2010 Issue

HSLS has upgraded our subscription to the journal Annals of Internal Medicine to include access to “Epubs ahead of print,” an option requested by many users. The notation “Epub ahead of print” appears when publishers submit citations for articles to PubMed that appear on the Web prior to their publication in final or print format.

You’ll also have access to the popular In the Clinic feature. In the Clinic provides evidence-based answers to frequently asked questions about the management of patients with common clinical conditions.

Parts of this article were reprinted from the Annals of Internal Medicine Web site and PubMed.

~ Leslie Czechowski

The HSLS Molecular Biology Information Service recently licensed two new bioinformatics resources from CLC bio. CLC Main Workbench supports researcher’s daily bioinformatics needs and CLC Genomics Workbench handles sequencing data from high-throughput sequencing systems.

CLC Main Workbench is an integrated software package that enables users to perform advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, seamless data management, and user-friendly graphical viewing and output options.  Noteworthy features include but are not limited to:

• Expression analysis including digital gene expression: support for both microarray and sequencing-based expression data, clustering algorithms, tools for Gene Set Enrichment Analysis
• DNA sequence analysis: primer design, in silico PCR, cloning, SNP annotation, restriction enzyme analysis and management
• RNA structure analysis: secondary structure prediction, symbolic representations
  Protein sequence analysis: antigenicity, PFAM domain search, transmembrane helix prediction, proteolytic cleavage detection
• Pattern search: motif searches for basic patterns, using regular expressions, and/or with ProSite patterns
• Database searches: GenBank Entrez, BLAST on local databases, PubMed
  Project and data management: detailed history log, full integration of data input, data management, calculation results, and data export
• Other bioinformatics features: multiple alignment of DNA, RNA, and proteins, sequence editor, local complexity region analyses

CLC Genomics Workbench is a cross-platform desktop application that incorporates cutting-edge technology and algorithms for analyzing and visualizing next generation sequencing data.  Some of its key applications are:

• Genomics: whole genome re-sequencing and targeted re-sequencing of genomes of any size and type, de novo assembly of an unlimited number of reads, SNP and DIP detection, identification of genomic rearrangements
• Transcriptomics: digital gene expression based on RNA-Seq, including a wide range of downstream gene expression analyses, novel transcript/exon discovery, interactive view of assemblies and derived gene expression data
• Epigenomics: ChIP-seq analysis, peak finding and refinement, false discovery rate and background distribution tables and graphs

To access CLC Main Workbench or CLC Genomics Workbench, visit Licensed Tools on the HSLS Molecular Biology portal.

For more information about CLC bio resources, call Ansuman Chattopadhyay at 412-648-1297, Carrie Iwema at 412-383-6887, or contact Ask A MolBio Librarian.

Parts of this article were reprinted from CLC bio.

~ Carrie Iwema

Multimedia resources for medical and patient education are becoming more widely available. MedlinePlus, from the National Library of Medicine, is a trusted source of freely accessible consumer health and drug information. It’s also a leader in providing high-quality illustrations and videos for patient education.  If you prefer to get health information from videos, tutorials, calculators, quizzes and games, the new Videos & Cool Tools is for you.

Videos & Cool Tools features three video collections: “Interactive Tutorials,” “Anatomy Videos,” and “Surgery Videos.” All videos and narrated tutorials are organized by topic and are also embedded in associated articles throughout MedlinePlus.

Interactive Tutorials
These easy-to-use, hands-on tutorials are arranged by diseases, tests and diagnostic procedures, surgery and treatment procedures, and prevention and wellness topics. Among the many tutorials you can choose from are “Heart Attack,” “Arthroscopic Surgery for Shoulders,” and “Back Exercises.”  Each interactive tutorial includes animated graphics, audio, and easy-to-read language.

Health Calculators and Quizzes
If you want to know how healthy you are, or where you might need to make improvements, try one of the health calculators or quizzes. Examples include the “Alcohol Calorie Calculator,” “Calculate Your Body Mass Index,” and “Risk Assessment Tool for Estimating Your 10-Year Risk of Having a Heart Attack.”

Anatomy Videos
The anatomy videos demonstrate how diseases and conditions can affect various parts of the body. You can watch videos on a wide array of topics from “Blinking” to “Ovulation” to “Snoring.”

Surgery Videos
The surgery videos are a licensed collection of over 120 videos of surgical procedures filmed at hospitals across the United States. It’s organized primarily by body system, and cross-indexed to more specific areas of interest, such as “Cancer” and “Child and Teen Health.”

Videos & Cool Tools also offers easy-to-use tutorials on understanding medical words and evaluating health information.  For anyone seeking reliable health information, Videos & Cool Tools can help.

