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

Red Flags, Yellow Flags, Blue Flags, Black Flags


This page was originally posted on September 21, 2006. It has been the most viewed page on this blog. Updated February 22, 2013.  

The other day a student asked me where the phrase “red flag” originated. He had also heard of yellow flags, and suspected that there were other colours of flags to indicate barriers to recovery. Well, we looked in various glossaries of medical and medical education terms, without success. So I e-mailed Dr. Shawn Thistle, and, sure enough, he helped. It is difficult to find where these terms originated (try Googling blue flags!) and Dr. Thistle thinks they may just be part of every doctor’s vocabulary. (Ever since I wrote the title above, I can’t get Dr. Seuss’s One fish two fish red fish blue fish out of my head.)


Red flags/clinical red flags (biomedical factors) ~
These help identify potentially serious conditions, and are often listed in practice guidelines. Here is a description from Chapter 13 of the
Clinical guidelines for chiropractic practice in Canada [Glenerin Guidelines]:
The main focus for the prevention of complications is the recognition of well-known and established indicators or “red flag” signs and symptoms which may require careful assessment and reassessment, changes in treatment plan, or other appropriate action, such as emergency care or referral to another health care specialist. Ignoring these “red flag” indicators increases the likelihood of patient harm. 

Yellow  flags/clinical yellow flags (psychological or behavioural factors/predictors) ~
These indicate psychosocial barriers to recovery. Here is a definition from

New Zealand acute low back pain guide: incorporating the Guide to assessing psychosocial yellow flags in acute low back pain:
Yellow Flags are factors that increase the risk of developing or perpetuating long-term disability and work loss associated with low back pain … Before proceeding to assess Psychosocial Yellow Flags it is important to differentiate between acute, recurrent and chronic presentations. Evidence suggests that treating chronic back pain as if it were a new episode of acute back pain can result in perpetuation of disability. 

Blue flags/occupational blue flags (social and economic factors) ~
These refer to conditions in the workplace that may inhibit recovery. Examples are
monotony, low degree of control, poor relationships or high work demands. 

Black flags/socio-occupational black flags (occupational factors) ~
These are also used for workplace issues, but refer to organizational issues such as financial reliance on disability benefits, workers’ compensation issues, or employer attitudes to the sick worker.


Helliwell PS, Taylor WJ. Repetitive strain injury. Postgrad Med J 2004;80(946):438-43.See An Approach to Diagnosis
Main CJ, Williams AC.  ABC of Psychological Medicine. Musculoskeletal pain. BMJ 2002;325(7363):534-7.

Click on the image below for The clinical flags approach to obstacles to recovery from back pain and aspects of assessment.

From:  Main CJ, Williams AC.  ABC of Psychological Medicine. Musculoskeletal pain. BMJ 2002 Sep 7;325(7363):534-7. PMC version

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New Page ~ Systematic Reviews

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

Christmas 2012


Every year at this time, some of the major medical journals publish special Christmas issues. The BMJ and the CMAJ offer some open access articles for our holiday reading. From this year’s December issues of the British Medical Journal: – Christmas 2012

The CMAJ’s Holiday Reading [open access]

The Medical Journal of Australia‘s Christmas Crackers [scroll down the page; full text by subscription]

See older Christmas issue entries   especially Christmas Songs for Christmas Eve
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Web Sites, Facebook, Twitter and LinkedIn ~ What I’m doing now

Hello, everyone out there ~
I haven’t been keeping this blog up to date but I am still very much involved in continuing health education and chiropractic. This is what I am doing now, and you can see the twitter feeds from this site ~

I am the Web editor for ICL and still have involvement with CACHE:


CE Measure: The Journal of Outcome Measurement in Continuing Healthcare Education

CE Measure is the first peer-reviewed journal dedicated specifically to the art and science of healthcare educational outcomes measurement.

Original manuscripts that address outcomes methodologies, results, practice-based protocols, CE conference highlights and abstracts, and case histories will be published to promote vigorous academic scrutiny of this important subject.

Sample articles (all available free online):

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Brand names make it to the OED!

I first created this post in 2007, and apart from the home page, it has been the most viewed page on my blog (over 6,000 views). So here it is again, with a link to the latest OED update.

