Mendeley: A Free Reference Manager, PDF Organizer & Academic Social Networking Tool

Looking for a tool to help you index and organize your research papers online? Described by some folks as “iTunes for researchers,” Mendeley is a free reference manager and PDF organizer. OK, you currently use RefWorks or EndNote for managing references, so why consider yet another one?

Mendeley is unique in that it’s designed to be an academic social networking tool as well as a platform-independent citation management application. Mendeley Web is a social network where you can create groups, invite friends (fellow researchers), and stay up to date on what other people are reading.  Mendeley combines an easy to use web-based interface with a desktop application for managing your citations and online documents. The Mendeley desktop tool is available for Mac, Windows, and Linux, and there are versions available for the iPhone and iPad.

Some of Mendeley’s main features include:

  • Automatically generates bibliographies
  • Easy to Collaborate with other researchers online
  • Easily import papers from other research software
  • Find relevant papers based on what you’re reading
  • Access your papers from anywhere online
  • Read papers on the go, with a new iPhone app

Use the following links to read more about Mendeley:

Main Mendeley web-site

MENDELEY FAQ (UCSF Library)

 

 

 

Posted in Citation management, Research, Scholarly Communication, Software, Tools & Technology, Uncategorized | Tagged , , , | Leave a comment

FRPAA proposes public access to all federally-funded research

In opposition to the publishing industry-backed Research Works Act (RWA), a bill was introduced in Congress yesterday to require public access to research articles resulting from funding from federal agencies with extramural research expenditures of over $100 million. The bill, Federal Research Public Access Act of 2012 (FRPAA), was introduced in the House of Representatives by Mike Doyle (D-PA) and two other Representatives as H.R.4004, and in the Senate by John Cornyn (R-TX) and two other Senators as S.2096.

FRPAA was previously introduced in 2006 in the Senate by Cornyn and in 2009 in both the House and Senate, but did not make it out of committee in either Congress. What’s different now? The bill has bipartisan support and an increasing number of supporters at that, not to mention the growing interest in open access to research articles in the interest of advancing science and improving health.

The National Institutes of Health Policy of 2008 also changed the game – NIH was the first U.S. federal agency to mandate publicly-accessible, online dissemination of research articles that come from research dollars it awards. FRPAA would take NIH’s policy even further, requiring all federal agencies awarding over $100M in total research grants to ensure public dissemination of published articles within six months, compared to NIH’s twelve months. A partial list of agencies FRPAA would apply to includes: the NIH, the National Science Foundation, and the Department of Health & Human Services.

Not only are scholars, libraries, and citizens paying attention to public access to scholarly works, it’s on the White House’s radar as well. In November 2011 the Office of Science & Technology Policy requested public input on “long-term preservation of, and public access to, the results of federally funded research”. The comments can be read here.

Take Action!FRPAA is beginning with even more support in 2012 than it did the last time it was introduced, however Congress needs to hear support for FRPAA – and against RWA/H.R. 3699 – in order for change to happen. Be part of that change by contacting Senators Cornyn, Wyden, and Hutchinson, and Representatives Doyle, Yoder, and Clay to voice your support for FRPAA. Use form letters created by the Alliance for Taxpayer Access’s to contact your legislators about both FRPAA and RWA, and sign ATA’s petition. Talk to your colleagues and involve your societies, too!

To learn more about FRPAA, see this Wired article and the FRPAA wiki.

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Research Works Act threatens public access to literature

A bill introduced in the House of Representatives in December 2011 could have enormous consequences for scientific and medical researchers if passed. Cited as the Research Works Act (RWA) (H.R. 3699), this legislation would prohibit any federal agency from engaging in any activity that :

  1. results in the dissemination of published articles without the prior consent of the publisher of the work; or
  2. requires that any actual or prospective author, or the employer of such author, assent to dissemination of a published research work.

Essentially, RWA would nullify the NIH Public Access Policy, which requires that the public has access to the published results of NIH funded research within 12 months of publication. This policy was implemented in 2008, and it was a significant move to ensure U.S. citizens’ right to read published results of research funded through taxpayer dollars, free of charge. Since so much of the research funding at UCSF comes from the NIH, our researchers are very familiar with this policy and making sure (sometimes painstakingly) that their articles get deposited in PubMed Central.

