PubMed Commons – A New Way to Share Information and Research Processes

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From a recent email  by Holly Ann Burt, Outreach and Exhibits Coordinator of the National Network of Libraries of Medicine (NN/LM) Greater Midwest Region

NCBI has released PubMed** Commons, currently in pilot phase, which is a new system that enables researchers to share their opinions about scientific publications indexed in the PubMed database. This is intended to be a forum for open and constructive criticism and discussion of scientific issues.

A new NCBI Insights Blog post provides more information and explains how researchers can join in!

For more information, please see:

PubMed Commons Homepage – http://www.ncbi.nlm.nih.gov/pubmedcommons
NCBI Insights Blog post: “PubMed Commons – a new forum for scientific discourse”-http://ncbiinsights.ncbi.nlm.nih.gov/2013/10/22/pubmed-commons-a-new-forum-for-scientific-discourse/

Here’s a mock-up

**PubMed  (a US government funded database) is the largest database of biomedical journals in the world. It comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related articles

• Enter PubMed Commons (blogs.discovermagazine.com)
• PubMed now allows comments on abstracts – but only by a select few (retractionwatch.wordpress.com)
• PubMed now allows comments on abstracts — but only by a select few (thestackscat.wordpress.com)
• New Online: NCBI Launches Pilot Version of PubMed Commons (infodocket.com)
• PubMed Commons: Post Peer Review System from NCBI (hslnews.wordpress.com)
• PubMed Commons: Post publication peer review goes mainstream (michaeleisen.org)
• Research Tools: PubMed Now Offers Relevance Sort Option (infodocket.com)
• Post-Publication Peer Review: PubPeer (hslnews.wordpress.com)
• How the NLM Justifies Linking to PubMed Central Versions Directly from PubMed Search Results Lists (scholarlykitchen.sspnet.org)

Looking for historical biomedical information? Try the redesigned IndexCat, a product of the US National Library of Medicine

In my last position as a medical librarian, IndexCat was the first place to go for finding historical biomedical articles and related information. Searches on IndexCat can find in minutes what took up to an hour or more in the print version, providing access to over 3.7 million items as information about books, journal articlesd,issertations, pamphlets, reports, newspaper clippings, case studies, obituary notices, letters, portraits, as well as rare books and manuscripts.

IndexCat has recently been redesigned for even easier access to the records of historical biomedical information.

IndexCat is “the [free!]online version of The Index-Catalogue of the Library of the Surgeon-General’s Office (Index-Catalogue) [, the]..multi-part printed bibliography or list of items in the Library of the Surgeon-General’s Office, U.S. Army. It contains material dated from the 1400s through 1950 and is an important resource for researchers in the history of medicine, history of science, and for clinical research.”[http://www.nlm.nih.gov/hmd/indexcat/abouticatalogue.html]

While IndexCat does not contain the full text of items, it provides enough information on them so they can be located at libraries.
If you need the full text of the items, the best place to start is your local public or academic library. Ask for a reference librarian.
He or she can help you find the item or assist you in getting a copy through interlibrary loan. And remember, most academic libraries will be happy to help those who are not affiliated with their institution. Just call ahead and ask how they assist the public.

Related blog post

How to obtain free/low cost medical and scientific articles (jflahiff.wordpress.com)

Open science: change is coming to how scientists communicate research findings

Image via WikipediaAuthor - art designer at PLoS, I converted a pdf into svg http://www.plos.org/

How Scientists Communicate Affects How Research Results Are Applied …as FDA approved drugs, nutrition values, violence prevention, and climate change models

Past blog postings (see below) here have often touched on the difficulties of  obtaining recent scientific and medical findings in original biomedical articles.  Most of these research articles are only found in journals that charge high annual subscription rates ($600.00/ year and up) or an access fee of about $20.00 per article.

Not only is this pricing arrangement making it difficult for scientists to get needed information, but it is becoming nearly impossible for even university and research libraries to buy subscription to the journals their customers want. Additionally article authors must pay publication fees to the journals which range from $1,000  to $5,000 per article.

Most stakeholders (researchers, librarians, publishing companies) believe that the relatively high costs of publishing articles is a major flaw of the current publishing system. These publishing costs used to be born by the researcher in centuries past and were relatively cheap and involved much fewer scientists in tight knit groups. But with the sheer numbers of those wanting information, the many biomedical specialities, and the sophistication of article content (images, videos, and audios), the cost per article has dramatically risen.

