Health Sciences Libraries

Posts by Amy Studer

US Department of Energy Launches PAGES

August 5th, 2014 by Amy Studer

Image credit:  Sergey Sus.  License:  CC BY-NC-SA 2.0. <br/> https://flic.kr/p/96iTMv

On August 4, 2014, the US Department of Energy (DOE) unveiled its plan to increase access to the research that it funds, as required by the White House OSTP directive of February 22, 2013.

Now available is a beta version of the Public Access Gateway for Energy and Science (PAGES). The DOE Office of Scientific and Technical Information website provides links to the full plan, FAQs, as well as this short summary:

” In response to the OSTP directive, OSTI has developed and launched the DOE Public Access Gateway for Energy and ScienceBeta – DOE PAGESBeta. When fully operational, this new resource will offer free access to the best available full-text version of DOE-affiliated scholarly publications – either the peer-reviewed, accepted manuscript or the published article – after an administrative interval of 12 months. ”

According to Nature News Blog (August 4, 2014), the PAGES approach will make up to 30,000 papers per year “free to read”, but open access advocates are concerned that the approach may not provide for bulk downloading, re-distribution or creative re-use, such as text-mining.

More description of the PAGES approach from the DOE Office of Scientific and Technical Information website:

” The portal that OSTI has prepared employs a hybrid model of centralized metadata and primarily decentralized full-text access to accepted manuscripts or articles hosted by DOE-funded national laboratories, universities, and other institutions or by individual publishers. In this way, the gateway builds on DOE’s existing scientific and technical information infrastructure and also integrates publishers’ public access efforts. For publisher-hosted content, OSTI has been collaborating with the publisher consortium CHORUS, or the Clearinghouse for the Open Research of the United States. OSTI is also engaging with other stakeholders’ initiatives to advance public access, such as the university and research library community’s Shared Access Research Ecosystem (SHARE). ”

For more information:

ScienceInsider Blog

The Chronicle of Higher Education

Shared Access Research Ecosystem (SHARE)

Clearinghouse for the Open Research of the United States (CHORUS)

Image credit: Sergey Sus. License: CC BY-NC-SA 2.0.  https://flic.kr/p/96iTMv

EndNote Capture Plug-In

May 7th, 2014 by Amy Studer

Did you know there’s a button you can add to your web browser’s toolbar that will quickly open an EndNote library record form and pull citation information in from a webpage?

This is a great feature if you happen upon a citation, book, or webpage that doesn’t offer an Import to EndNote option.
To learn more and install the Capture plug-in:
1.  Sign in to EndNote Web
2.  Select the Options tab –> Download Installers
3. Follow the instructions for the “Capture Reference” button to install it on your toolbar:

 

EndNote_Plug_In

When you find a webpage that you would like to add to EndNote, click on the “Capture Reference” button and a new EndNote record will be populated.  You may need to manually enter some of the information (for example, in the following case author needs to be added.)  You then have the option of saving the record to EndNote Web or EndNote installed on your computer.

EndNote_Capture_2

For EndNote questions, contact a librarian at:  hslref@lib.ucdavis.edu or mclref@ucdavis.edu

 

Scopus: Access for 2014

February 23rd, 2014 by Amy Studer

During the 2014 calendar year, UC faculty, staff, and students will be able to access the Scopus database.   Scopus is an abstract and citation database of peer-reviewed literature, including some 50 million records, 21,000 titles and 5,000 publishers, and includes tools to track, analyze and visualize research.

Scopus search interface (UC Davis computer network or VPN access required):

http://www.scopus.com/

See the Facts and Figures flyer or Content Overview page for more information about Scopus.

The NIH Public Access Policy: What it Means for You and How to Ensure Compliance

February 4th, 2014 by Amy Studer

The NIH Public Access Policy: What it Means for You and How to Ensure Compliance
Wednesday, February 19, 2014
12:15 pm – 1:45 pm
Education Building Room 2206
To Register: http://lib.ucdavis.edu/dept/instruc/classes/descriptions.php#class134

In 2008, the National Institutes of Health (NIH) announced that investigators funded by the NIH must submit a copy of their final, peer-reviewed manuscripts to PubMed Central (PMC) upon acceptance of publication, to be made publicly available no later than 12 months after the date of publication. Failure to comply with the Public Access Policy will result in funding delays.

