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.
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
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)
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):
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.
“Exact phrase” is an option in both advanced search screens; enter phrases in quotation marks in basic searches.
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)
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.
You can specify date ranges in Scholar; broad ranges only are available in Google.
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 …)
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).
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).
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.
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
This article adapted from grand rounds presented by faculty from the Mt. Sinai Medical Center and published in the October 2006 issue of the Mount Sinai Journal of Medicine provides a nice overview of the services currently offered by medical libraries. The authors discuss the following myths, issues I deal with every working day:
Myth #1: Everything is online
Myth #2: Everything online is free
Myth #3: MEDLINE is difficult to use
Myth #4: Google can replace MEDLINE databases
Myth #5: Textbooks are out of date before they are published
Beam PS, Schimming LM, Krissoff AB, Morgan LK. The changing library: what clinicians need to know. Mt Sinai J Med 2006; 73(6):857-863. PubMed Related Articles
Abstract: Over the last two decades, changes in technology have allowed academic medical center libraries to bring the world of biomedical information to the physician’s computer desktop. Because digital libraries have grown so rapidly and in so many ways, some clinicians may be uncertain about the services and resources that are available to them. This article explains how clinical faculty can best utilize their library to support their research and patient care. It addresses some of the most common myths about the “new” medical library, and it highlights innovations in library resources and services that can help physicians to better access, use and manage medical information.
Here is an abbreviated version of the authors’ Top ten tips for getting the most from your medical library (see p. 862 for the full version):
1. You don’t need to visit your library to use your library.
2. Most recent biomedical journal articles are available online; most older articles are available in print only.
3. Databases such as PubMed are getting “smarter” and easier to use.
4. To find current, accurate information about the latest research and best practices, check resources that cover peer-reviewed journals (e.g., Medline/PubMed) or that provide regularly updated, peer reviewed, evidence-based summaries.
5. Online resources such as MD Consult are streamlining your ability to keep up with changes in your field—and with what your patients are reading.
6. Full-text linking is now available from many library databases.
7. Faculty can now enter requests for books or articles not held at their local library through online interlibrary loan services.
8. Bibliographic management programs, available through many academic libraries, can help to organize the references for your publications.
9. Your library’s homepage is a gateway to your library’s services as well as its resources.
10. Ask a librarian—in person, by phone, by e-mail, or by an online chat service—to show you the quickest, easiest ways to get the best information.
I wasn’t going to write about the study published recently in the BMJ, mainly because everyone else has. So what I’m going to write about is some of the reaction to the study. First, here is the abstract; free full text is available online:
Tang H, Ng JHK. Googling for a diagnosis–use of Google as a diagnostic aid: internet based study. BMJ 2006; 333(7579):1143-1145.
Objective: To determine how often searching with Google (the most popular search engine on the world wide web) leads doctors to the correct diagnosis. Design: Internet based study using Google to search for diagnoses; researchers were blind to the correct diagnoses.
Setting: One year’s (2005) diagnostic cases published in the case records of the New England Journal of Medicine.
Cases: 26 cases from the New England Journal of Medicine; management cases were excluded.
Main outcome measure: Percentage of correct diagnoses from Google searches (compared with the diagnoses as published in the New England Journal of Medicine).
Results: Google searches revealed the correct diagnosis in 15 (58%, 95% confidence interval 38% to 77%) cases.
Conclusion: As internet access becomes more readily available in outpatient clinics and hospital wards, the web is rapidly becoming an important clinical tool for doctors. The use of web based searching may help doctors to diagnose difficult cases. PubMed Record Related Articles
One of my favourite alerting services, MedPage Today, wrote the following in a teaching brief:
- Explain to interested patients that for physicians search engines may be less helpful in diagnosing complex diseases with non-specific symptoms or common diseases with rare presentations.
- Caution patients that while Google is good at finding documents describing signs or symptoms, the judgment and clinical experience of physicians are still needed to determine relevance and make the diagnosis.
[It's interesting to note that after I suggested to the MedPage Today reviewers that they link to the abstracts of the papers they review, they sent me a lovely gift of fruit and cheese.]
The BMJ rapid responses to this article provide some fascinating reading. In an Authors’ Reply, the study’s authors write:
To state the obvious for those who seem to have missed the point, there is no danger of “Google misdiagnosing life-threatening disease” as search engines cannot make diagnosis. Only doctors are capable of making diagnoses (and misdiagnoses). If the probability of a diagnosis exceeds the testing threshold , then tests would be performed to prove or disprove the diagnosis. However the diagnosis has to be considered in the first place and search engines may act as a diagnostic reminder.
