EBM and Clinical Support Librarians@UCHC

A blog for medical students, faculty and librarians about their use of evidence based medicine, clinical literature, Web 2.0, sources and search strategies

Tag Archives: Medical Literature

News, Academic Libraries, Medical Literature: For Wiley Journals, A New Look

Image Source:  http://info.onlinelibrary.wiley.com/view/0/index.html – All rights reserved – Copyright 2010.

In a next week, those who rely on subscription journals or database content from John Wiley Company – one of the largest sci-tech-medicine international publishers – will notice a major redesign of their website.

The familiar Wiley Interscience page is going to be replaced by their new portal, Wiley Online Library. While plans are put into place for the switch-over on Saturday, Aug 7, 2010, users may notice some downtime on the Interscience site.  (Both sites cannot run simultaneously.)

Following is a screenshot of the company announcement made in April 2010:

Image Source:  http://info.onlinelibrary.wiley.com/view/0/index.html – All rights reserved – Copyright 2010

Note:  The implementation of the new portal includes our subscription to the Cochrane Library.

Any major migration in technology can present some access or usability challenges.  (Forewarned is forearmed, the old saying goes.)  If you have bookmarked specific links to Wiley journal articles or e-textbooks, you will need to update the URLs to the new site…  as the old links will stop working within a few weeks.

Here’s hoping for a smooth transition for Wiley!

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Teaching & Learning in Medicine, Research Methodology, Biostatistics: Show Me the Evidence (Part 3)

This post is the third in a series entitled Show Me the Evidence. It is about the evidence gained from bibliometric data and journal impact factor analysis.

Let’s start with an excerpt from an 2008 article:

The assumption that Impact Factor (IF) is a number absolutely proportional to science quality has led to misuses beyond the index’s original scope, even in the opinion of its devisor*. When the IF is inappropriately attributed to all articles within a single journal, it leads to false applications regarding the  evaluation of individual scientists or research groups. This is, unfortunately, a common practice, especially among governmental funding boards and academic institutions entitled to judge scientists for positioning and grant allocation. The IF has thus accumulated huge strength and importance, mainly implied by its, at least to a degree, undue application as an index of overall scientific quality“.

Excerpt on page 1 from “The Top-Ten in Journal Impact Factor Manipulation” by ME Falagas and VG Alexiou, published in Arch Immunol Ther Exp (Warsz). 2008 Jul-Aug;56(4):223-6 – All rights reserved – Copyright 2010

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This post was sparked by a recent reference question from a retired professor who needed some assistance on how to find and search the Journal Citation Reports® database*, which is described by its’ producer, Thomson Reuters,  in this way:

Journal Citation Reports® (JCR) offers a systematic, objective means to critically evaluate the world’s leading journals, with quantifiable, statistical information based on citation data. By compiling articles’ cited references, JCR® helps to measure research influence and impact at the journal and category levels, and shows the relationship between citing and cited journals. “

Text source: Thomson-Reuters –http://wokinfo.com/products_tools/analytical/jcr/ – All rights reserved – Copyright 2010

So let’s take a look ways to find current evidence about publication patterns in the biomedical literature.

There were two things about JCR® that needed explanation for the professor.  First, the latest annual edition of JCR® was released in June 2010 and indexes journal citation data for the 2008 calendar year only (not 2009).  Second, only those journal titles indexed in the Web of Science database* are searchable in JCR®.

As one example: Let’s say that you’re a scientist working on stem cell research and you subscribe to ten international journals that are critical to your continuing professional knowledge, lab work and research.  It’ll be a good idea to check the list of 6,600+ journals that are included in the Web of Science database in order to determine if your “best” journals are searchable in Journal Citation Reports®.  If those titles are not covered in JCR®, you’ll be missing essential facts for comparing bibliometric data.

Here is a screenshot of a search done on the 2009 JCR® database for journals indexed under Cell and Tissue Engineering:

Image source: Thomson-Reuters – All rights reserved – Copyright 2010

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Some folks assume that “every journal in the world” is included in Journal Citation Reports, but that’s not the case.  9,100 journal titles were indexed in the 2009 edition.

Another thing to know is that there are six subsets available for annual subscription from  JCR® and UConn Libraries subscribes only to these two: Science Citation Index Expanded (indexing of 7,100 major journals across 150 disciplines and Social Sciences Citation Index (2,474 journals across 50 social science disciplines).

Below is a screenshot from an online tutorial about ways to search Journal Citations Reports® (with my added comment in the upper left-hand corner):

Image source: Thomson-Reuters – http://thomsonreuters.com/products_services/science/science_products/a-z/journal_citation_reports – All rights reserved – Copyright 2010

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Next, the professor asked: “I have a manuscript to submit for publication.  Is this the only place I should use to look at statistics about specific journal titles? “.

While JCR® is an important reference resource, it’s neither free or the only one available worldwide for researchers to search.  Below are sites which provide evidence that there are other ways to do citation analysis in year 2010 (some are free, some are via subscription).

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SCImago Journal & Country Rank Indicator (SJR). I like this site – it is easy to learn to use.  There are many ways to search their datasets (ranked by country, by journal title, by countries grouped by continent, etc.).  I also found their Map generators intriguing, which show comparative relationships between discipline or subject-specific citations.

Below is a screenshot of the SCImago Journal & Country Rank page showing a search done on Year “2008”,  “Medicine” as a general category, “Emergency Medicine” as a specialty and USA for the “country, with a limit for displaying journals that had at minimum 12 citable documents over 8 years:

Image source: http://www.scimagojr.com/journalrank.php – All rights reserved – Copyright 2010

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Link here to a 2007 paper written by the creators of SCImago which describe the process by which journals are ranked on their site.

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Those who have access to the Scopus database* through their library may have already discovered the Scopus Journal Analyzer, where allows one to select a discipline (shown below as “Biochemistry, Genetics and Molecular Biology”) and a journal title (“Cell” was searched below) and then choose method of analysis to determine journal impact.  Elsevier is the producer of the Scopus database. 15,000 journal titles are indexed for inclusion in Scopus analytics.

A screenshot below shows results of a search performed in Scopus Journal Analyzer recently for the broad topic of Biochemistry, Genetics and Molecular Biology.  The journal Cell holds the most-cited place in the list (no surprise there):

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The journal analyzer can be sorted using the following criteria: SJR versus SNIP.  I  found out that four years of data are necessary for sorting results using these filters.  Below, see a different screenshot:  rankings by SJR and SNIP for the same subject area:

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Explanations for SJR and SNIP were easily found in the Scopus Help section (screenshots shown below):   

Credit for all Scopus Images shown above: Elsevier B.V. – All rights reserved – Copyright 2010

Want a different way to search Scopus analytics for evidence? Use the search feature in Journal Analyzer to select and compare up to ten Scopus sources on number of citations, documents, and percentage not cited.

A 12-page PDF white paper (from 2006) is available to download from Scopus, entitled “Using Scopus for Bibliometric Analysis: A Users’ Guide“.  Following is an excerpt from that document:

Introduced in January 2006, the Scopus Citation Tracker enables users to easily evaluate research by using citation data. This tool offers at-a-glance
intelligence about the influence of a set of articles, an author or group of authors over time, so users can quickly spot trends using a visual table of citations broken down by article and chronology
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Text Source:  Courtesy of Elsevier B.V. – All rights reserved – Copyright 2010

Two other Scopus pages which I found useful were the Scopus Top Cited page and Scopus Journal Metrics Factsheet.

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No use trying to make this post pithy.  It would be an error not to mention the following means of assessing the scientific literature:  Eigenfactor, h-index and JANE.

University of Washington biology professor Carl Bergstrom and colleagues created the  Eigenfactor Project™.   The main webpage is  http://www.eigenfactor.org.

Give the interactive map a try: click here. Here is an example for Molecular & Cell Biology Map:

Image Credit:  http://www.eigenfactor.org/map/ –  All rights reserved – Copyright 2010

Following is an excerpt from a May 2007 article that Dr. Bergstrom wrote for the Association of College and Research Libraries publication, College & Research Library News:

We can view the Eigenfactor score of a journal as a rough estimate of how often a journal will be used by scholars. The Eigenfactor algorithm corresponds to a simple model of research in which readers follow citations as they move from journal to journal. The algorithm effectively calculates the trajectory of a hypothetical “random researcher” who behaves as follows: Our random researcher begins by going to the library and selecting a journal article at random. After reading the article, she selects at random one of the citations from the article. She then proceeds to the cited work and reads a random article there. She selects a new citation from this article, and follows that citation to her next journal volume. The researcher does this ad infinitum.

” Since we lack the time to carry out this experiment in practice, Eigenfactor uses mathematics to simulate this process.

” Because our random researcher moves among journals according to the citation network that connects them, the frequency with which she visits each journal gives us a measure of that journal’s importance within network of academic citations. Moreover, if real researchers find a sizable fraction of the articles that they read by following citation chains, the amount of time that our random researcher spends with each journal may give us a reasonable estimate of the amount of time that real researchers spend with each journal.

Text source: College & Research Library News – Vol 68:5 (May 2007) – All rights reserved – Copyright 2010

A slideshow presentation created by Dr. Bergstrom and presented at a conference hosted by Microsoft in 2009 can be viewed here.

Professor Alan Fersht wrote an article in 2009 published in PNAS Vol. 106(17):6883-4 (Apr 28 2009) entitled “The Most Influential Journals: Impact Factor and Eigenfactor” which is available free online on the PubMedCentral website.

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Physics professor Jorge E. Hirsch wrote a paper published in 2005 in PNAS entitled “An Index to Quantify an Individual’s Scientific Research Output“, in which he outlined the algorithm known as the Hirsch Index (or h-Index).

And – LOL – according to Scopus, that PNAS paper by Dr. Hirsch has been cited 575 times!

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JANE (or Journal Author/Name Estimator) is a software tool created in 2007 by members of the Biosemantics Group, a collaborative group at the Medical Informatics department of the Erasmus MC University Medical Center of Rotterdam and the Center for Human and Clinical Genetics of the Leiden University Medical Center.  Following is  how the creators of JANE describe the purpose of the tool:

Have you recently written a paper, but you’re not sure to which journal you should submit it? Or are you an editor, and do you need to find reviewers for a particular paper? JANE can help!  Just enter the title and/or abstract of the paper in the box, and click on ‘Find journals’ or ‘Find authors”.  JANE will then compare your document to millions of documents in Medline [over 10 years] to find the best matching journals or authors. ”  —

Source: http://www.biosemantics.org/index.php?page=jane – All rights reserved – Copyright 2010

M. J. Schuemie and J.A. Kors – two of the creators of JANE – published a paper about the software in the journal Bioinformatics – Vol 24:5 (Mar 1 2008).

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* Dr. Eugene Garfield was a co-founder of the Institute for Scientific Information, the producer of Science Citation Index.  A professor at the University of Pennsylvania and a prolific author, Dr. Garfield is now 85 years old.  Here is a link to his website.

In 1955, he wrote a paper titled “Citation Indexes to Science: A New Dimension in Documentation through Association of Ideas“, published in the journal Science (Vol. 122:108-111).  The online version is available to be read at this link.

From looking around on his Library website (url above), I think he has a sense of humor and the soul of an archivist. A great deal of his professional life has been taken up thinking about information management, and the ways in which scientists use their literature. I – and other librarians everywhere – should thank him for being an early adopter!

For example, in a commentary he wrote in 1963 published in the journal Science (Vol. 141:3579 – Aug 2 1963), titled “Citations in Popular and Interpretive Science Writing“, he admonishes mainstream periodical editors for not including basic volume and issue information.  Here is a direct quote: ” Librarians and scientists spend hundreds of hours tracking down precise literature citations which are missing in articles published in otherwise reputable publications like Scientific American, the New York Times, or The Sciences-a task that could be eliminated if brief but complete citations were given. This is certainly false economy and annoying “.  Garfield… You go!

The text of a presentation he gave at the International Congress on Peer Review And Biomedical Publication (2005) can be read online at  “The Agony and the Ecstasy: The History and Meaning of the Journal Impact Factor“.

I performed an author search on PubMed for his publications and created a small group of citations, those search results can be viewed here.

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In addition to thanking Dr. Garfield for creating this field of citation analysis, there are many fellow health science or academic librarians whose work has helped me understand this complex subject, or who have made public their own instruction for others to benefit from. These folks deserve recognition (and applause!).

Thanks to UCHC collection management librarian, Arta Dobbs, for her suggestions and explanations of sources and methods of bibliometric analysis.

Thanks to Janice Flahiff and Jolene Miller, librarians at Mulford Health Science, University of Toledo (Ohio) who have written a great fact sheet on the uses and misuses of interpreting journal impact factors.

Props to Kathi Sarli, health science librarian at Bernard Becker Medical Library of Washington University of St. Louis,  wrote a very useful library guide called “Tools for Authors“… check the section-tab for “Preparing for Publication“.

I enjoyed watching an excellent tutorial on Journal Impact Factors produced by librarians at the Ebling Library for the Health Sciences, University of Wisconsin-Madison.

Finally, remember this is all about Publish or Perish.


* Subscription via UCHC Library.  If off-campus, use your library proxy number to connect.

Search Engines, Genomics, Medical Literature: Tag Clouds come to PubMed via LigerCat

LigerCat is a search tool for NCBI’s PubMed that uses tag clouds to provide an overview of important concepts and trends. LigerCat aggregates multiple articles in PubMed, summing their MeSH descriptors and presenting them in a cloud, weighted by frequency “.

Except from:  http://ligercat.ubio.org/about#contact_us

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LigerCat is an abbreviation for Literature and Genomics Resource Catalog, which is a free PubMed search tool developed in 2009 as part of the Biology of Aging project at the MBLWHOI Library at the Woods Hole Marine Biological Laboratory.

LigerCat is great news for geneticists or anyone involved in translational research, a fairly effortless means of data mining for dynamic links to a very complex literature.

LigerCat can be used to search in several ways: 1) to locate and select a list of individual journal titles indexed in PubMed, 2) search using terms from the National Library of Medicine’s Medical Subject Heading (MeSH) list, 3) search using keywords, 4) search on Genes found in the NCBI databases.

Following is a screenshot of the LigerCat start page:

LigerCATfullscreen

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A screenshot of the “in process” retrieval process using LigerCat for the MeSH term “pancreatic neoplasms” and keyword term, “pain“,  is shown below.

Notice that LigerCat provides the searcher two choices for getting the results, which could take a few minutes: the option of simply waiting a few moments for the search to execute, or save the shortened URL of the search-strategy to revisit the results at a later time.  That’s nice!

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ligerCatPancreaticNeoplasmsandPain

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.Here is a screenshot of the retrieval from LigerCat – which took about 20 seconds to execute:

ResultsLigerCat

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.Next:  I used LigerCat do a Gene Search for specific protein sequences.  This is how the site authors described the process of searching genes:

LigerCat is performing a live BLAST to find similar sequences to your query. Once the sequences are identified, LigerCat will use its indices to map the genes into a set of PubMed articles that reference those genes, and extract all the MeSH terms for those articles. “

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I went to NCBI to  find the Entrez Protein page and then searched FASTA for P53 and Homo Sapiens.  The search statement I found looked like this:

>gi|14993572|gb|AAK76358.1| P53 [Homo sapiens]
VGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDS

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This string was copied-and-pasted into the LigerCat Gene search box for the following result:

LigerCatBLASTP53HomoSapiensresult

All images above – Courtesy  of LigerCat – All rights reserved – Copyright 2009

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As a medical librarian, I think LigerCat is a great step forward — but because the value of information lies in the eye of the beholder — I’ll wait to hear the opinions of geneticists and research scientists as they weigh in on this new search engine.

For a different example of using this resource, see this link from the blog Biology of Aging, dated Aug 21 2009.

News, Searching the Medical Literature: Two Expert Opinions on Searching, or PubMed and Beyond

Today is a great day to highlight the recent posts of two fellow medical bloggers:  the first is from Laika’s MedLibLog, written by a Dutch research-scientist/medical-librarian; the second post is from Life in the Fast Lane, a blog written collectively by a group of Australian physicians.

Each author has written definitive posts about the mechanics – and utility – of searching the medical literature, and evaluating what has been found.

These posts should be seen as instant classics – and required reading for new graduate students in medicine, dental medicine or biomedical research or just about anyone with an interest in finding more-pertinent clinical information (in less time).

Their descriptive clarity in explaining what to search, and how to search is pitch-perfect.

Thank youLaika and SandNSurf – for writing them!

Please read:

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Next: Following are several quite different compilations of medical information resources written by librarians.

Elena Giglia, a medical librarian from Central Library of Medicine, University of Turin, Italy,  wrote in 2007 an excellent overview of the medical literature entitled “Beyond PubMed: Other Free Biomedical Databases.  This 11-page article was published in the European Journal of Physical and Rehabilitation Medicine (Europa Medicophysica) – Vol. 43(4):563-9 (Dec 2007). It is available online for anyone to read.

Ms. Giglia is the author of a very recent article, “Medline/PubMed revisited: new, semantic tools to explore the biomedical literature“, published June 2009 in Eur J Phys Rehabil Med – Vol. 45(2):293-7 (subscription required).

Law librarian Gloria Miccioli wrote a summary of medical sources targeted for legal professionals, entitled  “Researching Medical Literature on the Web” (published Sept 22 2008), found on LLRX.com.

The LLRX website also offers a list of links for librarians (or others) doing legal research.

My own Home Week: Evidence Based Medicine Resources page on Libguides.com was created – and is updated annually – as a source-sheet for third-year medical students at UCHC as they rotate throug h their clinical clerkship year.

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Finally:  Librarians working in academic health science libraries offer a variety of digital training tutorials or subject lists for orienting their students, residents and faculty to the technical aspects of searching the literature of medicine.