If you are involved with NIH-funded research in any capacity, consider attending this workshop to learn more about the Public Access Policy and how to be compliant with it. It will cover:

* what it is and what it means;
* who has to comply;
* how to determine the copyright policy of the journal publishing your manuscript, and;
* the various methods of article submission into PMC, including the NIH Manuscript Submission System (NIHMS).

To register:  http://lib.ucdavis.edu/dept/instruc/classes/descriptions.php#class134

Due to space restrictions, this workshop will be limited to 30 attendees on a first-come, first-served basis.

If you have any questions, please contact:

* Raquel Abad, Health Sciences Librarian, 916.734.3870 | rjabad@ucdavis.edu OR

* Amy Studer, Health & Life Sciences Librarian, 530.752.1678 | astuder@lib.ucdavis.edu

2014 West Virginia Elk River Chemical Release: Information Resources

February 3rd, 2014 by Amy Studer

Adapted from NLM Tech Bull. 2014 Jan-Feb;(396):b5.:

You may be aware from multiple news sources that little information was available about 4-methylcyclohexanemethanol at the time of the spill in West Virginia’s Elk River in early January 2014.

Since the spill, government and private sector scientists have contributed to collecting and verifying information about the chemical.

Here are some new resources about the chemical and the government response:

Please note that in some social media and early news reports, the chemical was MISIDENTIFIED as Methylcyclohexanol (CASRN: 25639-42-3). This is NOT the correct chemical.

In chemical incidents, it is unusual for little online information to be available about a substance. Chemicals can often be readily identified using online resources such as TOXNET and WISER. In the absence of published information, local and state officials request consultation with local, state, federal and industry experts. Typically, following such an incident there is immediate, ongoing, extensive consultation and communication among responders and experts to determine appropriate actions.

When planning for providing health information following chemical incidents, it is critical for institutions and government agencies to know who to contact in uncommon situations as well as knowing the authoritative published sources of chemical information.

Sources

PLoS Medicine article: Good reasons to search in ClinicalTrials.gov

December 9th, 2013 by Amy Studer

A new article out of PLoS Medicine (December 6, 2013) provides some good reasons for adding ClinicalTrials.gov to the list of resources consulted routinely for evidence-based treatment decisions:

Riveros, C., et al., Timing and Completeness of Trial Results Posted at ClinicalTrials.gov and Published in Journals. PLoS Med, 2013. 10(12): p. e1001566.

Access at:  http://www.plosmedicine.org/article/info%3Adoi/10.1371/journal.pmed.1001566

The authors compared the reporting on clinical trials of drugs in ClinicalTrials.gov with corresponding journal publications for timeliness of publication and completeness (flow of participants, efficacy results, adverse events, and serious adverse events) of posted results.  Reporting in ClinicalTrials.gov was significantly more complete than in the published journal articles.

Accessing drug information from ClinicalTrials.gov may help address potential publication, reporting, and time-lag biases that have been identified in journal literature, thereby supplementing information gathering for evidence-based practice.  ClinicalTrials.gov is “designed to complement, not replace, the journal publication” because results are presented as tabular data, without interpretation, and are not peer-reviewed (Zarin, Tse, Williams, Califf, & Ide, 2011, page 3).

Reference:

Zarin, D. A., Tse, T., Williams, R. J., Califf, R. M., & Ide, N. C. (2011). The ClinicalTrials.gov results database–update and key issues. N Engl J Med, 364(9), 852-860. doi: 10.1056/NEJMsa1012065.

Links to Resources:

ClinicalTrials.gov website:  http://clinicaltrials.gov/

For help with finding information in ClinicalTrials.gov, contact hslref@lib.ucdavis.edu

Try searching for a drug by name in DailyMed, and then link to related ClinicalTrials.gov information from the menu on the left side of the page.

Project Tycho: Data for health

December 5th, 2013 by Amy Studer

Announcing Project Tycho™, a web site which provides open access to newly digitized and integrated data from the entire 125 years history of United States weekly nationally notifiable disease surveillance data since 1888.  Read more about it:

The goal of Project Tycho™ is to aid scientists and public health officials in the eradication of deadly and devastating diseases. A recent NEJM article, documents how the Project Tycho team digitized and made public all weekly surveillance reports of nationally notifiable diseases for U.S. cities and states published between 1888 and 2011. The project derived a quantitative history of disease reduction in the United States over the past century, focusing particularly on the effect of vaccination programs.

