Visualizing PubMed

There are a number of sites where you can do a PubMed search and display the results in interesting and sometimes quirky ways.

Here is a KNAKIJ search on low back pain[mh] AND laser therapy, low level[mh]. You can click on the circles and link to PubMed records.


Here are some of these visualizing sites:

  • PubMed PubReMiner
    PubReMiner is a front-end for the popular PubMed literature database at the NCBI. When you submit your query (which can be any query that can be processed by PubMed), PubReMiner will process the result of that query and display its results (in the form of selectable “keywords”) in frequency tables, which can be added/excluded from the query to optimize the results.
  • KNAKIJ – information visualization
    KNALIJ PubMed: KNALIJ is a real-time infographic engine. The KNALIJ PubMed web application is built to visualize and explore the connections within medical research. KNALIJ PubMed draws upon more than 22 million abstracts as a unique knowledge discovery tool  More
  • LigerCat: Literature and Genomics Resource Catalogue
    Search PubMed using words or even a DNA/protein sequence to create a tag cloud showing an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, combining the associated MeSH descriptors into a cloud, weighted by frequency.
  • Genes2WordCloud [Click on PUBMED SEARCH]
    Create Word Clouds using PubMed searches  Help

New Page ~ Systematic Reviews

This new page contains links to resources that will get you started on preparing systematic reviews …

Twittering for chiropractic, continuing health education and fun

I maintain three Twitter accounts, one for CACHE/ACEMC, one for the Index to Chiropractic Literature, and one just for fun stuff I find on the Internet. You can follow them from any page on this blog (right and left sides of the screen) at

The new, improved PubMed


On September 30, NCBI mounted the preview site for the redesigned PubMed. When I first looked at it, I thought they had omitted some key resources like the MeSH and Journals Databases. But I think I entered the site just as they were putting it up, and today, on October 1, there are some great features on the site.

Check out this record:

The default display is now Abstract, with links to the MeSH terms/Publication Types and LinkOut directly below each record. I had heard a rumour that they were going to eliminate the Single Citation Matcher, but apparently there was an uproar among librarians (a terrifying thought) and the feature was retained. There is a simple search and an Advanced Search, and links to the PubMed Tools and More Resources are right on the home page. I think this is an improvement on the current site, where the only way to see MeSH terms is to use the Citation Display. This was not intuitive, and now all users will be able to view the MeSH terms easily.

Read more about the redesign in the September-October 2009 NLM Technical Bulletin.

The Cochrane Library is now free for all Canadians!

cclogo.gif  About a year ago, I wrote a blog post entitled Cochrane Library: Free access for all?  Well, this has come to Canada, as a pilot project.  The Canadian Cochrane Network and Centre announced on April 15 that everyone in Canada is now able to access the full contents of the Cochrane Library. From the announcement:

The Canadian Cochrane Network and Centre, in partnership with the Canadian Health Libraries Association, has successfully secured a national license to The Cochrane Library. In essence, the license provides a subscription for every Canadian with access to the Internet to benefit from the immense volume of health information found in The Cochrane Library. Everybody will be one click away from the best available evidence on the effectiveness of treatment procedures including which ones may be harmful.

Access the Cochrane Library at

ROAR & DOAR: Registry / Directory of Open Access Respositories

writing.jpg  I started to look for open access repositories and was getting absolutely overwhelmed until I discovered ROAR and DOAR.
See also eScholarship Respository (California Digital Library)

Directory of Open Access Repositories – OpenDOAR
OpenDOAR is an authoritative directory of academic open access repositories. Each OpenDOAR repository has been visited by project staff to check the information that is recorded here. This in-depth approach does not rely on automated analysis and gives a quality-controlled list of repositories.
United States    Canada    Search or Browse for Repositories     FAQ   
Example: Health and Medicine/English/Multimedia

Registry of Open Access Repositories (ROAR)
We are promoting open access to the research literature pre- and post-peer-review through author self-archiving in institutional eprint archives. Open access to research maximises research access and thereby also research impact, making research more productive and effective.
Search     Google Custom Search    Help (WIKI)

