Discovering Biology in a Digital World

tags: PubMed, PubMed Central, medical informatics, bioinformatics, finding scientific articles

This three part series covers the problem of finding scientific articles, compares results from a few different methods, and presents instructions for the best method.

A day in the life of an English physician

In April, I had the great fortune to attend (and speak at) a conference on scientific publishing sponsored by the Association of Learned and Professional Society Publishers. One of the first speakers was an English physician who described his trials and a typical ordeal in trying to use the medical literature.

What is peer-reviewed scientific literature?
Before I go further, I should explain that this doctor wasn't looking for popular web sites on healthy living, he wanted to find research or review articles that had been subjected to peer-review. Unlike the white-papers that we write in the software industry, peer-reviewed articles are not published until they have been read and accepted by other scientists. Many times, the reviewers also ask the authors to do extra work and rewrite sections of the paper. Consequently, getting an article published in a peer-reviewed journal can takes one or more years, depending on the article, the authors, the reviewers. Although slow and imperfect, peer-review is a form of quality control, designed to minimize the publication of poor quality science.

Back to our story
This doctor, a thoughtful and well meaning young man, had reviewed the X-ray results for one of his patients. She listened quietly and asked if him if her results could mean lung cancer.

He went to the internet to find out.

First, he tried PubMed.

But many of the papers were in journals that he couldn't access because his hospital didn't have subscriptions.

Next, he tried Google.

But his Google results all seemed to be same, and they failed to provide his answer.

Last, he tried Google scholar and finally found a place to begin. Luckily, he happened on a paper, written by someone that he knew worked in the field. After several tries and several minutes, he had at last, found a place where he might at least start looking.

The audience attacks
The talk was over and it was time for questions. One of audience member, an older gentlemen with a crisp English accent, angrily questioned the young man, in disbelief. How could it be that he, a doctor , couldn't access this information? Surely, he must have access through his University?

Calmly and carefully, the young physician explained that he worked in a hospital, run by the National Health Service. Yes, he said, he could access publications if he were at the University. But he works long hours in a hospital and doesn't have the luxury to spend time traveling back and forth to the University in the middle of his workday to use the University computers.

Furthermore, he explained that the computer he uses is situated in a central work station, shared with the nurses, and other doctors; and used for multiple tasks. With others waiting to access to patient records, check medication details, and review lab results, it's impossible for him to monopolize the computer for more than a few minutes at a time. If he can't find the answer quickly, he can't answer his patient's questions.

I sat in the audience, simply amazed. Not that he couldn't access information for free, mind you, but that he didn't know how to find freely accessible information in PubMed. I really wanted to raise my hand and give him some advice, but we were on a schedule. We quickly moved on to the next talk and the young doctor was gone before the coffee break.

Read the whole series:

• part I A day in the life of an English physician,
• part II Comparing different methods,
• part III My new favorite method,
• part IV One last experiment