Though several publications were already making all articles freely accessible 12 or fewer months after initial publication, many publishers opposed the NIH Policy since it makes some of their published content free that would otherwise only be accessible through a subscription or other paid access.  In 2008 and 2009 publishing interests got the “Fair Copyright in Research Works Act” introduced into Congress; it died both times in committee.

Two years later, the publisher-backed RWA is back, demonstrating that some publishers are willing to keep fighting the NIH Policy and prevent other government agencies from implementing something similar. Who is behind RWA? The Association of American Publishers (AAP) is the primary backer, though not all of AAP’s members support RWA. MIT Press, AAAS, Nature, and BioMed Central are among the publishers opposing RWA.  One of AAP’s members – Elsevier Science – is receiving most of the blame for getting this bill introduced by Representatives Carolyn B. Maloney, Democrat of New York, and Darrell Issa, a Republican from California. So much so that more than 4,500 researchers have signed a petition vowing to boycott Elsevier publications.

Whether or not it’s fair to single out Elsevier as the bad guy, it’s clear that scholars around the world are beginning to take a different stance on their role in the scholarly publishing cycle. Scientists are behind many of the innovations in publishing and online communications tools such as the Public Library of Science, arXiv, and ResearchGate.

Take Action! As of January 11, the RWA bill has been referred to the House Oversight and Government Reform Committee, and may or may not make it to the House floor for a vote.

 

Want to get involved? Here are some steps:

  1. If you are a member of a society, check if your society supports or opposes RWA, and start a dialog with the society decision-makers and other members.
  2. Contact the Representatives who introduced RWA to let them know your opinion:  Carolyn B. Maloney, New York, and Darrell Issa, California.
  3. Write a letter of opinion to a newspaper.
  4. Leave a comment to let us know what you think about RWA and the NIH Policy.
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A Quick Way to Find Information on Dietary Supplements in PubMed

If you’re searching for information on, say, supplements used by athletes, or the efficacy of glucosamine and chondroitin extracts in treating rheumatoid arthritis, use the relatively new PubMed Dietary Supplements subset to refine your search.  This subset of records is designed to limit search results to citations from a broad spectrum of dietary supplement literature including vitamin, mineral, phytochemical, ergogenic, botanical, and herbal supplements in human nutrition and animal models. The subset will retrieve dietary supplement-related citations on topics including, but not limited to:

  • chemical composition
  • biochemical role and function — both in vitro and in vivo
  • clinical trials
  • health and adverse effects
  • fortification
  • traditional Chinese medicine and other folk/ethnic supplement practices
  • cultivation of botanical products used as dietary supplements
  • surveys of dietary supplement use

To use this subset you just go to the PubMed Limits page and select Dietary Supplements from the Subset menu:

A search for peer-reviewed papers on the use of dietary supplements in sports:

 

The subset is a collaboration between the NIH Office of Dietary Supplements and the National Library of Medicine.

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Annotating PDFs with EndNote X5

If you’re wondering whether or not to upgrade to EndNote version X5 you might want to consider this great new feature that’s been added to the application. X5 now includes a PDF window that not only allows you to view PDFs within EndNote but also allows you to annotate text with highlights and/or text:

 

 

 

 

 

 

 

 

 

 

 

You annotate text by adding “stickies” to the document:

 

 

 

 

 

 

 

 

 

View this online tutorial for more information about version  X5.

 

 

 

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Beyond MEDLINE: Biomedical Information in Patents

You’re doing in depth research on, say,  artificial knee implants. Perhaps you’re applying for a research grant or thinking about applying for a patent. You need to do a comprehensive search and find everything that’s out there. You’ve searched PubMed, then other databases such as Web of Science (WoS) and BIOSIS Previews.  That’s it then, isn’t it?  Unfortunately, no isn’t! If you really want to do a comprehensive search and find as much scientific or technical information as you can about any topic, you would have to search the patent literature. Databases such as Chemical Abstracts and BIOSIS Previews include some patent records, but if you want access to the complete patent literature you have to go beyond bibliographic databases and the peer-reviewed literature.