Some related statistics (from the posting How many science journals at Science Intelligence and InfoPros)

• Estimation: <> 25-40,000 journals
• 96% are published online
• 8-10% are published under Open Access models
• 20% of science articles are available free of charge
• How many articles have been published ever (means since 1665)? est. 50 millions
• Growth: 1.4 million of articles per year
• There are 2,000 publishers but Top 3 (Elsevier, Springer, Wiley)  account for 42% of articles published

The open science model is one initiative which may reduce costs and increase readership. This approach may well also drastically reduce the time from article completion by the scientist to article publication. It is currently not uncommon for an article in a peer reviewed journal to take up to  1 1/2 years to be published after submission.

In a recent New York Times article (Cracking Open the Scientific Process), the conservative culture of science is outlined, as well as the plausibility of using social media as vehicles of communicating research results. The article also summarizes another fear of scientists. While social media is a less costly and speedier way to communicate research approaches and results, it currently lacks the quality control and trustability of the peer review process in selecting and editing articles for publication.

While Open Science overwhelmingly is geared for  scientist participation only, the way scientists communicate does ultimately affect the application of research. Examples in consumer health  include the drugs we take, the way treatments are prescribed, and the make up of a well balanced diet.  Current questions about the Open Science model include how wise is the scientific equivalent of crowdsourcing? and who will pay for the costs involved and how much?

Some excerpts from the article

The system is hidebound, expensive and elitist, they say. Peer review can take months, journal subscriptions can be prohibitively costly, and a handful of gatekeepers limit the flow of information. It is an ideal system for sharing knowledge, said the quantum physicist Michael Nielsen, only “if you’re stuck with 17th-century technology.”

Dr. Nielsen and other advocates for “open science” say science can accomplish much more, much faster, in an environment of friction-free collaboration over the Internet. And despite a host of obstacles, including the skepticism of many established scientists, their ideas are gaining traction.

Open-access archives and journals like arXiv and thePublic Library of Science (PLoS) have sprung up in recent years. GalaxyZoo, a citizen-science site, has classified millions of objects in space, discovering characteristics that have led to a raft of scientific papers….

…a social networking site called ResearchGate — where scientists can answer one another’s questions, share papers and find collaborators — is rapidly gaining popularity…

  …On Thursday [January 19] , 450 bloggers, journalists, students, scientists, librarians and programmers will converge on North Carolina State University (and thousands more will join in online) for the sixth annual ScienceOnline conference. Science is moving to a collaborative model, said Bora Zivkovic, a chronobiology blogger who is a founder of the conference, “because it works better in the current ecosystem, in the Web-connected world.”…

…[The Research Gate] Web site is a sort of mash-up of Facebook, Twitter and LinkedIn, with profile pages, comments, groups, job listings, and “like” and “follow” buttons (but without baby photos, cat videos and thinly veiled self-praise). Only scientists are invited to pose and answer questions — a rule that should not be hard to enforce, with discussion threads about topics like polymerase chain reactions that only a scientist could love….

Related past postings at Health and Medical News…

• The White House Calls for Information on Public Access to Publications and Data  (via The Scholarly Kitchen)
• Many NIH-funded clinical trials go unpublished over two years after completion (with ClinicalTrials.gov link for many trial study results)
•  Impact of free access to the scientific literature, including empowerment of health care consumers

Related articles (basically an indicator of how hot this topic is)

• ‘Open Science’ Challenges Journal Tradition With Web Collaboration – Thomas Lin via NYTimes.com (stoweboyd.com)
• Advocates For Open Science Say Systemic Change Is Inevitable (keptup.typepad.com)
• Cracking Open the Scientific Process (InnovationToronto.com)
• ‘Open Science’ Challenges Journal Tradition With Web Collaboration (nytimes.com)
• ‘Open Science’ Challenges Journal Tradition With Web Collaboration (nytimes.com)
• Open science: change is coming… (scienceintelligence.wordpress.com)
• ‘Open Science’ Challenges Journal Tradition With Web Collaboration – NYTimes.com (policyabcs.wordpress.com)
• Open science: why is it so hard? (downes.ca)
• Open science: why is it so hard? (lemire.me)
• Michael Nielsen: SPARC Innovator [Confessions of a Science Librarian] (scienceblogs.com)
• Taking a Closer Look at Peer Review (r-bloggers.com)
• I’m on peer review strike! (ucfagls.wordpress.com)
• Cracking Open the Scientific Process (3quarksdaily.com)
• University PR offices need to make peer review process clear (jodymacpherson.wordpress.com)
• The Research Works Act: Is It Time For a Rally To Restore Sanity? (scholarlykitchen.sspnet.org)
• Open Science And The Econoblogosphere (krugman.blogs.nytimes.com)
• Elsevier and Federation of Biochemical Societies Launch New Journal: FEBS Open Bio (prnewswire.com)
• Scientists, Share Your Secrets Or Lose Funding (junkscience.com)
• Publishing and the open-access model (bindingobsession.com)
• How many science journals? (scienceintelligence.wordpress.com)
• Are publishers the enemies of science? (scienceintelligence.wordpress.com)

