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Data Management Planning: Metadata, Part 2

Metadata: it is so much more than data about data! When a dataset is included in an online collection or database, the standardized structure and vocabulary of metadata makes it “findable” when users query the search interface. Metadata also supports interoperability between databases, providing the semantic power necessary for sharing datasets and enabling collaboration.

At its simplest level, metadata provides a standardized description of the content of any form of data, such as a book, an image, or a dataset. The metadata elements for a book include title, author, and publication year, whereas the elements for a dataset can include contributor/creator, unique identifier, format, file size, type of data (survey, microarray), subject, abstract, version, source, and ownership. Use metadata elements as headings in spreadsheets or databases to facilitate and standardize data collection.

Pre-existing sets of elements are readily available, such as Dublin Core, with 15 repeatable core elements, and DataCite, with 17 repeatable elements. Both are designed especially for scientific datasets. DataCite also supports registration of a persistent Digital Object Identifier (DOI), which serves to increase the exposure and citation count of your dataset.

Some biomedical journals require raw data to be deposited in an approved public repository, such as UniProt or ArrayExpress, prior to peer review, and an acquisition number assigned by the repository must then be submitted along with the manuscript. The metadata standards for those datasets are determined by the repositories. An excellent resource for biomedical metadata standards is “MIBBI: Minimum Information Guidelines from Diverse Bioscience Communities.”

Metadata is a brief but required section of the National Institutes of Health (NIH) and National Science Foundation (NSF) data management plans. The free resource DMPTool provides a framework for describing the metadata used in projects funded by NIH, NSF, and other organizations.

Part 1 of this six-part series appeared in the February 2013 HSLS Update and gave an introduction to data management planning.

~ Andrea Ketchum

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PubMed Mobile

PubMedMobileSearchPubMed Mobile provides a simplified, mobile friendly Web interface for accessing the National Library of Medicine’s Standard PubMed/MEDLINE database. The mobile version searches the same content as Standard PubMed and does not require an account or registration.

To search PubMed Mobile, simply enter your search terms in the search box and then click on Search. Continue reading

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Teaching the ABCs of DNA for NN/LM MAR

IMAGE BY Amanda Van Buren
IMAGE BY Amanda Van Buren

In this genomic era, many people are eager to learn about personal genomics and personalized medicine, yet feel overwhelmed by the sheer volume of information. These complex topics encompass not only scientific and medical concerns, but also ethical, legal, and social issues. To assist in the dissemination of awareness about these issues, the National Network of Libraries of Medicine is offering a four hour continuing education class, “ABCs of DNA: Unraveling the Mystery of Genetic Information for Consumers,Continue reading

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Police Line: Do Not Cross!

Caution TapeI must be imagining things! I walk into the library and not only have the books and journals switched places, but now part of the library looks like a crime scene from CSI…have I bumped my head or have I been studying way too much?

You’re not alone if things are feeling a little out of place. But fear not—this “crime scene” is actually a step in the second phase of remodeling at Falk Library. The books from the upper floor are now on the main floor, exchanging places with the journals. The extra journal shelves that were formerly in the middle of the main floor have been removed, opening up space on the floor. In the next step, the nearby computer desks and furniture will be rearranged to make those areas more spacious for our patrons. So if you’re a victim of too much studying, you can at least get a change of scenery once the main floor remodeling is complete!

~ Julia Jankovic

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HSLS Staff News

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

News

Linda Hartman, reference librarian, moderated a paper session on “Health Care for Children” at the fifteenth annual meeting of The Southern Association for the History of Medicine and Science, February 21–23, 2013, in Charleston, South Carolina.

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March Classes

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 on the upper floor of the library in Classroom 2. All classes are open to faculty, staff and students of the schools of the health sciences at the University of Pittsburgh. They are also open to UPMC residents and fellows.

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.

Faculty, staff and students of the schools of the health sciences will need a valid Pitt ID or e-mail account to attend these classes. UPMC residents/fellows will need to show their UPMC IDs.

 

HSLS ORIENTATION

Introduction to HSLS Resources and Services at Falk Library
(Meet inside entrance to Library)
Offered upon request to groups or individuals. Call 412-648-8866.

 

SEARCHING DATABASES

Painless PubMed* (Falk Library Classroom 1)

Monday, March 4 4:30-5:30 p.m.
Thursday, March 21 11 a.m.-noon
Wednesday, March 27 3-4 p.m.