Reference

van Panhuis WG, Grefenstette J, Jung SY, Chok NS, Cross A, Eng H, et al. Contagious diseases in the United States from 1888 to the present.N.Engl.J.Med. 2013 Nov 28;369(22):2152-2158.

Project Tycho Image

About Project Tycho

In the United States, cases of contagious diseases have been reported at weekly intervals to health authorities for more than a century, but these data have not been publicly available in a computable format, so their use and value have been limited. The University of Pittsburgh has released a collection of surveillance reports about diseases in the United States going back 125 years. “The researchers obtained all weekly notifiable disease surveillance tables published between 1888 and 2013 – approximately 6,500 tables – in various historical reports, including the U.S. Centers for Disease Control and Prevention’s Morbidity and Mortality Weekly Report. These tables were available only in paper format or as PDF scans in online repositories that could not be read by computers and had to be hand-entered. With an estimated 200 million keystrokes, the data – including death counts, reporting locations, time periods and diseases – were digitized. A total of 56 diseases were reported for at least some period of time during the 125-year time span, with no single disease reported continuously.”

Blog entry re-posted from Rudolph Mata Library Blog by medref@tulane.edu, with permission.

New from AHRQ: Patient Education Materials Assessment Tool

December 4th, 2013 by Amy Studer

For those providing health education to patients, families, or communities, this new resource is freely available online from AHRQ:

The Patient Education Materials Assessment Tool (PEMAT) and User’s Guide:

An Instrument To Assess the Understandability and Actionability of Print and Audiovisual Patient Education Materials

Pill Bottle

Description from website:  The Patient Education Materials Assessment Tool (PEMAT) is a systematic method to evaluate and compare the understandability and actionability of patient education materials. It is designed as a guide to help determine whether patients will be able to understand and act on information. Separate tools are available for use with print and audiovisual materials.

Additional AHRQ resources designed to support improving patient health literacy:

AHRQ Pharmacy Health Literacy Center

Self-Management Support Video and Library

Health Literacy Topics (choose For Professionals)

Image credit:  subsetsum from Flickr.  License:  CC BY-NC-ND 2.0

 

NCBI Discovery Workshops @ UC Davis Library [Webinar Edition]

November 15th, 2013 by Amy Studer
Image:  Light Helix by BloodLight
 
The UC Davis Library is pleased to announce:

2013 NCBI Discovery Workshops @ UC Davis Library [Webinar Edition]

The workshops will focus on the following areas:

1.      Sequences, Genomes, and Maps:  December 17, 2013 from 12:30-2:30pm PT
2.      Proteins, Domains, and StructuresDecember 18, 2013 from 12:30-2:30pm PT
3.      NCBI BLAST ServicesDecember 19, 2013 from 12:30-2:30pm PT
4.      Human Variation and Disease GenesDecember 20, 2013 from 12:30-2:30pm PT

You are welcome to register for one or more workshops, each emphasizing different sets of NCBI resources.  Specific examples will be used to highlight important features of the resources and tools under study and to demonstrate how to accomplish common tasks.  Electronic copies of detailed handouts for each session will provide step-by-step instructions and additional information about each example.

All workshops are taught by NCBI staff and will consist of 1.5 hours of instruction followed by a Q & A period.

Due to the US Government sequester, the workshop instructors will not be able to present in person at UC Davis, as in previous years.  Instead, you are invited to attend all sessions via webinar, using your own computer or perhaps collaborating with your department or research group to view together.

NCBI Discovery Workshops Website:  http://www.ncbi.nlm.nih.gov/education/workshops/

Questions?  Contact bioagquestions@lib.ucdavis.edu or hslref@lib.ucdavis.edu

Image credit: Light Helix by BloodLight.  License:  CC BY-NC-ND 2.0

PubMed Relevancy Sort

November 5th, 2013 by Amy Studer

PubMed now includes a new relevance sort option.

The “Relevance” sort option is available from the “Display Settings” menu under the “Sort by” selections.  Initially, easy access to relevance sort will also be provided under a “New feature” discovery tool (see red boxes on image).

The relevance sort order for search results is based on an algorithm that analyzes each PubMed citation that includes the search terms. For each search query, “weight” is calculated for citations depending on how many search terms are found and in which fields they are found. In addition, recently-published articles are given a somewhat higher weight for sorting.

PubMed Relevancy

For additional information, please visit the NLM Technical Bulletin.

This blog entry was adapted from NewsBits Blog from NN/LM Pacific Southwest Region, October 23, 2013.