In Plain Sight

Many who search in PubMed do not find what they seek. Frustrated by off-topic, too few or too many results they look elsewhere for answers. They know they “should” use PubMed as part of finding biomedical information but can’t seem to make it work for them.  If that sounds familiar, then read on!

Several alternative search interfaces attempt to solve these problems. Do they work? The answer depends on what you are trying to do. Are you looking for a few good articles? Are you doing exhaustive searches? Are you looking for articles about the psychosocial aspects of biomedicine? To find the right solution for you, it is likely you will need to “test drive” some of the possibilities. Search two or three questions with which you are already familiar, take a look at your results and then decide. This is the first installment of a series of postings in which several of these alternative interfaces will be introduced.

First, let’s be clear about the difference between PubMed and MEDLINE.  MEDLINE (Medical Literature Analysis and Retrieval System Online) is a literature database of life sciences and biomedical information. The database has more than 22 million records from approximately 5,200 selected publications from 1950 to the present. MEDLINE is maintained by the National Library of Medicine (NLM).  Each record in MEDLINE is manually indexed with NLM’s controlled vocabulary, the Medical Subject Headings (known as MeSH). PubMed is the NLM’s free search interface for the MEDLINE database. However, there are a number of third-party search tools that can be used to access and interact with MEDLINE.

Quertle (the name is derived from the word query) is a website that is a relatively new third-party tool for interacting with PubMed. It was designed by biomedical informatics researchers who wanted a search engine that would be able to pinpoint the most relevant citations for their research. Sign up here for a free account.

Why Quertle? It claims to understand acronyms (e.g., NO for Nitric oxide), have a built-in understanding of biology and chemistry, and understand word relationships. Quertle suggests wording your search using a sentence with subject-verb-object construction. This is a “relationship” search, which we will touch on further below . Quertle also uses Power Terms, e.g., $Disease searches for disease names. The search “caffeine affects what $Diseases” looks for diseases affected by caffeine without have to list each disease. Quertle has many other features, which left me with the question of whether Quertle is that much easier than PubMed to learn.

The recurring example for this series of blog articles: “Is acetaminophen or ibuprofen  better for fever control in children?” I would enter the search seen below:

- tylenol or motrin treats fever in children

Quertle yields 2 articles using Focused Results and 189 articles using Broader Results. The same search run in PubMed using MeSH  yields 257 hits. The second of the two Focused Results looks promising, but I would like to see a bit more about the topic than this. Quertle sorts by relevance; the first page of Broader Results looks pretty good.

When viewing search results note that Quertle not only retrieves MEDLINE records but also full-text articles from PubMed Central.

Two take home points from comparing Quertle with PubMed:

• Quertle appears to be good at finding a few good relevant articles from MEDLINE.
• The PubMed search engine is better for exhaustive, “leave no stone unturned searches”.

Quertle is definitely worth a look if you don’t mind somewhat of a learning curve and are seeking a few to several good articles about a topic. Here is a quick guide to using Quertle.  You can also view this Youtube video.

Future posts in this series will address:

• SUMSearch 2
• TRIP database
• HubMed
• NextBio
• For Mobile devices
  • o PubMed on Tap
  • o PubMed for Handhelds
  • o PubMed Mobile

Installment two will be coming soon. Until then, stay well.

Evans Whitaker, MD, MLIS, Education and Information Consultant for Medicine.

Thomson Reuters has just launched a free online version of EndNote:

EndNote Basic includes storage for 2 gigabytes of attachments and 50,000 references, as well as the top 20+ most frequently used styles. I haven’t explored it in depth yet but it seems to replace what was formerly known as EndNote Web.

If you want a little background on why EndNote has decided to release a free version  you can read this Wall Street Journal article.

BrowZine works by organizing the articles found in Open Access and subscription databases, uniting them into complete journals, then arranging these journals on a common news-stand.  The result is an easy and familiar way to browse, read and monitor scholarly journals across the disciplines:

Click here for more information on how you can help the Library evaluate this research tool.

If you are frustrated with wasting time while trying to find the right research instrument, HaPI is the database for you. Health and Psychosocial Instruments (HaPI) is an easy-to-use database that provides users access to information on measurement instruments (i.e. questionnaires, interview schedules, checklists, coding schemes, rating scales, etc.) not only in the fields of health and psychosocial sciences, but also in organizational behavior and education.

Although the full text of the instruments is not included in the database, HaPI can help you with the following tasks:

• Discovering the landscape of existing instruments in your field of study;
• Determine the availability of reliability and validity evidence;
• Track the history of an instrument;
• Locate ordering information for a known instrument.

Additionally, there are several useful limit options highlighted below that can help you find specific information about the instruments.

• Use “Primary Source” to look for the original articles where the instrument was first published or a source that contains the full text of the instrument.
• Use “Secondary Source” to look for articles that use a particular instrument.

• Use “Review Source” to find articles that review ta specific instrument.
• Use “Translated Source” to find the instruments in different languages.

A good practice is evaluating the reliability and validity of a specific instrument before you decide to use it. To do this, use “Search Field” from the top of the search screen. Enter the name of the instrument and then select the following fields: Reliability, readability index and validity (see below)

Utilizing these HaPI tools will help you be able to quickly and efficiently identify the research instrument appropriate for your field of study.

Clinical Queries (CQ) is somewhat hidden on the PubMed homepage, but allows you to quickly narrow your search for clinical information to systematic reviews and controlled clinical trials. Medical genetics results are also shown in a third column.

Using CQ is easy. Type in the search box, click on Search and look at your results. You can fine tune your results by choosing a Category (as “Therapy” in the example) and Scope (“Broad” or “Narrow”).

That is all there is to it. CQ is useful when you are looking for a few good articles on which to make evidence-based clinical decisions.