MOLECULAR BIOLOGY AND GENETICS RESOURCES

Microarray Data Analysis* (Falk Library Classroom 2)

Wednesday, March 6 1-3 p.m.

Sequence Similarity Searching* (Falk Library Classroom 2)

Wednesday, March 20 1-3 p.m.

Introduction to CLC Main Workbench* (Falk Library Classroom 2)

Wednesday, March 27 1-3 p.m.

 

SOFTWARE TRAINING

Advanced PowerPoint for Presentations (Falk Library Classroom 2)

Thursday, March 7 1:30-3:30 p.m.

EndNote Basics (Falk Library Classroom 2)

Tuesday, March 12 2-4 p.m.

PowerPoint for Conference Posters (Falk Library Classroom 2)

Monday, March 18 noon-2 p.m.

Prezi for Presentations (Falk Library Classroom 2)

Tuesday, March 26 1-3 p.m.

CUSTOMIZED CLASSES

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

 

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Stricter Standards for NIH Public Access Policy Compliance

In an effort to improve compliance with the NIH Public Access Policy, the National Institutes of Health (NIH) recently announced that more stringent standards will soon take effect. As described in the NIH guide notice, Upcoming Changes to Public Access Policy Reporting Requirements and Related NIH Efforts to Enhance Compliance,

“…in Spring, 2013, at the earliest, NIH will delay processing of non-competing continuation grant awards if publications arising from that award are not in compliance with the NIH public access policy. The award will not be processed until recipients have demonstrated compliance. This change will take effect in tandem with NIH requiring the use of the Research Performance Progress Report (RPPRs) for all Streamlined Non-competing Award Process (SNAP) and Fellowship awards in the Spring of 2013.”1

The NIH Public Access Policy requires researchers to submit final peer-reviewed journal manuscripts that arise from NIH funds to PMC upon acceptance for publication. The policy requires that these papers be accessible to the public through PMC no later than 12 months after publication.

There are three submission methods for final published articles:

  1. A number of journals automatically deposit the final published article to PMC without author involvement.
  2. The author can make arrangements to have the publisher deposit a final published article in PMC—usually for a fee.
  3. The author deposits the final peer-reviewed manuscript in PMC via the NIH Manuscript Submission System.

HSLS maintains a Scholarly Communication Web site that provides information and guidance on the NIH Public Access Policy, including policy basics, compliance, article submission, and more.

1. “Upcoming Changes to Public Access Policy Reporting Requirements and Related NIH Efforts to Enhance Compliance,” National Institutes of Health Office of Extramural Research, accessed January 3, 2013, http://grants.nih.gov/grants/guide/notice-files/NOT-OD-12-160.html.

~ Jill Foust

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The Values of Libraries Study: An Update

In the fall of 2010, UPMC physicians, residents, and nurses were invited to participate in the initial phase of a multi-site survey of the role of library information resources in improving patient care. The results of the full study were recently published.1 In this study, clinicians from 118 hospitals completed an online survey that asked them to think of an occasion when they required additional information for a patient care issue, and to then answer questions about the impact of access to library information resources on patient outcomes for that particular case.

Nearly every study participant agreed that information resources available from their libraries were relevant (99 percent), accurate (99 percent) and current (97 percent). The high quality of information available was not just appreciated, however—75 percent of participants agreed that access to the information definitely or probably changed how they handled an aspect of patient care, including advice given to a patient (48 percent), drug choice (33 percent), and diagnosis (25 percent). Participants (85 percent) indicated that having access to the information saved them time, with the average amount of time saved estimated to be 2.5 hours.

In addition to these positive impacts, clinicians believed the information provided by libraries helped to avoid negative events such as patient misunderstanding of disease (23 percent), misdiagnosis (13 percent), adverse drug events (13 percent), medication errors (12 percent), patient mortality (6 percent), and hospital acquired infections (3 percent).

In follow-up interviews, a subset of participants reiterated the clinical value of having access to current and accurate information, and the impact such access has on patient safety. Clinicians also commented on the value of having access to professional librarians who can assist with patient care, either through provision of literature searches for busy clinicians, or through education of clinicians in the most efficient use of library resources.

1. J.G. Marshall, J. Sollenberger, S. Easterby-Gannett, L.K. Morgan, M. Klem M, et al., “The Value of Library and Information Services in Patient Care: Results of a Multisite Study,” Journal of the Medical Library Association 101 no. 1 (2013): 38-46.

~ Mary Lou Klem

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Director’s Reflections…Does Access to Information Make a Difference?