~ Andrea Ketchum

In the last year, HSLS users consulted over 30,000 documents from e-books available through the vendor Stat!Ref. For example, Sparks and Taylor’s Nursing Diagnosis Reference Manual had over 7,000 downloads during the year. These statistics give evidence that HSLS users want and use our e-book collections.

However, we face one troubling issue–our users also experience turnaways from time to time. That is, when trying to click through to a Stat!Ref e-book, they receive a notice that the e-book is in use and unavailable. This occurs because most of our e-books allow a limited number of concurrent users (number of people who can be viewing the same e-book at the same time).  For example, Stat!Ref allows  10 concurrent users, which is not always adequate. If you do get turned away from a Stat!Ref e-book or any other e-book, please try again in a few minutes, as the situation generally doesn’t last long. However, if it happens for too long or repeatedly, e-mail Ask A Librarian. It may be possible to increase the number of users for specific titles if they are extremely popular. For example, we will increase the concurrent users allowed for Sparks and Taylor this fall because the book will be used in a course assignment.

Stat!Ref also contains a number of other vital texts, such as ACS Surgery: Principles & Practice, AHFS Drug Information, Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR),  Goldfrank’s Toxicologic Emergencies, and the ICD-9-CM. All of our e-books can be accessed in numerous ways:

• Search for the title in the Pitt Resources Quick Search box
• Search for the title in PITTCat for the Health Sciences
• Browse e-books by subject
• Search the full text of HSLS e-books in the E-Book Full Text search box

~ Leslie Czechowski

Not sure where to submit your manuscript? Try consulting JANE: Journal/Author Name Estimator, a freely available Web-based tool, to identify suitable journals. In addition to locating journals, JANE can also locate relevant articles to cite in your paper and even help find manuscript reviewers.

To search in JANE, enter the title, author, and/or abstract of the paper in the search box, and click on “Find journals,” “Find authors,” or “Find articles.” JANE will then compare your document to millions of documents in MEDLINE to find the best matching journals, authors or articles. JANE can also be searched by keyword.

JANE is updated monthly and includes papers with abstracts that were published in the last 10 years. The database works by searching for the 50 articles that are most similar to your input. For each of these articles, a similarity score between that article and your input is calculated. The similarity scores of all the articles belonging to a certain journal or author are summed to calculate the confidence score for that journal or author. The results are ranked by confidence score.

JANE also calculates an Article Influence (AI) score. The AI measures how often articles in the journal are cited within the first five years after its publication. These citations are weighted based on the influence of the journals from which citations are received: being cited in an article in Science can boost a journal’s AI more than being cited in an article in an obscure journal.

No need to worry about submitting your abstract to JANE. The information sent to the JANE server is not stored. It is kept in memory for as long as needed to calculate the scores and formulate the response page, and then it is discarded from memory.

JANE is produced by the The Biosemantics Group.

Parts of this article were reprinted from the JANE: Journal/Author Name Estimator Web site.

~ Jill Foust

HSLS and the University’s School of Information Sciences (iSchool) recently enrolled our first cohort of students in a newly created Certificate of Advanced Study in Health Sciences Librarianship (HealthCAS) program. This online post-Master’s degree program, funded by a grant from the Institute of Museum and Library Services, allows librarians to expand and enhance their knowledge of the theory and practice of health sciences librarianship. The HealthCAS program is a unique collaboration between faculty in the Department of Library and Information Sciences at the iSchool and practicing faculty librarians at HSLS.

Over the course of the year-long program, HSLS faculty librarians will teach classes on topics such as understanding the current health care environment, management of health sciences resource collections, and provision of information services and instruction to health care providers.  In addition to taking these courses, students will complete a 3-credit research project relevant to the topic of health sciences librarianship. Librarians in this first cohort will graduate from the HealthCAS program with a firm understanding of current trends in health sciences research and education, an enhanced awareness of the information needs of clinical care providers, and the skills needed to manage and provide access to the expanding knowledge base in health care and the health sciences.

For more information about HealthCAS, contact Ester Saghafi, reference librarian and project manager, at 412-648-1973 or esaghafi@pitt.edu.

~ Mary Lou Klem

In March 2010, UPMC Shadyside was designated as a Magnet Hospital by the American Nurses Credentialing Center (ANCC).  Magnet hospitals are recognized for strong leadership, exemplary professional practice, innovation, and quality patient care.  Only 6% of hospitals in the United States have earned Magnet status.

HSLS librarians were active participants in UPMC Shadyside’s journey to Magnet recognition. Embedded within the hospital are two libraries managed by HSLS: the James Frazer Hillman Health Sciences Library and the Hopwood Library, a health resource center for patients and families.