Give it a try!

Evans Whitaker, MD, M.L.I.S.,  Education and Information Consultant for Medicine, UCSF Library.

See below for important updates to this posting.

An impressive number of open access initiatives have recently come from the federal and California government. These efforts have the potential to significantly broaden public access to government-funded research publications. On February 13, 2013, the Fair Access to Science & Technology Act (FASTR) was introduced with bipartisan support in both the U.S. House of Representatives (H.R. 708) and Senate (S. 350). FASTR would require federal agencies with an annual extramural research budget of at least $100 million to provide free online access to published articles resulting from the funds, no later than six months after publication. Affected agencies include (among others) the Department of Health and Human Services (including the NIH), the National Science Foundation, NASA, and the Department of Education.

FASTR is the successor to the Federal Research Public Access Act (FRPAA), which did not make it out of committee in the 112th Congress (2012). UCSF scientists are familiar with the NIH Public Access Policy, which stipulates public access no later than twelve months after publication. FASTR would not only shorten that period to six months, but it also stipulates that the article versions deposited in repositories be distributed “in formats and under terms that enable productive reuse, including computational analysis by state-of-the-art technologies.” (bill, 4.b.5)  This type of usage addresses current research needs beyond simply reading articles to mine large amounts of data.

Then, on February 22, the White House Office of Science & Technology Policy (OSTP) directed federal agencies with at least $100 million in research & development expenditures to develop plans to make the results of federally-funded research publicly available, free of charge, within 12 months after original publication. Obama’s directive was a response, in part, to a We the People petition signed by over 65,000 people asking the government to make all publicly funded research results free.

While having FASTR and the Obama directive at the same time might seem duplicative, the two efforts complement and strengthen each other. If FASTR passes, it would become the law and could not be overturned as could a future presidential directive.  It would reduce the public access embargo period from 12 to six months. The White House directive also specifies that data associated with an article must be made open access. Both efforts call for green open access, whereby authors publish in the journal of their choosing and then deposit a final version of their article in an open access repository. These U.S. initiatives contrast with the United Kingdom’s approach decided by the Research Councils UK, mandating paid, immediate (gold) open access to funded research.

At the same time, California Assemblyman Brian Nestande introduced a similar measure for state-funded research publications to be made open access within six months after publication. The California Taxpayer Access to Publicly Funded Research Act (AB-609) would mandate public access to articles funded through California state agencies and universities, and through the California Institute for Regenerative Medicine (CIRM). The California State Library would host the articles.

Will FASTR and the California Act pass? Nobody knows for sure, though legislator and public support for such legislation continues to increase.  Meanwhile, the American Association of Publishers (AAP) has predictably come out against FASTR.  What’s certain is that the Obama initiative requires a plan to be in place by August 2013. Some say that the White House hasn’t gone far enough to broaden access, however it is difficult to argue against it being progress toward opening access to research publications.

Voice your opinion on FASTR and the California Access to Publicly Funded Research Act.

Update, April 12, 2013: California bill AB-609 (California Access to Publicly Funded Research Act) will have its first hearing on April 17. To voice your opinion on this bill, contact Assemblyman Nestande’s staff. For more information, contact Anneliese at the Library.

Update, April 16, 2013: The hearing for CA AB-609 has been moved to May 1st at Assemblyman Nestande’s request to allow for supporters to be present at the hearing by the Assembly Accountability & Administrative Review Committee. The University of California Office of the President (UCOP) requested two amendments to the bill, which the author has agreed to. See the UC letter of support.

Update, May 14, 2013: CA AB-609 cleared the hearing by the Accountability & Administrative Review Committee on May 1 and is headed for review by the Appropriations Committee. The hearing received seven votes in favor and three against the bill. See a summary here. It’s not too late to provide feedback to the CA Assembly.

A previous post outlined one procedure for capturing bibliographic information for a Web page using EndNote/EndNote Web. It’s a little easier for RefWorks users since you can download the RefGrab-It plugin that’s specifically designed to do this. You download it from the Tools menu in your RefWorks account:

RefGrab-It is available in two versions: as a bookmarklet that works with either Internet Explorer or Firefox, or as downloadable plug-ins for Internet Explorer and Firefox. Say you want to reference the following CDC page:

You select RefGrab-It and it captures the basic bibliographic information:

You then import this into a RefWorks folder:

Note that in some cases RefGrab-It can look up standard numbers such as an ISSN or DOI to retrieve more complete records about the content you are viewing, which is why it works particularly well with PubMed and Amazon records. However, in most instances citation information captured using RefGrab-It is not as complete as records exported from databases such as PubMed, so you may have to do a little bit of editing.

Complete information for installing and using RefGrab-It is available in the online help section of your RefWorks account.

For an online tutorial click here.

The move from print to online copies of books continues as the UCSF Library expands its collection of ebooks and our annual purchase of ebook titles starts to outstrip print titles. Already UCSF faculty and students often request ebooks in favor of print.

As with print books, the best way to find whether we have access to an ebook is to search the Library Catalog. And as with ejournals, users must be on the campus network or logged into VPN to get to the full-text. And that’s where the similarities end. Navigating the various publisher and content-host provider platforms for printing, downloading, and reading offline is varied, and, in some cases, a little challenging.

Susan Boone, the UCSF Library’s  E-Resources Specialist, has developed an Electronic Books at UCSF LibGuide subject guide for the ebook collections. This  is a great way to get an idea of what’s available, and get quick directions for access, printing, and downloading of the Library’s  most heavily used ebooks.

You can now download the EndNote for iPad application from iTunes if you want to try it out. It’s on sale until February 11 by the way:

Watch a short video: EndNote on iPad: EndNoteSync, PDFs, and Groups