Elsewhere in this issue, Mary Lou Klem reports on the newly-published results of the Value of Libraries project, a multi-site study aimed at determining the impact of the library’s information resources and services on patient care. UPMC participated in the pilot phase of this project. In this survey study, clinicians were asked to think about an occasion in the last six months when they looked for information resources for patient care (beyond what is available in the eRecord or lab results) and to answer questions regarding that occasion.

A total of 1,473 UPMC physicians, residents, and nurses responded to the survey. Continue reading

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Trial Access to Data Citation Index

Free trial access to the Data Citation Index from Thomson Reuters will be available during the month of February. You can use the Data Citation Index to discover research data available in a growing number of data repositories worldwide. About 80 repositories are currently indexed by Data Citation Index. Roughly 60 percent of the indexed repositories focus on life sciences research; physical and social sciences, as well as arts and humanities, are also represented.

The Data Citation Index is organized by three record types: repository, data study, and data set. Each record also includes a recommended citation for the resource, helping to make data easier to cite.

You can access the Data Citation Index on the Web of Knowledge platform, under the “Select a Database” tab. More information about Data Citation Index is available here. If you have any feedback you would like to share, please e-mail Ask A Librarian.

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STAT!Ref’s Mobile App

E-books from STAT!Ref are available in a convenient mobile app for on-the-go access for Pitt and UPMC users.

Contents

The STAT!Ref Mobile App provides access to the following e-books: Continue reading

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Changes in HSLS Collections for 2013

The economic climate of recent years demands that libraries build and manage their collections in more cost-effective ways. Subscription costs continue to rise—at rates far above general inflation—leaving libraries with little budgetary room to maintain their existing collections, let alone grow them. In response to the changing needs of their diverse user populations, libraries often add new resources while canceling others.

The following electronic journals have been added to the HSLS collection for 2013:

  • Applied Clinical Informatics
  • Augmentative and Alternative Communication
  • Best Practice and Research: Clinical Anaesthesiology
  • Biofactors
  • British Journal of Health Psychology
  • Canadian Journal of Urology
  • Clinical Journal of Oncology Nursing
  • Cold Spring Harbor Perspectives in Biology
  • Comparative Immunology, Microbiology and Infectious Diseases
  • Developmental Cognitive Neuroscience
  • Disruptive Science and Technology
  • Endocrine-Related Cancer
  • Focus: the Journal of Lifelong Learning in Psychiatry
  • Hastings Center Report
  • Health Care: the Journal of Delivery Science and Innovation1
  • International Health
  • International Journal of Medical Microbiology
  • IUBMB Life
  • JACC: Heart Failure1
  • Journal of Addictions Nursing
  • Journal of Chromatographic Science
  • Journal of Comparative Effectiveness Research
  • Journal of Forensic Nursing
  • Journal of Health Administration Education
  • Journal of Health Communication
  • Journal of Interprofessional Care
  • Journal of Molecular Cell Biology
  • Journal of Obsessive-Compulsive and Related Disorders
  • Journal of Pediatric Rehabilitation Medicine
  • Journal of the Pediatric Infectious Diseases Society
  • Journal of Vascular Access
  • JoVE Bioengineering
  • JoVE Clinical and Translational Medicine
  • JoVE Immunology and Infection
  • JoVE Neuroscience
  • Lancet: Respiratory Medicine1
  • Methods of Information in Medicine
  • Neurorehabilitation
  • Pancreatology
  • Pharmacogenomics
  • Research Synthesis Methods
  • Sleep Medicine Reviews
  • Stereotactic and Functional Neurosurgery
  • Thrombosis and Haemostasis
  • Transactions of the Royal Society of Tropical Medicine and Hygiene
  • Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine

1.  Publication forthcoming later in 2013.

Please note that the new subscriptions may not yet be active for some journals.

Below is a list of cancelled e-journals and print journals. Cancellation decisions were primarily based on usage statistics and cost-per-use, though other factors were considered in the process. The savings realized through these cancellations allow us not only to absorb the cost increases on our existing resources, but also to add some new resources. HSLS made a concerted effort to add new electronic journals that have been requested by our users.

The following electronic journals were cancelled for 2013. University of Pittsburgh users may order individual articles for a small fee through the HSLS Document Delivery Service.