A Google Scholar Primer

 Almost a year ago I wrote A Google Primer, which some of you have told me you have found useful. This week I took a careful look at Google Scholar, and I’ll pass on some of the things I discovered. Scholar’s advantages and disadvantages have been well documented and I won’t go into them in detail here. See also A little Google history from the Internet Archive

See Shultz M. Comparing test searches in PubMed and Google Scholar. J Med Libr Assoc 2007; 95(4):442-445. [Open Access]

Google Scholar is terrific for serendipitous searching, especially if you use the Cited By feature. This is what I tell my students:

  • Use Google Scholar as a starting point, keeping in mind limitations such as lack of subject indexing and undeterminable coverage
  • Use the Advanced Scholar Search to take advantage of several advanced search features at the same time, and use the Scholar Preferences
  • Enrich your searches by using other (free) databases such as PubMed or TRIP  (Turning Research Into Practice) or the Index to Chiropractic Literature because Scholar’s coverage of MEDLINE, for example, is incomplete (although Scholar does cover a lot of “grey literature” absent from PubMed)

If you compare the search features on the Google Advanced Search and Google Scholar Advanced Search pages, some puzzling differences appear. Some features may be used in both. Here are some highlights of Scholar and Google search features:

Downloading into bibliographic software

I have been frustrated by what I thought was the inability to download references from Scholar. Well, this week I discovered that you can download from Google Scholar, and into 5 different software managers. Outstanding! Simply go to Scholar Preferences , scroll down to Bibliography Manager and choose one.  See the link Import into RefMan on the bottom line in this screen shot (click on the image to enlarge it):

 kroenke1.png    Link to search (Turn on the bibliography manager in Google Scholar to see all the links.)

Boolean searchingWords and phrases in both Googles are automatically ANDed. OR can be used (uppercase). You can NOT words or phrases by using  – .Truncation or wildcard searching

In Google, use * to capture all forms of a word, e.g. chiropract*. Oddly, this does not work in Google Scholar.

Phrase searching

“Exact phrase” is an option in both advanced search screens; enter phrases in quotation marks in basic searches.

Author searching

This is a search feature in Google Scholar advanced search; au:  in basic search also works, although results may be incomplete (e.g. au: taylor-vaisey)

Publication searching

This is a search feature in Google Scholar advanced search. Caution: Titles are entered in the form in which they appear in publications, and the search screen only gives one chance to enter titles. Publication:  seems to work in some cases, but is unreliable. There is no way to capture all forms of a title in one search, as far as I can see.

Date searching

You can specify date ranges in Scholar; broad ranges only are available in Google.

Language searching

Google has a long drop box for countries on its advanced search screen. You can also choose from many languages in Google preferences. Scholar has no language feature on its search page, but you can choose 8 language limiters in Scholar Preferences. (A puzzling difference that may have to do with bias …)

File type

This is a choice on the Google advanced search page, not on Scholar. But you can limit by file type in Scholar basic search (e.g. filetype:pdf).

Domain limiting

This is a feature on the Google advanced search page, not on Scholar. But you can limit by domain in Scholar basic search (e.g. site:edu).

Citation searching

The “Cited by” feature is only in Google Scholar (see above screen shot). Also use the Related Articles feature. I don’t know how they create the latter but they seem to pick title words and authors. I tried to figure out how to find all the “cited by” records for a particular author, but this seems to be pretty random, unlike PubMed, which uses a formula.

Refining results

Google Scholar includes broad subject categories in its advanced search. In Google,  however, I just discovered that you can refine a search on a topic like “chronic fatigue syndrome” by the categories below. (These appear only after you do a search.)

Treatment; Tests/diagnosis; For patients; From medical authorities; Symptoms; Causes/risk factors; For health professionals; Alternative medicine; Patient handouts; Clinical trials; Continuing education; Practice guidelines