Throughout the Magnet recognition process, librarians assisted nurses and administrators with literature searches, provided resources to support clinical research, and served on relevant committees.  During the Magnet appraisers’ site visit, librarians participated in Q&A sessions, describing available services and resources, and communicating the importance of libraries and librarians in providing quality health care to patients. The Shadyside team concurred, as Rachel Nechyba, RN, Chair of the Evidence-Based Practice Council commented, “The EBP Council’s success is due in large part to the dedication and in-depth investment exhibited by our library system.”

HSLS librarians at UPMC Shadyside are Michelle Burda, consumer health librarian; Melissa Ratajeski, reference librarian; and Charles Wessel, head of Hospital Services.

~ Michelle Burda and Melissa Ratajeski

The Online Bioinformatics Resources Collection (OBRC) is a freely searchable collection of over 2,600 bioinformatics databases and software tools on the Web. The HSLS Molecular Biology Information Service created the tool and maintains it regularly.

A criticism of OBRC is, “Why bother [searching OBRC]? You can just use Google!” To answer this question, a research project was developed comparing Google to OBRC for locating bioinformatics tools. The project intended to answer three questions:

1. Is OBRC superior to Google at locating bioinformatics resources quickly, easily and successfully?
2. Does OBRC leave users more satisfied than Google with the results of their search and the overall experience?
3. Do users want to use OBRC again for their research?

Ten biology graduate students were recruited. Each was assigned three tasks to find bioinformatics resources, using both Google and OBRC. Their searches were recorded using screen capture software, and they narrated their actions and thoughts while searching. The time spent searching, number of search queries, and number of sites visited were recorded. If they gave up without locating a resource, that was recorded as well. Afterward, they completed a survey regarding their opinions about both Google and OBRC. Specifically, they were asked how appropriate the results were, how easy each tool was to use, and then rated their entire experience. They were also asked how likely they were to use the OBRC again for their own research.

On average, the users spent twice as much time searching Google as they did searching OBRC. They visited slightly more sites with Google and used slightly more search queries. Users failed to find relevant information using Google 30% of the time, while they were 100% successful using OBRC. They had overwhelmingly positive reactions to OBRC, while Google only garnered negative or neutral ratings. The majority of students plan to use OBRC again in the future, and many asked when it would be available, not realizing it already was. Their comments suggested that they felt that Google was too time consuming and frustrating, while OBRC was very direct.

OBRC’s success shows that libraries can and should produce niche search tools, and they must aggressively market them to users.

~ Katrina Kurtz

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

Publications

Michele Klein Fedyshin, reference librarian, published “It Was the Worst of Times, It Was the Best of Times:  Positive Trends Influencing Hospital Libraries” in Journal of the Medical Library Association, 98(3): 196-199, July 2010.

Leslie Czechowski, assistant director, Collections and Technical Services; Renae Barger, assistant director, Access Services; Malgorzata Fort, head of Technical Services; and Gretchen Maxeiner, cataloging librarian, published “Letting Go: Closing a Branch Library of the Health Sciences Library System, University of Pittsburgh” in Library Resources and Technical Services, 54(3): 153-163, July 2010.

Barbara A. Epstein, director; Nancy H. Tannery, associate director for User Services; Charles B. Wessel, head of Hospital Services; Frances Yarger, assistant director for Computing Services; John LaDue, knowledge integration librarian; and Anthony B. Fiorillo, medical director, ambulatory eRecord, University of Pittsburgh Medical Center published “Development of a Clinical Information Tool for the Electronic Medical Record: A Case Study” in Journal of the Medical Library Association, 98(3): 223-227, July 2010.

Jonathon Erlen, history of medicine librarian published “Dissertations Recently Completed in Related Fields” in Journal of the History of Sexuality, 19(2): 382-383, May 2010.

Presentations

Leslie Czechowski, assistant director, Collections and Technical Services, presented a talk “The Problems with Use Statistics for Electronic Books” at the American Library Association annual meeting, Washington, D.C. on June 26, 2010.

Congratulations

Linda Hartman, reference librarian, has been approved for membership in the Medical Library Association’s Academy of Health Information Professionals at the Distinguished Member level.

Tricia Connell and Katrina Kurtz successfully presented certificate research projects on July 15, 2010, to complete their year-long Traineeships in Biomedical Informatics and Health Sciences Librarianship.  The Traineeship is sponsored by the Department of Biomedical Informatics and HSLS, with funding from the National Library of Medicine. Connell presented “The Information Needs of Physicians at the Point of Care When Making Prescribing Decisions.”  Kurtz presented “Going against Goliath: Knowledge Discovery Using a Library-Developed Specialized Search Tool versus General Web Search Engines.”

HSLS offers classes on database searching, software applications such as Adobe Photoshop, bibliographic management, molecular biology and genetics, and library orientations.  For more information visit the online course descriptions.