  • Acta Oncologica
  • American Journal of Nephrology
  • Animal Genetics
  • Annals of Clinical Psychiatry
  • Annals of the Royal College of Surgeons
  • Autoimmunity
  • Bioanalytical Reviews2
  • Biorheology
  • Canadian Journal of the Neurological Sciences
  • Cancer Investigation
  • Caries Research
  • Clinical and Experimental Allergy Reviews2
  • Clinical Medicine
  • Clinical Neuropsychologist
  • Clinical Toxicology
  • Cognition and Emotion
  • Comparative Biochemistry and Physiology
  • Current Eye Research
  • Current HIV Research
  • Cytoskeleton
  • Dentomaxillofacial Radiology
  • Dermatology
  • Digestion
  • Drug Metabolism Reviews
  • Eating Disorders
  • European Neurology
  • Foot and Ankle International
  • Free Radical Research
  • General and Comparative Endocrinology
  • Health Care for Women International
  • Hospital Pharmacy
  • Human Heredity
  • Journal of American College Health
  • Journal of Analytical Psychology
  • Journal of Asthma
  • Journal of Biopharmaceutical Statistics
  • Journal of Cognitive Psychotherapy
  • Journal of Community Health Nursing
  • Journal of Empirical Research on Human Research Ethics
  • Journal of Family Therapy
  • Journal of Nursing Measurement
  • Journal of Pain and Palliative Care Pharmacology
  • Journal of Personality Assessment
  • Journal of Sports Sciences
  • Molecular and Cellular Probes
  • Molecular Membrane Biology
  • Mount Sinai Journal of Medicine2
  • Neuroepidemiology
  • ORL: Journal for Oto-Rhino-Laryngology
  • Pediatric and Developmental Pathology
  • Pediatric Hematology and Oncology
  • Pediatric Neurosurgery
  • Psychiatric Rehabilitation Journal
  • Research and Theory for Nursing Practice
  • Scandinavian Journal of Clinical and Laboratory Investigation
  • Scandinavian Journal of Rheumatology
  • Seminars in Ophthalmology
  • Technology and Health Care
  • Xenobiotica

2.  Ceased publication.

The following print journals were cancelled for 2013:

  • Antiviral Therapy
  • Clinical and Experimental Rheumatology
  • Facial Plastic Surgery Clinics of North America
  • Rhinology

~ Jeff Husted

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Data Management Planning, Part 1

This is the first article in a six part series which will describe the various aspects of data management planning.

All data has a “lifecycle.” It’s created, processed, analyzed, preserved, shared, and potentially re-used by you or others in the research community.

Data management is the development and execution of policies Continue reading

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Increase Your Research Productivity: Try JoVE

JoVE, the Journal of Visualized Experiments, is the first and only peer-reviewed video journal for biological, medical, chemical, and physical research indexed in PubMed/MEDLINE. Via a global network of videographers, JoVE films and edits videos of researchers demonstrating their experimental techniques. As of mid-January 2013, JoVE has published 2,176 video protocols by 7,267 international researchers from prestigious universities at a rate of 50 articles per month.

JoVE articles are generally 10-15 minutes long and provide step-by-step descriptions of protocols/techniques to enable other researchers to easily reproduce them. Each article is accompanied by a written component containing introductory remarks, a written description of the protocol, representative results, discussion, and references. JoVE publishes novel techniques, novel applications of existing techniques and gold standard protocols.

The JoVE Editorial Board consists of world renowned scientists, physicians, professors, and key opinion leaders, including three members of the University of Pittsburgh community:

  • Neil Hukriede, PhD, associate professor and vice chair of the Department of Developmental Biology
  • Joseph Newsome, DVM, research associate professor of the Department of Pathology and clinical director, Division of Laboratory Animal Resources
  • Kimimasa Tobia, MD, PhD, research assistant professor of the Department of Developmental Biology and director of Animal Imaging Core

There are multiple ways to find articles of interest in JoVE. The homepage provides a rotating slide show of highlighted video articles as well as lists of the most recently published and most popular video articles. Articles may be located by keyword search or by browsing one of the many JoVE sections:

  • A = All
  • G = General
  • N = Neuroscience
  • i2 = Immunology & Infection
  • CTM = Clinical & Translational Medicine
  • B = Bioengineering

The purpose of JoVE is to encourage rapid knowledge transfer, elucidate the complexity of life science research, address the time- and resource-consuming process of learning experimental techniques, and expand the parameters of scientific publishing.

Give JoVE a try! For more information, contact the HSLS Molecular Biology Information Service.

*Parts of this article were reprinted from JoVE.

~ Carrie Iwema