Google googling for a diagnosis and you will find huge numbers of responses. In the morning of December 10 there are about 10,700 hits. (!!) Here are some more specialized hits, from Google News and Google Blog Search. (I wonder if I will show up here?)
Note: I wrote this post in the morning of December 10. Google picked it up about 12 hours later. Those are quick little spiders, eh?
See also A Google Primer
See also A Google Scholar Primer; A little Google history from the Internet Archive
A recent Google search revealed that the word google was first used in the 1927 Little Rascals silent film Dog Heaven (according to Wikipedia, anyway), and the word meant having a drink of water. However, my Shorter OED identifies google as a cricket term first used in 1904. (See A little Google history from the Internet Archive to discover what the founders of Google meant by the term.)
On June 15 of this year, the verb to Google was included in the Oxford English Dictionary, and Googling is now such a part of our daily lives that many of us use the search engine several times a day. At any time of the day I can walk through my library and see students typing words into the basic Google search box, the one that has the I’m Feeling Lucky button below it.
But there is a more efficient way to use Google, in my humble opinion. I use the Google Toolbar for quick searches and the Advanced Search for more complex searches. (See the end of this post for several advanced search forms.) But because the Advanced Search doesn’t include all the Google search features, I am pulling them all together in this, my Google primer.
Below are the Advanced Search features listed in bold, followed by how to perform the same search in the Basic search (that search box on the home page). (Do keep in mind the limitations of machine-made search engines, and search literature databases when appropriate.)
All of the words [Advanced]
Basic: use + to indicate words that must be included in your search example
Exact phrase [Advanced]
Basic: use “quotation marks” to search exact phrases example
Without the words [Advanced]
Simple: use – to exclude words or phrases example
Language [Advanced: choose language from a drop-down menu] example
Basic: not an option
File Format [Advanced: choose desired format from a drop-down menu]
Basic: use filetype: (e.g. filetype:pdf) example
Date [Advanced: choose from three options in the drop-down menu] example
Basic: use daterange: (but this is for Julian only)
Numeric Range [Advanced]
Basic: not an option
Occurrences [Advanced: choose where in the Web page you want your terms to occur; five options in the drop-down menu]
Basic: use the following tags, with no spaces after the colon
allintitle: [restricts results to words in title] example
allintext: [searches text of pages, not links or title]
intitle: [searches at least one of the words in the titles]
inurl: [includes a word in the URL] example
allinlinks: [searches only within links, not text or title] example
Domain [Advanced: include or exclude specific domains]
Basic: use site:[URL] example
Usage Rights [Advanced: choose from five options in the drop-down menu] example
Basic: not an option
SafeSearch [Advanced: choose from two options]
Basic: use safesearch: [exclude adult content]
Similar [Advanced: find pages similar to a URL you specify]
Basic: use related:[URL] example
Here are some pretty neat search features that are not included on the Advanced Search page.
define: [locate definitions for a word or phrase] example
movie: [find movie reviews] example example
stocks: [insert symbol, name] example
info:[URL] [goes directly to “about” pages] example
weather: [find weather for a particular city] example
Want to print this page? Do a Print Preview first; depending on your browser, pages 3-4 will likely be the pages you will want to print. Read Google’s Cheat Sheet to learn some finer points of searching syntax. A warning: some of these things don’t work and I know because I tested them.
A new column presenting case studies in health sciences information provision made its first appearance in the October 2006 issue of the Journal of the Medical Library Association (JMLA). The column will be curated by Rebecca Jerome of Vanderbilt University. The editors invite comments on these articles through its online forum.
Jerome RN, Miller RA. Expert synthesis of the literature to support critical care decision making. J Med Libr Assoc 2006; 94(4):376-381.
Excerpt: In this new column, the editorial team will address challenging situations in health sciences information provision. The column will provide narrative and insight from expert commentators drawn from librarianship, informatics, medicine, research, and other areas that inform the development of a given case situation. This feature will share commentary and practices for a variety of scenarios with the intention of prompting discussion of the issues facing health sciences librarianship as a developing profession and the development of potential solutions.
Health sciences librarians are increasingly being challenged to expand their skills in information retrieval and assessment into the clinical and other domains to foster the integration of evidence into decision making. The current column undertakes a complex clinical question drawn from the intensive care setting and explores the process of searching and synthesizing the evidence for application to a critical patient care decision. Coauthored by a clinical librarian and a clinician well versed in the fields of internal medicine and biomedical informatics, this case illustrates how clinical expertise and a detailed understanding of the literature can be applied. It has relevance to current and future potential directions for advanced development and application of librarian skill sets.
Full Text PubMed Record Blog Read all articles in this issue of JMLA