, related federal grant information, and access to full research data sets.

New Year, New Learning Goals

Image from Pixabay.

I started this blog a little less than a year ago, mainly to track professional development activities, but I’ve also found a space to explore other library-related interests like open access digital resources and intellectual property.  I’ve also occasionally gone a bit off topic with cats in libraries and my obsession with the Internet Archive digital collections.

So to get back on topic a bit, I want to take a look back at what professional development goals I’ve met this year and list a few new learning goals for 2018.  I’m happy to say that I’ve met a number of my learning goals I set for 2017:

The one learning goal I didn’t make much progress on was learning to code with R.  I’ve done a bit of practice with creating very basic graphs using the ggplot2 package, but I’d like to complete an actual online course about using R.

So there’s my first learning goal for 2018 – complete an online course that offers an introduction to R.  I’m thinking I’ll probably try to take the course Introduction to R for Data Science from edX (which is free but costs $99 for a certificate).

My other main goal for 2018 is to learn more about research data management (RDM) strategies for health science libraries.  I hope to take one of the courses or workshops recommended by NNLM to learn more about RDM strategies and tools.  I may start with the Research Data Management for Health Sciences Librarians training developed by librarians at the NYU Health Science Library.

I’ve got a few goals for 2018 in place…I guess I better start learning!


How Libraries are Using GIS Mapping

I first learned about geographic information system (GIS) mapping on the Community Health Maps blog from the National Library of Medicine, which offers training materials to teach community organizations how to create low-cost maps related to public health. GIS mapping is used in many creative ways for public health purposes (such as identifying health disparities or visualizing the locations of dangerous environmental hazards). GIS seems like an incredibly useful method for displaying and exploring data on local, national, and international levels, so I wanted look into how academic and public libraries are involved with teaching and using GIS.

Libraries Teaching GIS

Many academic libraries offer GIS mapping services, such as GIS software access, in-person training for students and faculty, and LibGuides that explain the basics about GIS.  For example:

  • At Duke University, the Brandaleone lab for Data and Visualization Services offers access to mapping software (like ArcGIS, QGIS, Google Earth Pro, and more).  Their GIS in the Library webpage offers tips about library workshops and academic courses on GIS and where students can find additional help related to data visualization and GIS.
  • John Hopkins University offers a LibGuide on GIS and Maps, access to ArcGIS software for students/staff, and their GIS and Data Services staff also offer training and consultation on GIS.

The only public library online resource I was able to find related to GIS was the Geographic Information Systems (GIS) Online Resources page from New York Public Library.  This online guide provides links to data sources, free software, lectures on GIS, and even NYC online maps.

Public Libraries using GIS for Assessment

While academic libraries seem to focus more on teaching GIS mapping to students and faculty, public libraries often use GIS mapping for assessment of services, facility use, and collection development.  The article Using GIS to Assess Public Libraries by Dilnavaz Mirza Sharma at Public Libraries Online discusses how public libraries “have embraced GIS as a tool for evaluating usage, collection development, and community impact by capturing GIS data to provide evidence of the library’s function in the community serviced.”  The article describes a case study “of how GIS maps were used to identify public library locations in Chicago that would be ideal for providing consumer health information materials to underserved populations.”

Interactive Maps as Exhibits

Some academic and public libraries also use GIS mapping to create interactive maps shared on their websites as digital exhibits or tools to explore useful data sets, such as:

  • The University of South Carolina library website offers a searchable map of locations from the 1956 Negro Travelers’ Green Book.
  • The College of Information Studies at the University of Maryland has created an interactive mapping tool that allows users to search for and view all libraries within a selected neighborhood, along with related local data on demographics, economics, education, health, and responses from local libraries from the 2013 and 2014 Digital Inclusion Survey.
Interactive mapping tool to explore Digital Inclusion Survey data, created by the University of Maryland College of Information Studies.
  • Brooklyn Public Library offers a literary map on its website, exploring local landmarks and locations related to children’s literature, fiction, and non-fiction.

There are so many potential applications for GIS mapping in both academic and public libraries, from workshops to teach students how to use GIS to interactive digital exhibits that allow users to explore data sets at a local level.  I hope in the coming year to learn more about use of GIS software, maybe using the Community Health Maps training materials.

