HSLS Update: Online Only

This issue of the HSLS Update introduces a new look and format for the newsletter. Just as library journals are moving from print to electronic, the Update is now “e-only” and will cease publishing print issues. You can receive the Update via an RSS feed or by email subscription by registering at: www.hsls.pitt.edu/updatereport/?page_id=227.

HSLS Account holders are automatically subscribed to ensure that you receive the latest information about new resources, upgrades and services. Feedback from our readers and suggestions for future articles are welcome! E-mail the editor at hslsnews@pitt.edu.

Director’s Reflections . . . Legislation Mandates Public Access to Reports of NIH-Funded Research

Barbara EpsteinDecember 26, 2007, President Bush signed into law a requirement that all reports of research funded by the National Institutes of Health (NIH) must be publicly available within 12 months of journal publication. The legislation requires researchers to deposit electronic copies of their final, peer-reviewed manuscripts, including all graphics and supplemental materials, into the National Library of Medicine’s online archive, PubMed Central (PMC) www.pubmedcentral.nih.gov.

Though some commercial scientific journals already have provisions for public access to research articles after a designated time period, most do not. Since the NIH calculates that there are approximately 80,000 articles published each year reporting on its funded research, the new mandate will dramatically increase access to the results of this research.

Specifically, the NIH Public Access Policy applies to all peer-reviewed articles that arise, in whole or in part, from direct costs funded by NIH, or from NIH staff, that are accepted for publication after April 6, 2008. Investigators and their institutions are responsible for ensuring that any publishing or copyright agreements concerning submitted articles fully comply with the Policy. Beginning May 25, 2008, all applications, proposals or progress reports to the NIH must include the PMC or NIH manuscript submission reference number when citing applicable articles that arise from their NIH funded research.

NIH estimates that submitting a manuscript usually takes less than ten minutes. Note that the Policy does not apply to non-peer-reviewed materials, such as correspondence, book chapters, and editorials. Authors who publish in an open access journal must still submit their article to PubMed Central if the journal does not have an articulated agreement to deposit articles in PMC.

Researchers are advised to consult the NIH Public Access Web site publicaccess.nih.gov for complete information and answers to frequently asked questions. Included are detailed instructions on how to comply with the policy, how to address copyright and publisher negotiations, how to submit a manuscript to PubMed Central, and a list of journals that submit articles on behalf of their authors. For a broader discussion of the policy’s implications, see the University Times article “NIH Mandates Open Access to Researchers’Publications“, 40(10), January 24, 2008.

Earn CME Credits by Watching TV

NCME-TVNCME-TV, a Web-based series of streaming CME videos, is now accessible through the HSLS Web site. Physicians familiar with NCME (Network for Continuing Medical Education) videos and DVDs will welcome this new Internet-accessible format that allows access to videos anytime, from any computer.

NCME-TV provides updates on topics relevant to physicians, including:

• Hospital quality, performance and credentialing issues, and programming to help meet Joint Commission requirements
• Master lectures on critical issues in medicine and disease states
• State-mandated topics such as HIV/AIDS management, domestic violence and pain management
• Topics in the news, such as avian influenza and bioterrorism

NCME-TV titles available through the internet will have a “Launch” icon. Older NCME programs in DVD or VHS format can be accessed through the Computer and Media Center at Falk Library. Search the library catalog, PITTCat http://pittcat.hsls.pitt.edu/, to check the title’s availability.

All NCME programs are certified for AMA PRA Category 1 Credit™ on an hour-for-hour basis. In addition, most programs are certified for prescribed credit by the American Academy of Family Physicians and Category 2A credit from the American Osteopathic Association. CME certificates are sent after receipt of the program’s evaluation.

To access NCME-TV visit: www.hsls.pitt.edu/resources/ncmetv. First time users must create an NCME-TV account, which allows them to receive monthly email notifications of new NCME-TV programs.

