Pubmed is LIVE on Social Media – Hashtags of the Week (HOTW): (Week of July 21, 2014)

Pubmed Social Media Icons
PubMed Update: Social Media Icons Added. NLM Tech Bull. 2014 Jul-Aug;(399):b2.

Have you been straddling the fence deciding whether or not social media is “a thing” in healthcare? Well, maybe this will tip the balance. Pubmed now includes social media sharing icons at the article level, as shown in the image above. This is in addition to NIH’s own active life on social media. Unfortunately, when I was testing it out, every now and then what it shared was not the link to the article, but a link to the search strategy from which I found the articles. Hopefully, they’ll get that fixed, but usually it was good. Here’s what it looks like when sharing something to Twitter.

Pubmed Social Media Sharing Example: Twitter

In honor of this noteworthy change, I thought I’d divert from actual hashtags to seeing what people are sharing from Pubmed this week. If you really want hashtags, take a look at what hashtags they are ADDING to the posts, since Pubmed doesn’t automatically add any.

PubMed Commons: New comment forum on PubMed

go-public-iconFrom the PubMed Commons Blog:

If you are one of the millions of people who visit PubMed today, be on the look-out for something different. On each abstract page, there’s now a section called PubMed Commons. It’s a forum for scientific discussion on publications open to any authors in the world’s largest biomedical literature database.

Several hundred comments have been made during a closed pilot in the last few months. But there are over 23 million articles in PubMed, with thousands more pouring in every day, from Tuesday to Saturday. So the chance of coming across an article with comments is still very low.

We’ll show you some interesting ones shortly, though – and you can learn how to look for articles with comments and set up alerts in one of last week’s blog posts. Or you can check out the stream of selected new comments – as well as articles that are trending in PubMed – at the PubMed Commons home page.

If you happen onto an article that has comments, the first sign will be in your search results. There will be a little icon letting you know an article has comments, and how many there are – like this:

Comment icon with number 7

Anyone can read the comments. Members may also have rated their helpfulness, which looks like this on the comment:

8 out of 8 found this helpful

Read more about PubMed Commons here.

Sharing Research on Twitter — Hashtags of the Week (HOTW): (Week of January 13, 2014)

Altmetrics: Top Articles of 2013

Last week in the #medlibs chat on altmetrics, Donna Kafel shared an interesting article on how research articles are shared in social media.

Haustein S, Peters I, Sugimoto CR, Thelwall M, Larivière V. Tweeting biomedicine: An analysis of tweets and citations in the biomedical literature. Journal of the Association for Information Science and Technology, Article first published online: 26 NOV 2013. DOI: 10.1002/asi.23101

This is the newest study of how real life sciences research is being used in social media. They analyzed a sample of over a million articles from Pubmed to reveal patterns associated with heavily shared articles, then compiling a list of the most tweeted articles. (There will be a sequel to this post about them.)

Meanwhile, the Altmetrics web site has also released a year-end overview of the most influential research articles of 2013 according to the Altmetrics score. What is an Altmetrics score? In their words, “We’ve created and maintain a cluster of servers that watch social media sites, newspapers, government policy documents and other sources for mentions of scholarly articles. We bring all the attention together to compile article level metrics.”

Altmetrics: Top 100 Papers that Received the Most Attention Online:

Let’s take a little closer look. For a richer understanding of how Altmetrics looks at articles, here is a screenshot of the Altmetrics report for the top ranked medical article from 2013.

Atmetrics: Sample Article Report
Primary Prevention of Cardiovascular Disease with a Mediterranean Diet:

As you can easily see, although Altmetrics looks at many sources of information (Twitter, Facebook, F1000, news media, videos, blogs, Google+, Reddit,Mendeley, CiteULike), Twitter activity far outstrips activity for the other sources.

Now, usually the HOTW posts track a hashtag with health, life science, education, or research interest. This week, as a diversion from the usual, I wanted to see what articles are being shared and how best to discover them. I found that neither “research” nor “#research” were terrible effective, although both were interesting, they didn’t retrieve actual research articles but rather articles about research funding and process. What did work was searching the word “Pubmed.” Here are some of the most popular research articles (including mentions of UM researchers!) from the past week.

What an amazing collection, and great way to discover articles of interest that I might have missed otherwise!

New publication model for PubMed citations

In mid-June 2013, a new publication model, Electronic-eCollection, was introduced for PubMed citations from electronic-only journals. “Electronic-eCollection” means that an article is published electronically on a specific date and is also associated with an electronic collection date (similar to an issue; this date can be a year or a year and month, but never a year, month, and day). NLM determines the publication model based on the data submitted by the publishers.

“eCollection” will be displayed preceding the collection date information in a citation. The specific article date will display after the journal title abbreviation while the collection date will display near the end of the source information.

Screen capture of a sample display for journal citation with PubModel = Electronic-eCollection.