Classes are held on the first floor of Falk Library (200 Scaife Hall) in classroom 1 and conference room B, and on the second floor in the Computer and Media Center classroom 2. Some classes are also held in the conference room at UPMC Shadyside Libraries. All classes are open to faculty, staff and students of the schools of the health sciences at the University of Pittsburgh and UPMC.

No registration is required for any of these classes.  Seating for classes is first-come, first-served, until the class is full.  Classes marked with an asterisk (*) qualify for American Medical Association Category 2 continuing education credit.  Class schedules are subject to change.  Please consult the online class calendar for the most current information.

HSLS ORIENTATION

Introduction to HSLS Resources and Services at Falk Library
(Meet inside entrance to Library)
Monday, Sep. 30                          1-2 p.m.
Also offered upon request to groups or individuals. Call 412-648-8796.

Introduction to HSLS Services at UPMC Shadyside
Offered upon request to groups or individuals.  Call 412-623-2415.

Finding Full-Text Articles at UPMC Shadyside
Offered upon request to groups or individuals.  Call 412-623-2415.

SEARCHING DATABASES

PubMed Basics* (Falk Library Classroom 1)
Tuesday, September 14                1-2:30 p.m.
Thursday, September 30               9-10:30 a.m.
Thursday, October 21                   10-11:30 a.m.

Searching in CINAHL* (Falk Library Classroom 1)
Wednesday, October 13                1-2:30 p.m.

MOLECULAR BIOLOGY AND GENETICS RESOURCES

Genome Browsers* (Falk Library Conference Room B)
Wednesday, September 1             1-3 pm.

Locating Protein Information* (Falk Library Conference Room B)
Wednesday, September 8             1-3 pm.

Locating Gene-centric Information* (Falk Library Conference Room B)
Wednesday, September 15            1-3 pm.

SNPs & Genetic Variation* (Falk Library Conference Room B)
Wednesday, September 22            1-3 pm.

Cancer Informatics* (Falk Library Conference Room B)
Wednesday, September 29            1-3 pm.

Introduction to Vector NTI* (Falk Library Conference Room B)
Wednesday, October 6                  1-3 p.m.

Microarray Data Analysis* (Falk Library Conference Room B)
Wednesday, October 13                1-3 p.m.

Pathway Analysis Tools 1* (Falk Library Conference Room B)
Wednesday, October 20                1-3 p.m.

Pathway Analysis Tools 2* (Falk Library Conference Room B)
Wednesday, October 27                1-3 p.m.

SOFTWARE TRAINING

EndNote Basics (Falk Library Classroom 2)
(Note: This class is usually full.  Please arrive 15 minutes in advance to ensure seating.)
Monday, September 13                 10 a.m.-noon
Wednesday, September 29           1-3 p.m.
Thursday, October 14                  10 a.m.-noon.
Wednesday, October 27               1-3 p.m.

Adobe Photoshop for Beginners (Falk Library Classroom 2)
Tuesday, September 7                 10 a.m.-noon
Tuesday, October 5                      10 a.m.-noon

PowerPoint for Beginners (Falk Library Classroom 2)
Wednesday, October 27                10 a.m.-noon

Advanced PowerPoint for Presentations (Falk Library Classroom 2)
Wednesday, September 22           10 a.m.-noon

The WOW Factor: PowerPoint for Posters (Falk Library Classroom 2)
Tuesday, October 19                    10 a.m.-noon

Lunch With A Librarian

Making a Dent in Your Personal Paper Silo
Thursday, September 30              noon-1 p.m.

Personal Genomics, Personalized Medicine, and You
Tuesday, October 19                   noon-1 p.m.

Get It To Go

These informal online sessions will quickly introduce you to a variety of free online tools for productivity, current awareness and organization.  Sessions are held in Falk Library Classroom 1. Each session is hands-on and consists of a lecture and optional practice.

Twitter: Power in the Universe of Current Awareness
Thursday, September 23              noon – 1pm

Classes @ UPMC Shadyside Libraries

PowerPoint for Beginners (UPMC Shadyside Libraries)
Wednesday, September 15           11 a.m.-1 p.m.

Why use PubMed? (UPMC Shadyside Libraries)
Wednesday, September 22           3:30-4:30 p.m.

Introduction to RefWorks (UPMC Shadyside Libraries)
Tuesday, October 19                    3:30-4:30 p.m.

Thursday @ Three HSLS UPMC Shadyside Libraries Information Series

These informal sessions are held in the Conference Room at UPMC Shadyside Libraries.

Twitter: Power in a Universe of Current Awareness
Thursday, September 16              3-4 p.m.

Searching for Dollar$: Grant Resources
Thursday, October 28                   3-4 p.m.

CUSTOMIZED CLASSES
Customized classes can be developed for your department, course, or other group.

LEARNING @ YOUR PACE
These online tutorials provide information on getting started at HSLS, focusing on the Web site and popular resources.