A patent is not just a legal document but is also a technical description of an invention, be it a new drug compound, an artificial knee joint or a new procedure for isolating DNA. The patent literature is an important, unique, and often overlooked source of technical and research data,  much of which is never published or disclosed elsewhere. It is estimated that up to 80%  of scientific or technical information disclosed in a patent application is not disclosed anywhere else.  Because a patent application needs to be applied for before the first publication of an invention,  patents and patent applications are often published earlier than academic papers.

Thankfully, the majority of the patent literature is now freely available on the web. The following are links to free key sources for patent information. These sites also provide general information about patents and the patent process:

The United States Patent and Trademark Office (USTPO) provides bibliographic details or access to the full text of US patents from 1976 and TIFF images for all patents from 1790 to the present

The patent database of the European Patent Office (EPO) offers free patent searching of documents from over 50 different countries and access to the full text of many via its esp@cenet interface.

The World Intellectual Property Organization (WIPO)’s PATENTSCOPE lets you search 10,078,403 patent documents, including 1,982,614 published international patent applications (PCT).

Google Patents searches over 7 million patents granted by the United States Patent and Trademark Office (USPTO) as well as patent applications submitted to the office.

Posted in Basic Sciences, Database, Drug info, General, Life Sciences, Medicine, Research, Uncategorized | Tagged , , , , , | Leave a comment

December 1st is World AIDS Day: Trustworthy HIV/AIDS Information from MedlinePlus

For trustworthy information on HIV/AIDS visit the MedlinePlus HIV/AIDS site. MedlinePlus is the National Institutes of Health (NIH)’s Web site for patients and their families and friends and offers reliable, up-to-date health information, anytime, anywhere, for free.

Posted in Drug info, General, Medicine, Nursing | Tagged , | Leave a comment

UCSF Profiles: A Research Networking and Expertise Mining Tool

The National Institutes of Health (NIH) has made translational medicine research a high priority. UCSF’s Clinical and Translational Science Institute (CTSI) is one of the 60 institutes nationwide awarded through the NIH Clinical Translational Science Award program in 2006 and was recently awarded a five-year, $112 million NIH renewal grant to help accelerate translation of research to improve health.

Cross-discipline collaboration has grown rapidly over the last few years. The CTSI promotes collaborative and interdisciplinary translational research.  To facilitate researchers not only locally but also nationally and internationally to find experts, collaborators or mentors from UCSF, CTSI created a “UCSF Profile”.


It’s very easy to use. You can find investigators by searching research topic or by name/department. Below is an example of Dr. E. Blackburn’s profile. You can see whom Dr. Blackburn networks with (who co-authored with her; who worked on similar research topics) and her publications.


Try this useful UCSF research expertise database to find mentors, collaborators and experts!

Posted in Basic Sciences, Dentistry, Medicine, Nursing, Physical Therapy, Research, Tools & Technology | Tagged , | 1 Comment

Dear RefWorks Users… Classic Interface is Going Away.

Many of you will have moved to the new RefWorks 2.0 interface. The new interface has the same features as the classic interface but is easier to navigate and use:

RefWorks "Classic" Interface

RefWorks 2.0 Interface

Up to now you’ve had the option to switch between the new interface and the old. However, if you haven’t started to use 2.0 you should switch as soon as possible because Classic is going away. It will no longer be available after December 31, 2011.  

You can view these quick online tutorials if you aren’t familiar with 2.0.

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Get PubMed PDFs Faster with PubGet’s PaperPlane tool.

PubGet’s PaperPlane

A previous post highlighted PubGet, a Web-based search engine for life sciences researchers for conducting searches of the medical literature and fast retrieval of full-text PDFs. However, if you don’t have the time or inclination to explore yet another biomedical search engine and just want to stick with PubMed, you can still get fast access to PubMed’s PDFs by using the PubGet PaperPlane tool.

It’s simple to use. First you add a PaperPlane bookmarklet  to your browser toolbar:

 

 

 

When you search PubMed, click on the title of an article to select the Abstract format:

Then  select the PaperPlane link from the Bookmarks menu/bar and PubGet opens a new window and gets you the PDF:

 

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