~ Charlie Wessel

RefWorks Q&A

RefworksRefWorks, a Web-based product for managing citations and creating bibliographies, is now available to HSLS’ University of Pittsburgh and UPMC patrons. Look for the RefWorks link on the HSLS More Resources page www.hsls.pitt.edu/resources.

What’s the difference between RefWorks and EndNote?

Both programs allow users to build personal databases of references to articles, books, chapters, and other publications. With Microsoft Word, these references can be inserted into documents. Formatted bibliographies can be created using various output styles, including journal specific or standard styles such as MLA.

The main difference is ubiquity. Since RefWorks is a Web-based product, you can access it and your saved references from anywhere. EndNote, a desktop-based program, must be separately installed on each computer.

I’ve used EndNote for years. Should I switch to RefWorks? I’ve never used any bibliographic citation management software before. Which is better for me: RefWorks or EndNote?

Answers to these questions: “Not necessarily” and “It depends.” A long-time EndNote user with a well-developed routine for updating the program and saving references on multiple computers has no compelling reason to change. A researcher who has written many papers using EndNote or attached a large number of PDFs to EndNote records also has a long-term investment to consider.

RefWorks might be right for a student who wants to streamline term paper writing or who is starting research for a dissertation, assuming reliable Internet access. It is also a good choice for anyone needing an easy way to share references with colleagues.

Consider using both products, depending on the circumstances. No decision is irrevocable: references saved with one product can be easily converted to the other.

Can I use RefWorks to search databases directly for references, the way I can with EndNote?

With RefWorks, you can search free sites such as PubMed, PITTCat, and the catalogs of many other institutional libraries; however you cannot directly search subscription-based products such as Ovid and EBSCOhost databases. References found through searching subscription databases independently of Refworks, however, can easily be exported into the program. For products that do not support direct export, save your references as a file and import the saved file into RefWorks.

Can I use RefWorks off-campus?

With your individualized account, you can access RefWorks and your saved references from any location. Remember you must first log into either HSLS remote access www.hsls.pitt.edu/services/remote/ or the University Library System’s SSLVPN service https://sslvpn.pitt.edu/dana-na/auth/url_default/welcome.cgi. Note that Write-N-Cite, the RefWorks utility used to create and edit citations in Word, must be specially configured for remote access.

More information on using RefWorks is located at HSLS’ How Do I? page www.hsls.pitt.edu/lore/. Type “RefWorks” in the search box located at the top.

~ Patricia Weiss

Learning @ Your Pace

Learning @ Your Pace
New to the Health Sciences Library System? Interested in learning how to search HSLS online resources more efficiently? Check out Learning @ Your Pace: www.hsls.pitt.edu/services/learning_at_your_pace, a Web page containing online tutorials developed especially for HSLS patrons.

Tutorials in the library basics section provide a brief overview of HSLS, instructions for accessing HSLS electronic resources from off-campus, and explanations of basic database concepts. Users can also view a series of tutorials detailing how to use the search.HSLS function to find full-text journal articles, search the PubMed database, or explore the HSLS electronic book collection. Note that all tutorials require the Flash plugin.

Instructors can add these modules to BlackBoard course sites by using the “external links” option. For questions about this option, contact HSLS at medlibq@pitt.edu or 412-648-8796.

~ Mary Lou Klem

Cardiosource Plus

Cardiosource Plus
HSLS now provides access to the institutional version of Cardiosource Plus, a specialized Web site, formerly available only to members of the American College of Cardiology. First time users may register for a free account to use premium services and resources listed below:

• More than 1000 clinical trials, including summary slides
• More than 4500 clinical images
• Expert interviews and case studies, offering over 100 hours in CME
• Heart Songs audio product
Journal of the American College of Cardiology (JACC) online
• ePocrates Rx Online Drug Database and Essentials for Cardiology
• The most recent self-assessment programs including ACCSAP 6, EchoSAP 5, CCTSAP, CV Drug Therapy, ECGSAP 3, HeartValveSAP and ArrhythmiaSAP
• Rapid news summaries from major cardiovascular meetings.