How many research papers are freely available? (About 28% in PubMed)- August 01, 2011

From the Nature.com Newsblog item

The chart shows the proportion of papers indexed on the (largely biomedical) PubMed repository each year that are now freely accessible: in 2009, it’s above 28%. (Some of this literature is not immediately available at the time that it is published, because of journal policies that impose embargo periods on when material can become free). Those numbers are even more impressive than a study last year which found that around 20% of research papers published in 2008 were freely available on the internet.

The growth is due to various public access mandates by federal government and by funding agencies – as well as the success of open access publishers like the Public Library of Science. “What’s interesting is the relatively stable linear slope here for more than 10 years,” says David Lipman, director of the US National Center for Biotechnology Information (NCBI) at the National Institutes of Health, which houses PubMed. “Would we expect that to continue at the same rate with around 50% of the literature published in 2021 freely available?”

Read entire article (with links) here

Related articles

• Should scientific articles be available free online? (slate.com)
• How to obtain free/low cost medical articles in medical and scientific journals (jflahiff.wordpress.com)

• Impact of free access to the scientific literature (Science Intelligence and InfoPros)

Impact of free access to the scientific literature, including empowerment of health care consumers

From the 21 July 2011 blog item at  Science Intelligence and InfoPros, by hbasset

An excellent review in the latest JMLA:

The paper reviews recent studies that evaluate the impact of free access (open access) on the behavior of scientists as authors, readers, and citers in developed and developing nations. (…)

• Researchers report that their access to the scientific literature is generally good and improving (76% of researchers think that it is better now than 5 years ago)
• Publishers (Elsevier and Oxford UP) reveal an increase in the number of journals available at a typical university and an even larger increase in the article downloads
• For authors, the access status of a journal is not an important consideration when deciding where to publish (journal reputation is stronger)
• The high cost of Western scientific journals poses a major barrier to researchers in developing nations
• There is clear evidence that free access increases the number of article downloads, although its impact on article citations is not clear
• Recent studies provide little evidence to support the idea that there is a crisis in access to the scholarly literature
• Author’s resistance to publication fees is a major barrier to greater participation in open access initiatives
• The empowerment of health care consumers through universal access to original research has ben cited as a key benefit of free access to the scientific literature
• overall, the published evidence does not indicate how (or whether) free access to the scientific literature influences consumers’ reading or behavior
• current research reveals no evidence of unmet demand for the primary medical or health sciences literature among the general public
• most research on access to the scientific literature assumes a traditional and hierarchical flow of information from the publisher to the eader, with the library often serving ans an intermediary betwwen the two. Very little has been done to investigate alternative routes of access to the scientific literature

Davis, Philip M. & Walters, William H. The impact of free access to the scientific literature: a review of recent research. J Med Libr Assoc 99(3):208-17 (2011).
http://www.ncbi.nlm.nih.gov/pubmed/21753913

available at:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133904/

Related posts

• How to obtain free/low cost medical articles in medical and scientific journals
• “Summaries for Patients” and other plain language summaries help patients and others understand medical studies and guidelines

 

 

 

Related articles

• Challenging the Access Crisis (scholarlykitchen.sspnet.org)
• Peter Suber, Open Access Overview (definition, introduction) (earlham.edu)
• Do we need an alternative to peer-reviewed journals? (arstechnica.com)
• Science Longevity Paper Retracted (news.sciencemag.org)
• How the quality of the scientific literature impacts the evidence (kevinmd.com)
• Should scientific articles be available free online? (slate.com)