Bioinformatics with NNLM is a BLAST!

Image from Pixabay.

I’m currently about six weeks into a 16-week online class from the National Network of Libraries of Medicine (NNLM), Bioinformatics and Biology Essentials For Librarians: Databases, Tools, and Clinical Applications, and so far:

  • I’ve gotten a very helpful basic overview of genetics, bioinformatics, and molecular biology concepts,
  • I’ve thought about the possible roles librarians can play in bioinformatics, and
  • I’ve started exploring some of the bioinformatics tools and resources from the National Center for Biotechnology Information (NCBI).

I was excited to take this class when it started at the end of January, especially because I recently changed jobs and now work mainly with clinical researchers, providing reference and instructional services.   I want to quickly get up to speed on topics like bioinformatics and research data management, so I can provide better training opportunities and more knowledgeable reference services to patrons.  My learning goals for the year may have shifted slightly, but I’m still using one of the best (and currently free!) training resources I have available to me: the online courses offered through NNLM.

This bioinformatics class from NNLM, which I’m taking through the online learning management system Moodle, has directed me to a number of interesting free learning resources about genetics, molecular biology, and bioinformatics in many different formats, including interactive text-based courses, videos, and even interactive games and labs.  Here are a few of my favorites so far:


Libraries Promoting Their Public Domain Content

Artists, academics, and students often want quick access to images and other forms of media for use in projects, and anyone online may want an image to include on social media or in a blog post.  Normally, you’d need to worry about copyright restrictions and licensing fees when re-using images or media, but some content falls under the public domain.  According to Stanford University Libraries, public domain is defined as “creative materials that are not protected by intellectual property laws such as copyright, trademark, or patent laws. The public owns these works, not an individual author or artist.”  Works can fall into the public domain for a number of reasons: because the copyright has expired (in the US, works published before 1923 or if the copyright owner fails to renew the copyright), if the copyright owner purposely dedicates the work to the public domain, or if copyright law doesn’t cover that type of work.

How can you quickly find these works in the public domain, though?

Some major libraries have created portals to publicize their public domain digital collections, and these portals can be a helpful way to quickly find interesting images and media that can be freely shared and re-used without copyright restrictions.

  • Library of Congress (LOC): The LOC recently announced the creation of a  Free to Use and Reuse page, which “features themed sets of content (such as travel posters, presidential portraits, Civil War drawings) that are all free to use and reuse.”
“Free to use and reuse” digital collections from LOC.
Public domain collections highlighted from New York Public Libraries.
Albums from the British Library Flickr page.

If you want to learn more about finding public domain works, check the following guides from university libraries:

February 2018 Library News Round-Up

I’ve found a few interesting odds and ends from the websites and blogs I regularly check for library news, ranging from a new copyright search resource to a really, really neat online collection of medieval manuscripts from the British Library.

Before I go into list mode with the news items, I first want to highlight a great library news website that a coworker introduced me to: Library Technology Guides, a site run by Marshall Breeding.  I’ve added the news section of Library Technology Guides to my morning news check, since it lists daily announcements from major library service and database vendors.  The site also has a wealth of information about database/library service vendors, such as a database of library automation companies and a collection of guides related to industry trends and products.

Now on to library news that caught my eye from the past few weeks:

      • Farewell, PubMed Commons:  The NCBI Insights blog announced on February 1 that comments would no longer be accepted through PubMed Commons after February 15, and comments from PubMed Commons will no longer be visible after March 2.  PubMed Commons always seemed like a really interesting idea (allowing researchers to comment on PubMed articles), but it unfortunately sounds like usage of the feature was too low to justify (“comments submitted on only 6,000 of the 28 million articles indexed in PubMed”).
      • Virtual U.S. Copyright Office Card Catalog: In late January, InfoDocket described a new Virtual Card Catalog proof of concept website released by the Library of Congress (LOC), where users can browse through almost 18 million scanned images of cards in indexes from 1955-1970 and 1971-1977.  The site isn’t very practical for fast, easy searching, but it sure beats actually going onsite to the Copyright Records Reading Room.  I’ve written in the past about what a pain in the neck it can be searching for pre-1978 copyright registrations, so I’m very happy to see that LOC is finally making the digitized versions of the catalog cards available online (even if the viewing options are a bit clunky).  To celebrate, you can browse through Walt Disney copyright registrations from 1955-1970.
Exploring Walt Disney copyright registrations from the 1960s on the new Virtual U.S. Copyright Office Card Catalog.
    • Medieval Manuscripts Online at the British Library: Information Today posted an announcement that the British Library “made 50-plus rare medieval manuscripts and early print editions freely available via its Discovering Literature: Medieval resource”, including “the single surviving manuscript of Beowulf, the first complete translation of the Bible into English, an illustrated print edition of The Canterbury Tales, and the first English-language work written by a woman.”  You can also read fascinating articles analyzing the works, such as a look at Monsters and heroes in Beowulf and an incredible article describing the evolution of Old English.


Sir Gawain and the Green Knight c. 1400 from the Discovering Literature: Medieval resources on the British Library website.

So much library news (and amazing digital collections to explore), so little time.

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.

Gamification at Health Science Libraries

Image via Pixabay.

Last year I occasionally saw the term “Gamification” pop up on the American Libraries Magazine website, and I was immediately intrigued. I’ve heard of board games and video games used in library programming, but what in the world was gamification?  In the article “Engaging Students Through Gamification”, Tasha Squires describes how “gamification  takes a process or learning target and sets it in a gaming format.”  Squires goes on to describe how she and the other staff at a middle school library created a game where students earned points through challenges involving “critical thinking, collaborating to solve puzzles, interacting with teachers outside their normal purview, and creating original work such as book trailers and creative writing pieces.”  Gamification seems like an incredible tool for school and public libraries who work with children and teens to promote learning and reading in a fun, creative way.

Can gamification also be used by health science libraries in academic, government, or hospital settings for outreach and training purposes?

Gamification for Health Outreach and Medical Training

I used a quick search of PubMed to see if I could find any reviews on the use of gamification for health or biomedical purposes.  Many of the reviews I found illustrated how gamification can be used promote healthy habits and provide health information to patients, such as:

Other reviews described how gamification can be used for training of healthcare workers:

One of the most interesting examples of gamification used specifically in a health science library is described in the article “Courting Apocalypse: Creating a Zombie-Themed Evidence-Based Medicine Game”, where health science librarians at the University of Iowa created a zombie-themed “choose your own adventure” game to teach students evidence-based medicine skills.

Health science libraries can use gamification methods to provide health information to patients and training for medical students and healthcare staff in an entertaining, memorable way.

If you’d like to learn more about gamification, I’d recommend reading the article “An Introduction to Gamification: Adding Game Elements for Engagement” by Tara Brigham (full-text behind paywall), or watch the free training webinar from the National Network of Libraries of Medicine (NNLM), Education Games and Health Sciences.


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!


The Best Gift For the Holidays: Digital Collections

It’s two days before Christmas, and I’ve just found the best gift I could ask for: digital collections of old holiday postcards.  Here are three to brighten your holiday:

Greeting card from 1881, with cats!
Santa cards from New York Public Library collection.
A bright and merry Christmas : once we were not very good, but that was a long while ago, ca. 1900-1910

As an added bonus, also check out this collection of Christmas dining menus from University of Nevada Las Vegas.  It might just give you some fun ideas for Christmas dinners.

Have a happy and safe holiday season!