This particular article was published online on January 25, 2013, yet was included in the Volume 3, 2012 collection as deposited in PMC.

New public health MeSH terms for 2014

Each year, PubMed adds, changes, & deletes terms in the Medical Subject Heading (MeSH) database, which contains all the terms used to index articles in Medline.  I’m always excited (yes, really!) to see what new terms are available for public health, since that makes searching so much easier & accurate.  I’ve gathered a list of the new terms that are particularly relevant to public health below.  To see the whole list of changes, go to Changes to MeSH – 2014 & select from the links at #4.

  • alcohol abstinence
  • biodegradable plastics
  • dataset
  • disaster victims
  • drug trafficking
  • ethnic conflict
  • hazard analysis and critical control points
  • hazardous waste sites
  • hope
  • human trafficking
  • International Classification of Functioning, Disability and Health
  • material safety data sheets
  • mindfulness
  • mobile applications
  • nurses, public health
  • nutritionists
  • nutritive sweetners
  • observational study
  • organ trafficking
  • pediatric obesity
  • physical conditioning, human
  • serving size
  • slave
  • slavery
  • social determinants of health
  • sports for persons with disabilities
  • sports nutritional sciences
  • teach-back communication
  • web browser
  • workplace violence



PubMed Commons: New Space for Discussion among Researchers

Earlier this week, NCBI announced the released a pilot of PubMed Commons, a feature that enables commenting on article abstracts by researchers. According to the NCBI blog, the new feature is in response to requests by the scientific community. Their goal is to encourage constructive criticism and discussion of scientific issues.

For now, PubMed Commons is only available to researchers who have been invited. Several (unnamed, to the best of my knowledge) organizations provided lists of email addresses of PubMed authors. Those individuals can create accounts and invite others to participate. Wondering if you’re on the list? You can go to the Join PubMed Commons page.

Users can also search for articles with comments with searches like: nature[journal] AND “has user comments”[filter]. You must be a PubMed Commons participant to see comments, but I hope that it’ll eventually open up to more users because the comments have the capacity to provide valuable insight to many different types of users.

Another interesting thing is that I’ve been noticing a decline in enabling comments on online articles. In Popular Science, for example, they even believe that comment sections are actively hurting the scientific community because it gives small minorities the power to negatively alter readers’ perceptions on important topics. The highly controlled method taken on by PubMed Commons is an  way of ensuring some quality control, but at the expense of a diversity of perspectives. I’m looking forward to seeing how PubMed Commons develops!


PubMed “relevance sort”

On October 22, a new option was added to PubMed:  Relevance sort.   This option is available from the Display Settings menu under Sort by.

The relevance sort is based on an algorithm that analyzes each PubMed citation that includes the search terms.  A “weight” is calculated for citations depending on how many search terms are found and in which fields they are found. In addition, recently-published articles are given a somewhat higher weight for sorting.

Easy access to the relevance sort will also initially be provided under a New feature discovery tool.

Screen capture of PubMed Summary results with Sort by Relevance feature discovery tool.

Users may either choose Relevance from the Display Settings Sort by menu or click the Sort by Relevance link in the New Feature discovery tool.

Screen capture of PubMed results sorted by Relevance.

The update to the sort by selections is combined with a new feature that retains the most recent sort by selection for subsequent search results until a different sort order is selected, or after eight hours of inactivity on the system.

Results for My NCBI users signed in to their account with a modified default sort order will be displayed in the modified order until a different sort order is selected. A “Relevance default sort” selection in My NCBI PubMed Preferences will be added after the initial implementation of this new feature.

Changes to My NCBI Saved Searches

The My NCBI Saved Search Settings page has been modified to let you edit search terms.


You can change the search in the “Search terms” box, and then click the “Test search terms” link to check the search in PubMed before saving your edited search.


Click the “Save” button after you make any changes to the search name, search terms, e-mail schedule, or optional text settings. The Saved Search Settings page e-mail update schedule selections has been streamlined.


In addition, an “Edit” link to the Saved Search Settings page has been added to the My NCBI automatic e-mail alerts.


Non-English abstracts in PubMed

Publishers will soon have the opportunity to submit non-English abstracts to PubMed. The additional language view(s) will be links on the Abstract display, with bold text indicating the language currently displayed (see Figure 1). The abstract text will default to English when a citation has an accompanying non-English abstract.

Figure 1: Abstract Language Display Options on the Abstract Display.Screen capture of Abstract Language Display Options on the Abstract Display

Users can click the language link to view the abstract in a different language (see Figure 2). If a citation has only a non-English abstract, PubMed will not display an abstract by default, and users can select the non-English option.

Figure 2: Non-English Language Selected and Displayed on the Abstract Display.

Screen capture of Non-English Language Selected and Displayed on the Abstract Display

NLM will not review non-English abstracts for accuracy. Non-English abstracts will not be available in the Summary, MEDLINE, or XML displays and will not be available for download via E-utilities or in the data distributed to licensees.