MAC-MLA 2017 – Themes, Resources, and Opportunities

The Mid-Atlantic Chapter of the Medical Library Association (MAC-MLA) 2017 Annual Meeting was held in Staunton, VA from October 21-24, and the meeting was a whirlwind of powerful, innovative ideas shared through presentations, posters, and even live-Tweeting.  Here’s a quick rundown of my key takeaways from the meeting, including important themes highlighted during the keynote presentations, interesting resources, and professional development opportunities from MLA and the National Network of Libraries of Medicine (NNLM).


The overarching theme of this year’s meeting was “facing your fears” (yes, it’s close to Halloween), and each of the four keynote speakers discussed different topics related to librarian, patron, and researcher fears:

  • Impostor Syndrome – Do you ever feel like you’re an impostor in your profession?  Dr. Michael Southam-Gerow of Virginia Commonwealth University (VCU) discussed how anyone (but especially women and students/professionals from minority populations) can suffer from “impostor syndrome/impostor phenomenon”, where they worry about the validity of their achievements in their chosen field. Dr. Southam-Gerow also discussed techniques to overcome these “impostor” feelings.  The slides from the presentation are available here.
  • Open Science – Dr. Maryrose Franko of the Health Research Alliance (HRA) presented on addressing funders’ fears about open science.  Dr. Franko outlined common fears about open science (cost, administrative burden, and burden/uncertainty for researchers) and described how HRA, the Center for Open Science, and other partners are working to promote and strengthen open science initiatives like open access publications, data sharing, and preregistration.  Her presentation slides can be found here.
  • Health Justice and Health Literacy – Dr. Beth St. Jean of the University of Maryland, College Park gave an introduction to health justice and its relationship to health literacy, health outcomes, and information avoidance. She also discussed strategies to help information professionals improve health literacy among patrons and decrease information avoidance.  Her presentation slides can be viewed here.
  • Critical Librarianship – Derrick Jefferson of American University provided an overview of critical librarianship, which “seeks to be transformative, empowering, and a direct challenge to power and privilege.” Jefferson provided examples of critical librarianship in action and resources to learn more about the movement through and the #critlib on Twitter.  Jefferson’s presentation slides can be accessed here.


These are a few of the interesting new resources I learned about at the meeting:

  • NNLM RD3 – This is a fantastic website created by NNLM to help health science librarians learn the fundamentals about data science and data management.  (I also wrote about this resource in my MLA 2017 takeaways post.)
  • PubMed Labs – Use this test site from the National Library of Medicine to explore new features and tools that may be added to PubMed, and provide direct feedback to the NCBI team.
  • Open Science Framework (OSF) – OSF is a “free, open source service of the Center for Open Science“.  Researchers can collaborate and manage projects through OSF, including storage of data and files, access control, and the ability to link third party services to the platform. Users can also search through collections of pre-prints, project registrations, and posters/presentations from conferences.
  • NEJM Resident 360 – This online resource from the Massachusetts Medical Society (publishers of the New England Journal of Medicine) can be used by residents and medical students to participate in discussions, find career and study tips, and find interesting learning resources from NEJM.  The  Learning Lab, Resident Lounge, Career, and Discussions sections are free to explore, while the Rotation Prep section is only accessible through NEJM institutional or individual subscriptions.
  • Systematic Review Tools – I learned about several interesting free systematic review resources from the poster “From screaming to screening: An evaluation of free systematic review software” by Elizabeth Moreton,  Jamie Conklin, Leila Ledbetter, Rebecca Carlson McCall, and Jennifer S. Walker. Users can search for systematic review software through the Systematic Review Toolbox, and free systematic review tools that may be useful to try include Colandr and Rayyan.
  • Burnout Libguide – During the paper presentation “Burnout, Professional”[MeSH]: A Study on the Subject of Medical Librarian Burnout” by Megan N. Kellner, Associate Fellow, National Library of Medicine & Elizabeth O. Moreton, Nursing Liaison Librarian, UNC Chapel Hill, I learned about this very useful Libguide for medical librarians to test if they’re experiencing burnout and resources to prevent burnout.


Updates from MLA and NNLM included training opportunities for health science library professionals: