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: Information Management

News, Health Science Literature: Elsevier introduces SciVerse

Wow! For those of us who use information resources produced by Elsevier on a daily basis, it’s been a bit of a shock to tune into Scopus®, SciTopics® or ScienceDirect® this week to see how different they now look. (Or as a corny analogy, that figurative, proverbial 800-pound gorilla sitting in the corner of the room has decided to move house in September 2010.)

On Monday, Aug 30 2010, Elsevier announced their plans to combine and morph these sites into one platform named SciVerse Hub®. Read their press release here. First, I wanted to provide some definitions from the company as to which resources will be combined by this single search engine:

Image Source: http://www.scitopics.com/faq.jsp – All rights reserved – Copyright 2010

In plain terms, SciVerse Hub is an entry point for library users to simultaneously search the contents of:

  • Scopus (a subscription database indexing 18,000 titles from more than 5,000 international publishers including coverage of 16,500 peer-reviewed journals in the scientific, technical, medical and social sciences literature)
  • Science Direct (a subscription access point for searching 10 million articles from over 2,500 journals and 6,000+ e-books, reference works, book series and handbooks issued by Elsevier)
  • SciTopics.org (a free online expert-generated knowledge sharing service for the global research community)

Scirus.org® is a scientific search engine (created and maintained by Elsevier).  Scirus currently indexes 38 million websites found on open-access and mostly educational, scientific or government sites, incorporating what librarians refer to as grey literatureScirus will search these sources separately and bring back a sorted list of retrievals (with duplicate citations removed) to the SciVerse Hub site.

(Note: When I teach a Google Scholar class, considerable time is spent comparing along with the class participants why retrievals using Scirus.org to search for scientific information tend to produce “better” results than G–gle Scholar. Time well-spent, IMHO.)

Following are two screenshots from the SciVerse site:

Image Source: http://www.info.sciverse.com/what-sciverse – All rights reserved – Copyright 2010

And this page:

Image Source: http://www.scopus.com/home.url – All rights reserved – Copyright 2010

Note that the capability of searching each individual resource separately has been retained.


An informational video on SciVerse is well worth watching (and short at 3.5 minutes in length)… link to it here.  Another helpful reference resource: an 8-page training handout for using the new site which can be downloaded here.

In promotional materials, Elsevier refers to SciVerse as a “new knowledge ecosystem“. Their information products are integral to the daily work of clinical, health science and scientific research library users worldwide. Here’s hoping this migration runs seamlessly (as in: invisibly and glitch-free).

Image Source: http://www.info.sciverse.com/what-sciverse – All rights reserved – Copyright 2010

Medical Literature, Data Architecture & Organization: Idioms, Lexicons and Acronyms of Medicine? NIH, NCBI, MeSH, PubMed and Entrez

Image Credit/Source: http://www.ldoceonline.com/dictionary/pithy – All rights reserved – Copyright 2009

Try as I might, I couldn’t make this post pithy.  Sorry.

Based on some in-depth questions I’ve heard at the Reference Desk this month, this is a short long post on the structure and organization of medical information developed by U.S. agencies which collect, organize, share and otherwise distribute biological information for the purposes of basic science, clinical or translational research.

Graduate medical, dental or PhD students already search MEDLINE and other literature sources from National Center for Biotechnology Information (NCBI) but the purpose of this post is to illustrate ways to search these resources more effectively, or at least more time-efficiently.  If the first part of the post is too basic for you, please shoot down to the second section.

National Library of Medicine (NLM) and National Institutes of Health (NIH) are the U.S. agencies responsible for managing and administrating the NCBI, whose stated mission is to: 

develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules “.

Text source: http://preview.ncbi.nlm.nih.gov/About/glance/ourmission.html
  • Click here and here to see the collections of information resources accessible via the NCBI website.

  • Please take a look at this nice visualization of digitally- interconnected resources available from NCBI servers.


Entrez – also called the “life sciences search engine” – was designed by NCBI staff as a means to enable users to search across multiple databases or indexes to retrieve integrated search results from sequence, mapping, taxonomy and structural data for both human and non-human subjects.

Below is screenshot showing results from a search done recently on Entrez for data from NCBI servers on Protein 53, a human transcription factor:

Image Source: http://www.ncbi.nlm.nih.gov/sites/gquery – All rights reserved – Copyright 2009

Wow – That search retrieved almost too much information!  What if your search requirements don’t include the need for data about genomics or DNA sequencing?


Then consider the list of open-access Literature Databases available from NCBI.  A few of the best are highlighted here:


Pithy Librarian says:  “Try searching MEDLINE first.”

Library User responds: “Do you mean search PubMed?

MEDLINE, another NCBI database, is a major component of PubMed* but there is more there than just that database.  Happily, librarians from NLM have written a good MEDLINE FAQ page that explains those details.

MEDLINE is a medical literature index containing 19,000,000 records indexing articles from 5,200 international biomedical journals (in 28 languages), and covering the time period of 1948 through 2009.  Each year, approximately 600,000 new records are added to the database.   In other words, it’s a big database to search–but not as big as Scopus, a real Godzilla of a database, weighing in at 38,000,000 records.  The printed precursor to MEDLINE was Index Medicus, which is no longer being produced.

A key concept to remember when searching MEDLINE is that the database is indexed using what librarians call a “controlled vocabulary” – officially called the Medical Subject Headings List (or MeSH), a standardized thesaurus of 300,000+ terms used to electronically index each new article.

Think of MeSH terms as “tags“… similar to tagging your photos in Flickr.

How does these tags get into MEDLINE?  Actual (i.e., human) medical librarians working at the National Library of Medicine read and digitally assign appropriate MeSH terms to describe the contents and scope of individual journal articles. These information scientists are trained indexers and generally have other advanced degrees in biology, molecular genetics and so on which enable them to “parse” the mechanics of what the published article is about.

The majority of MEDLINE citations are tagged with 8 to 12 MeSH terms**. Because of those hand-crafted tags attached electronically to each journal article, when we search for a specific MeSH term, those records are retrieved into our citation list.  It is a scientific way to search. It is definitely not Googling.

A different way of constructing a precise search statement is to select MeSH terms in combination with the  list of clinical subheadings which combine with MeSH terms to narrow a search in an elegant way.  Clinical qualifiers are defined by NLM as:

83 topical qualifiers used for indexing and cataloging in conjunction with [MeSH] descriptors. Qualifiers afford a convenient means of grouping together those citations which are concerned with a particular aspect of a subject. Not every qualifier is suitable for use with every subject heading…. Subheadings are linked to the full record in the MeSH Browser.”


Following is a screenshot of the MeSH page showing the list of qualifiers which can be combined with the MeSH term “Pancreatic Neoplasms“:


Image Source: http://preview.ncbi.nlm.nih.gov/sites/entrez?db=mesh – All rights reserved – Copyright 2009


Sailors in old Hollywood movies sometimes were heard to yell, Land Ho!”

That is what I thought after scanning the 201o New MeSH Headings List recently released, and seeing a few new terms that medical librarians really like – such as this one:


Image Source: http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&index=25567&field=all&HM=&II=&PA=&form=&input= – All rights reserved – Copyright 2009


The list of new MeSH Descriptors is always interesting to browse.  National Library of Medicine states that currently there are 25,186 descriptors in the 2009 MeSH List.   Read the Introduction to 2010 MeSH List here.


Many excellent handouts and links to tutorials about using information resources from NCBI can be viewed at this link, and thanks to the librarians at the National Networks of Libraries of Medicine-Greater Midwest Region for creating this page.


Finally, please note that there are many more resources on the NCBI server than those explained above.  Gene libraries, DNA, RNA, proteins analysis or sequencing are very much out of the scope of my expertise.

One example is the link shown below – for DNA & RNA Resources – as one place to start exploration of genes, protein and sequence analysis (screenshot below):


Image Source: http://preview.ncbi.nlm.nih.gov/guide/dna-rna/ – All rights reserved – Copyright 2009


* PubMed has undergone recent design changes this month, although the “old” and the “new” PubMed versions will co-exist for the present.

** MEDLINE is a database comprised of 19,000,000 individual records.  Indexing a new citation requires careful attention to detail; tagging (indexing) for MEDLINE is never done by bots to create links based on the number of hits of a given term.  Each record is considered and evaluated by hand, which accounts for the indexing backlog (i.e., the difference between the moment when a new journal citation is delivered from the publisher to NLM and is put into the database, versus the period of time that it takes for that individual citation to show up in MEDLINE with a complete set of tags).  The whole indexing process generally is completed at NLM within 45-60 days.

News, Medical Students, Social Network Analysis: Digital Histories can’t be Deleted

The goals of this study were to describe reported incidents of medical students posting unprofessional content online at U.S. medical schools, describe current policies and views of medical school leaders regarding Web 2.0 use by medical students, and assess the relationship between unprofessional incidents and presence of policies.

Excerpt from an article published Sept 23/30, 2009 in JAMA (Vol. 302, No. 12: 1309-1315) written by Katherine Chretien, S. Ryan Greysen, Jean-Paul Chretien and Terry Kind


Medical Education is the theme of  this week’s issue of JAMA: Journal of the American Medical Association*.  Published in this issue is a seven-page article entitled “Online Posting of Unprofessional Behavior by Medical Students” written by four physicians affiliated with George Washington University and the Washington VA.

The questionnaire was sent out in March and April of 2009 to medical school deans or student affairs administrators at 130 allopathic schools of medicine accredited by the Association of American Medical Colleges.  The data was designed to be collected anonymously.  Staff from 78 medical schools chose to participate, with a return rate of 60%.

The questions in the survey focused on four principal areas: “School & respondent characteristics,  incidents of student-posted unprofessional online content, level of concern among student affairs deans or proxies and institutional policies and resources“.

About one-half of the deans or student affairs personnel who returned the survey reported that documented unprofessional behaviors by medical students were observed.

Following is a paragraph from the Commentary section of this article:

There are a number of actions that medical schools could take that might address some of the concerns raised by these findings. The formal professionalism curriculum should include a digital media component, which could include instruction on managing the “digital footprint,” such as electing privacy settings on social networking sites and performing periodic Web searches of oneself.  This is important given that residency program directors, future employers, and patients may access this information.

Excerpt from the above-referenced article published in JAMA (Vol. 302, No. 12: 1314).


The article will likely be read by many medical school administrators in the U.S. and abroad.  The literature is small but growing about what long-term effects one’s digital footprint (or captured misbehaviors) may have on a career in medicine. (As an example, two articles on this topic are linked here and here.) There were no social networking sites to capture a person’s online presence twenty years ago; the story is being told in the Now.

The JAMA article may serve as a wake-up call for those institutions of higher education who have yet to set up – or enforce existing – policies addressing online student profiles and conduct.

This week’s press coverage and subsequent discussions might also serve as a wake-up call to American medical students:   When is a good time to review your online profile? Answer: Quite likely, now.


Following are two related links.  First: click here for a collection of news stories or blog postings about this article, medical students and online behaviors compiled from Google.

Next: A different aspect of online identity and personal privacy issues was described by Carolyn Y. Johnson, who wrote an article published in The Boston Globe on Sept 20 2009.  Her report describes a 2007 research project conducted by two students at MIT enrolled in an ethics and law class.  Their software program, named Gaydar“, was used to import data from individual males’ Facebook pages, analyzing the relationships between stated  “interests”, “gender” and “groups of  friends” in order to make a statistical prediction about whether those men were gay.


.* JAMA is a subscription journal; if off-campus, use your proxy account number to connect in order to read full-text articles.


Searching Technologies, Cultural Evolution, Web 2.0: Slight Nostalgia for Olden Days, and Don’t Diss Librarians

Tis far better to be thought a fool than to open your mouth and remove all doubt.

-Quote variously attributed to Benjamin Franklin, Galileo, Socrates and Abraham Lincoln

You get the network that you deserve.

-Written by Brian Morressey


Being in the library/information business for more than a decade has taught me to take a long-term perspective about new companies or products (and possibly, a somewhat jaded outlook as well). What do I mean by this?

The technologies of Web 2.0/3.0 distribute your website, saves your comments on Twitter, immortalizes your blog-postings, shares your photos (for good or ill), exhibits your conference presentations or business plans, allows you to create an instant survey on Google Docs… each of these become instantly visible by those in your network, or worldwide.  (As YouTube.com famously advises, “Broadcast Yourself”.)  This connectivity has been described as ambient intimacy.

One of the first lessons a new blogger learns is how ridiculously easy it is to trip up online… when you make a mistake in a public and highly-distributed way, such an online event can make one very glad for the solitude of the workplace cubicle (while your face turns a deep, burning and lasting shade of red).  But that’s also a shared experience.  By joining up into the collective “we”,  it is possible to be anonymous yet harder to be invisible.  In digital life, these terms are elastic, relational, relative.  And Google never forgets.

Two recent examples of the downside of all that connectivity come to mind.   In 2008, a PhD student/blogger wrote on her Nature Network blog LabNotes that “I hate PubMed. I hate it with a burning passion.”  As seen in the comments garnered by that post, she was given a mild dressing-down by a variety of scientists, bloggers and medical librarians.  Some of us even offered to teach her how to search the database better.

Another more recent example involves the June 2009 roll-out of a clinically-oriented website named Clinical Reader.com, as medical librarian-blogger EagleDawg describes it, with additional commentary found at The Health Informationist blog.

These events have been Twittered about aplenty. One could take the view that the  company’s response to the librarian was that of a newbie… turn the prism, see it as free publicity.


By taking the long-range view, it’s not surprising to appraise commercial or non-commercial web sites as they come and go, in a literal sense*. Some sources stay the distance, some disappear quickly, some just can’t deliver a quality array of information, some sites are just plain ugly to use or to teach others to use, some crash frequently (thus losing your data), or are so difficult to navigate for results that users simply give up (and so then turn to Google Scholar).

For librarians, the perspective is a bit different than that of a researcher or medical student.  We are highly concerned with the content, scope and utility of individual information sources for our unique clientele.  That is why the mission of the librarians is to spend funds wisely, distribute the information efficiently along networks, assist those who have questions or problems with “digesting” the data, and to train our users to search well, collect and analyze their data.

Librarians aren’t the end-consumers of the information assembled by our subscriptions; we are more like information brokers and, to some extent, strive for impartiality.


Talk to almost any librarian with decades of experience, and they will tell you how it was before Google.  It was different.

The first library I worked in after graduate school was an academic library where the database subscriptions were delivered on CD-ROMs and loaded on an IBM server for distribution throughout the local area network.  Each month a new CD-ROM arrived and the old one was either returned to the company or discarded.

If a faculty member or student needed a comprehensive literature search, a librarian would use a dial-up modem to connect to a commercial information services corporation, Dialog, which charged by the minute for connection time, and charged individual fees for seaching a database, displaying citations, and for downloading each and every item.  Before even connecting to the site, the librarian had to check the so-called Dialog bluesheets to learn the scope and arrangement of fields for an individual database (or, which one of 300 individual databases were the best to search?).  It was all too easy to spend $100 of the library’s money on a search which might take 8-10 minutes.  And I still miss SilverPlatter.

Any student doing research had to physically be in the building in order to do any work.  Once the search was completed, they then had to trek around the stacks to locate the individual article in the journal.  They could read it in the building, or make a copy of it to take along for later reading.  After typing up a finished copy, the students handed-in a copy to their professor at the end of the term.  There was no TurnItIn then.

Sounds like ancient history, doesn’t it?

It was an analog world.   Our digital natives wouldn’t recognize the place.

And truly, it is so great in 2009 to offer our users Harrison’s Principles of Internal Medicine online.  What would our residents or students do without their ability to search and access medical information via Up to Date, PubMed or dozens of other sources?


* To take a brief “time-capsule” look at just how far academic libraries and collections have evolved over a decade can be appreciated by reading this ERIC Digest from 1990.

Finally… getting back to the feeling-jaded comment?  There are some who might feel a bit over-stressed by this always-on technological connecting.  If that applies to you, then check out the 2009 Cultural Dictionary (2nd edition) created by the ad agency Cramer-Krasselt, where the following definition was recently found:


Image credit: C-K Cultural Dictionary – Copyright 2009 – All rights reserved

News: October 2007 article in Journal of the Medical Library Association


Published in the October 2007 issue of The Journal of the Medical Library Association (Vol. 95, Issue 4: pages 381-387), this article is entitled “Decreased Hospital Length of Stay Association with Presentation of Cases at Morning Report with Librarian Support“. Four of the seven co-authors are librarians. Here is their summary of this research project:

Presentation of a case at Morning Report (MR), followed by the timely dissemination of the results of an online literature review, resulted in a shortened Length of Stay and lower hospital charges compared with controls. MR, in association with a computerized literature search guided by the librarians, was an effective means for introducing evidence-based medicine into patient care practices”.

There’s good news here for everyone involved: patients, physicians and hospital librarians!

Link here to the full-text of this article, available on open access via PubMed Central.