It’s fascinating to peruse the new words added to the OED. (Here is the latest update, December 2010.) Brand names often enter the language as generic terms, and I’ve listed a few of them below. (I wonder who they have in mind with the word “flip-flopper”. And what on earth is a cotylosaur? I thought “chicklet” meant a little piece of gum, but I was disappointed to discover that it means a small chick or girl.)

Goo·gle – verb: to use the Google search engine to find information on the Internet.

botox.jpg Botox
bo·tox – noun or verb – A proprietary name for: a preparation of botulinum toxin which is injected into specific muscles to create temporary paralysis, as part of the treatment of various medical conditions and in the cosmetic treatment of wrinkles of the face (esp. frown lines and crow’s feet). Also: treatment by this means; a course of such treatment.

popsicle.jpg Popsicle
pop·sicle – noun – A proprietary name for: an ice lolly.

hoover2.jpg Hoover

hoo·ver – verb: to clean with a vacuum cleaner (Chiefly British)

kleenex.jpg kleenex2.jpg Kleenex [see more ads]
klee·nex – noun: the proprietary name of an absorbent disposable cleansing paper tissue.

xe·rox – noun or verb: a name for a copying machine or the act of reproducing printed, written, or pictorial matter by xerography.

thermos_jug.jpg Thermos
ther·mos –noun: a vacuum bottle or similar container lined with an insulating material, such as polystyrene, to keep liquid hot or cold

pro·zac -noun: a brand of fluoxetine hydrochloride
spandex.jpg Spandex
span·dex –noun: a synthetic fiber composed of a long-chain polymer, used chiefly in the manufacture of garments to add elasticity

jello.jpg JELL-O
jell·o -noun: brand of dessert made from a mixture of gelatin, sugar, and fruit flavoring, dissolved in hot water and chilled until firm

band-aid_small.jpg Band-Aid
band·aid -noun: adhesive bandage with a gauze pad in the center, used to cover minor abrasions and cuts

viagra_hockey.jpg Viagra
vi·ag·ra -noun: sildenafil citrate, used to treat impotence

frigidaire.jpg Frigidaire
frig·i·daire – noun: the proprietary name of a brand of refrigerator.

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This blog on Wordle – January 8, 2010

These word clouds are fun to make on Wordle. This is a representation of this blog, today (atvtoronto).

The MMR-Autism Connection

Clear evidence of falsification of data should now close the door on this damaging vaccine scare
In a series of articles starting this week, and seven years after first looking into the MMR scare, journalist Brian Deer now shows the extent of Wakefield’s fraud and how it was perpetrated.

The  alleged MMR/autism fraud was exposed this week by the British Medical Journal. Below are the links to the main documents in this case.

The original article:
Wakefield AJ, Murch SH, Anthony A, Linnell, Casson DM, Malik M, et al. Ileal lymphoid nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet 1998;351:637-41.  Full Text

The retraction:
Retraction–Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet 2010 Feb 6;375(9713):445.

The BMJ editorial:
Godlee F, Smith J, Marcovitch H. Wakefield’s article linking MMR vaccine and autism was fraudulent [editorial]. BMJ January 5, 2011;   342:c7452.

Journalist Brian Deer’s article in the BMJ:
Deer, Brian. Secrets of the MMR scare: How the case against the MMR vaccine was fixed. BMJ January 5, 2011;342:c5347

Brian Deer’s blog entry:
Piltdown medicine: The missing link between MMR and autism. Jan. 6, 2011.

Globe & Mail article:
Picard A.  Medical fraud revealed in discredited vaccine-autism study. The Globe and Mail, Jan. 6, 2011.

Determination on Serious Professional Misconduct (SPM) and sanction [of] Dr Andrew Jeremy WAKEFIELD. This case is being considered by a Fitness to Practise Panel applying the General Medical Council’s Preliminary Proceedings Committee and Professional Conduct Committee (Procedure) Rules 1988. Date: 24 May 2010
Fitness to Practice Hearing – General Medical Council. Date: 28 January 2010

Issues in CME – Minnesota Medicine, November 2010

Most of this issue is devoted to discussing various aspects of continuing medical education. Here are some highlights:

  • Deye DL. CME ASAP. Minn Med 2010 Nov;93(11):30-1.

View the PubMed records for the above articles.    View Minnesota Medicine.