Cardiosource Plus’ target audience includes students, practitioners and researchers, but any health care professional with interest in cardiovascular information will find it helpful.

The information is organized for easy use with drop down menus and quick links on the sidebar. Interactive features like “Analyze This Image” and “Talk Back” engage casual browsers. The “Journal Scan” feature is updated daily. The Cardiosource Video Network allows users to watch news briefs, conversations with experts, a featured articles program, and updates from the JACC editor-in-chief.

To access this resource type “Cardiosource Plus” into the search.HSLS box on the HSLS home page.

~ Michele Klein Fedyshin

Ovid’s New Look

In January, HSLS introduced Ovid’s redesigned interface, now called OvidSP. Although visually quite different, the updated interface commonly used to search databases such as MEDLINE and PsycINFO, maintains the same functionality.

Search options are brought together under five tabs. Through the HSLS Web site, the Advanced Ovid Search is the default tab, opened automatically when OvidSP is launched. The advanced search allows for searching with a controlled vocabulary, such as Medline’s Medical Subject Headings (MeSH). If a search term entered is not in the controlled vocabulary, the search interface will suggest the appropriate term(s), or allow for free-text keyword searching. Search results are displayed in reverse chronological order, i.e. most recent citations are displayed first.

The Basic Search tab allows users to search by entering free text terms or questions such as “weather related migraine” or “ekg changes in hyperkalemia”. The search can include “related terms”, as defined by OVID, or check for misspellings. These options can be chosen via checkboxes below the search box. Quotes, hyphens, or parenthesis should not be used in the search. It is important to note that Basic Search is designed to find the most relevant results, not all possible results. Results are sorted by relevancy, not publication date.

The Find Citation tab locates missing citation information (e.g., page or volume numbers). Enter known information and then search. The complete citation will appear.

The Search Tools tab explores the relationship between terms and subjects within the context of the database being searched. Enter a term and then select map term, tree, permuted index, scope note, explode, or subheadings for more information.

The Search Fields tab allows the search to be narrowed to specific fields, such as grant number or institution.

Other new features in OvidSP include the ability to create RSS feeds for new citations in an area of interest, or the table of contents of a current journal. The Search Aid box, which appears on the left of the screen once a search has been run, allows searches to be narrowed by the subjects, author, or journals found in the retrieved citations.


For more information about OvidSP, view the short HSLS-produced tutorial available at www.hsls.pitt.edu/resources/ovid/.

~ Linda Hartman

HSLS-supported Pathway Analysis Software

• Are you engaged in basic science or translational research?
• Do your experiments include microarray expression, proteomics profiles, SNP/haplotype and mutation maps, or siRNA knockouts?
• Does your data include huge lists of genes or protein IDs?

Research in biological sciences has moved from primarily single gene-focused to biological systems-based experimentation. Advances in high-throughput (HT) technologies (e.g., protein or microarrays) are producing large-scale protein/gene data sets. The biological significance of these complex data sets can be uncovered by exploring biological pathways, functions, and molecular interactions associated with the genes or proteins derived from HT expression experiments. This requires systematic comparison of these large data sets with knowledge drawn from the published literature. The number of articles and journals published is increasing at an exponential rate, so much so that it is impossible to manually analyze the HT experimental results set. To help researchers with this challenging task, powerful systems biology tools commonly known as pathway analysis software have been developed. These tools search databases of gene or protein information culled from published literature.

The Molecular Biology Information Service at HSLS is pleased to offer access to major leading commercial pathway analysis packages. The list includes Ingenuity Pathways Analysis (IPA) from Ingenuity Systems, MetaCore from GeneGo, Inc., and PathwayArchitect from Stratagene.

IPA enables biologists and bioinformaticians to identify the biological mechanisms, pathways, and functions most relevant to their experimental datasets or genes of interest.

MetaCore is an integrated software suite for functional analysis of experimental data covering microarray & SAGE gene expression, SNPs & CGH arrays, proteomic, metabolomics, pathway analysis, yeast 2 hybrid, and other custom interactions.