A quick search on Google for “tutorials searching medical literature” brings up an eclectic group of 968,000 retrievals.

The same search using Bing f0und 1,530,000 well-filtered retrievals.

News, Search Technologies: Give Mednar a Try

Mednar [a federated medical search engine introduced in 2008] promises to become a standard tool of power searchers in the health sciences (e.g., medical librarians, physicians, health care researchers) and for savvy consumer searchers who seek supplements to such standard tools as MedlinePlus or PubMed “.

Quote from AltSearchEngines.com writer Hope Leman, who ranked Mednar as her Number 1 choice in the list published Dec 29 2008 entitled “Top Ten Health Search Engines of 2008

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After reading good reviews about Mednar recently, it seemed like a good idea to try it out. Below is a screenshot of what was retrieved on a recent search  for “inoperable pancreatic cancer” using the federated search site:.

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mednar1

Image credit/source: Mednar.com – All rights reserved – Copyright 2009

Once the search is processed, you’ll get a prompt asking if you want to include all sources, which I clicked Yes for.  The search is then reprocessed including all retrievals from those sources searched by the engine.

This screen capture shows some of the MEDNAR ‘top retrievals’ from all sources. It is a good sign that the most hits were found in PubMed:.

mednarssearchsources

Image credit/source: Mednar.com – All rights reserved – Copyright 2009

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This fall, I began teaching a Google Scholar class.  One of the exercises I ask the group to do is to compare results from different sources by running searches using identical “same-search-terms”.  Currently Google Scholar and Scirus.com (from Elsevier) are the compare-and-analyze search sites.

The more I use Scirus, which is a free database, the more value I find there for locating material found in what librarians call “the gray literature“. It has been improved a great deal since it was first introduced. If you’re not currently using Scirus, you might want to add it into your tool-kit of clinical research sites.

Here is a quote from the Scirus “About” page:

is the most comprehensive scientific research tool on the web. With over 450 million scientific items indexed at last count, it allows researchers to search for not only journal content but also scientists’ homepages, courseware, pre-print server material, patents and institutional repository and website information…. 

How Does Scirus Rank Results? Search results in Scirus are, by default, ranked according to relevance. It is also possible to rank results by date. You can do this by clicking the Rank by date link on the Results Page.

Scirus uses an algorithm to calculate ranking by relevance. This ranking is determined by two basic values:

  • Words – the location and frequency of a search term within a result account for one half of the algorithm. This is known as static ranking.
  • Links – the number of links to a page account for the second half of the algorithm – the more often a page is referred to by other pages, the higher it is ranked. This is known as dynamic ranking.

Overall ranking is the weighted sum of the static and dynamic rank values. Scirus does not use metatags, as these are subject to ranking-tweaking by users.

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480 million websites indexed!  This makes for a lively comparison of results… and as they are projected on the overhead, everyone in the class room can examine (on the big screen) how results are ranked, currency of the retrievals and how results (or links) differ from these two sources. 

Scirus search results for scientific information are (IMHO) better, consistently and over time, than those found via Google Scholar.  And most of the time in this class, I manage to persuade the group to begin using Scirus over Google Scholar.

Academic librarians are reminded every day how fortunate we are, as a group, to have the financial resources that allow us to offer world-class (and costly) subscription information resources to our researchers, clinicians, hospital administrators, graduate students or the general public. There are many  resources available to answer those difficult patient care or research questions. Google Scholar and Scirus are just two of the many resources available.

So will I start using Mednar?  I liked the results well-enough, but won’t give up using the precise technical limits and search filters available in PubMed, or the comprehensive, deep searches available by using the 15,000 journals indexed in Scopus.

But maybe for the next Google Scholar class, we’ll add Mednar to the mix.

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Lastly: here is another link from AltSearchEngine.com offering up a three-part primer on the subject of the Deep Web and how federated search engines operate (Jan 12 2009).

Editors note: Deep Web Technologies, which is a for-profit corporation, is the producer of Mednar.  Deep Web also sponsors a blog called FederatedSearchBlog.com.

News: MD Consult – Four E-Textbooks Updated (UCHC only)

Earlier this month, I posted about updated content from the UCHC subscription database, MD-Consult (click here to read Oct 5 2007 post).

Today, MD Consult posted a news notice regarding another four standard medical texts now online in the current 2007 edition. Updated titles include the 23rd edition of Cecil Medicine (Goldman), Practice of Geriatrics (Duthie – 4th edition), Obstetrics: Normal and Problem Pregnancies (Gabbe – 5th edition) and Textbook of Clinical Neurology (Goetz – 3rd edition).

mdconsultnews.jpg