PathwayArchitect uses curated and automatically created databases to identify relationships among genes, small molecules, cell objects, & processes, build networks, and create pathway diagrams suitable for publication.

Exploring your data with all three software packages serves to reinforce and provide confidence in your results. These tools can be used as complementary resources to:

  • discover biological and chemical information relevant to your research
  • explore context by building customized pathways, overlaying drug, biomarker and toxicity information, and computing cellular and molecular function
  • identify biological interactions among genes of interest from the published literature and link to the supporting sentences in the matching journal article citations
  • connect two molecules by the shortest possible path
  • import a list of genes and arrange them into a pathway
  • find common upstream and downstream regulators of a group of genes
  • display array results according to subcellular localization

To access these resources visit www.hsls.pitt.edu/guides/genetics/licensed_tools.

The HSLS Molecular Biology Information Service offers access information, hands-on workshops, and group or individual consultations for these resources. For more information, visit www.hsls.pitt.edu/guides/genetics or contact Ansuman Chattopadhyay (ansuman@pitt.edu, 412-648-1297) or Carrie Iwema (iwema@pitt.edu; 412-383-6887).

~ Ansuman Chattopadhyay and Carrie Iwema


www.antimicrobe.org is a reference tool for physicians, microbiologists, and pharmacists who are interested in pathogens and antimicrobial agents.
Victor L. Yu, professor of medicine, University of Pittsburgh, and chief, Infectious Disease Section, VA Pittsburgh Healthcare System, is editor-in-chief of this resource. Content is based upon his textbooks Antimicrobial Therapy and Vaccines, Vol. I: Microbes, Antimicrobial Therapy and Vaccines Volume II: Antimicrobial Agents, and the in-process title Empiric. Also contained in this resource is HIV Clinical Manual, edited by David D. Ho.

These titles are searchable together or can be browsed independently by clicking on the specific book link. A “sliding table of contents” is available to allow simplified navigation through titles.

A unique feature of www.antimicrobe.org is the Smart Search, designed to retrieve specific microbe information including microbiology, susceptibility, epidemiology, antimicrobial therapy, clinical manifestations, vaccines, laboratory diagnosis, and more. Also displayed is a “Guided PubMed Search” link that retrieves relevant references. Smart Search can be accessed through links following the name of any individual pathogen in the Microbes textbook or through the “advanced search screen” link located on the main page.

To access www.antimicrobe.org, type “www.antimicrobe.org” into the search.HSLS quick search box at www.hsls.pitt.edu. Once on the resources main page, users must click on the link “Institutional Users Access Here”, located on the right of the page.

This article is adapted from a December 2005 HSLS Update article written by Charlie Wessel.

HSLS Staff News

The HSLS Staff News section includes recent HSLS conference presentations, citations to HSLS published articles, staff changes, staff promotions, degrees earned, etc.


Farewell to Nicole Muehlbauer, operations specialist in the Computer and Media Center and productions/graphics editor of the HSLS Update newsletter. Muehlbauer left HSLS to finish her MLIS degree with School Library Certification from the University of Pittsburgh.

Welcome to Mary Jo Dorsey who joins HSLS as a visiting reference librarian. Dorsey earned a BS degree in Biology from Carlow College, an MLS from the University of Pittsburgh School of Information Sciences (SIS), and will receive a Ph.D. from SIS later this year. For the past five years, she has been director of the Richard M. Johnston Health Sciences Library at West Penn Hospital.

The HSLS Molecular Biology Service was featured in the article “Pitt Scientist-Librarians Guide Researchers” in University Times, 40(8), December 6, 2007.


Ester Saghafi, reference librarian, presented a talk, “Show Me the Evidence: Helping Mental Health Professionals Track Down the Best Evidence” at the Association of Mental Health Librarians conference, October 26-28, 2007, in Orangeburg, N.Y


John Erlen, history of medicine librarian, published “Dissertation/Theses” in Canadian Bulletin of Medical History, 24(2): 505-507, 2007.