PubMed’s Shutdown Averted… For Now.

12 04 2011

MEDLINE is the National Library of Medicine‘s (NLM) premier bibliographic database of citations from biomedical journals. The content of MEDLINE is available via commercial, fee-for-service MEDLINE vendors, like OVID.

On June 26, 1997, Vice President Al Gore officially announced free MEDLINE access via PubMed. This was one of the consequences of  the Freedom of Information Act (FOIA), a federal law that allows for the full or partial disclosure of previously unreleased information and documents controlled by the United States Government. (http://www.nih.gov/icd/od/foia/index.htm). National Library of Medicine (which is “just” one of the NIH web servers) gives access to many other databases besides PubMed/MEDLINEMeSH, UMLS, ClinicalTrials.gov, MedlinePlus, TOXNET.

I may complain about PubMed once in a while and I may criticize some of its new features, but I cannot imagine a working  life without PubMed. Probably this is even more true for biomedical scientist and physicians who have only access to freely available PubMed and not to OVID MEDLINE, EMBASE and Web of Science, like I do. PubMed and many other NLM databases have become an indispensable source of Medical Information.

We are so used to these free sources, that we take them for granted. Who would imagine that PubMed -or any other great free NLM/NIH database would cease to exists? Still, shutdown of these databases was imminent last weekend. Remarkably it largely went unnoticed, especially for people outside the U.S.

Did you know that there was a great chance of PubMed being killed this weekend?

I happened to get the news via my Twitter stream. I joined in around Friday midnight -Dutch time, 3-4 days ago.

Here are some selected tweets. Have a look. See and feel the panic:

As somebody far from the epicenter  it is hard for me to unravel the logic (?) behind the shutdown threat.

I understand that the near-breakshutdown is the result of the disagreement between the democrats and republicans on the ways to cut the federal costs. By refusing to pass a bill allowing the federal government to be funded, the Republican dominated House of Representatives was forcing a showdown with the White House and Barack Obama. The arrows of the Republicans were mainly directed at Planned Parenthood, the health organisation that Republicans portray as primarily focused on performing abortions, using American taxpayer dollars to do it. However, Planned Parenthood provides an array of services, from screenings for cancer to testing for sexually transmitted diseases (see Huffington post).

Well the tweet of Sarah Palin illustrates the view of the Tea Party (in typical Palin style).

For now, the threat has been averted. The Republicans forced the Democrats to agree to $39bn (£23bn) in spending cuts in this year’s budget to September, $6bn more than the Democrats were prepared to accept earlier this week. In return, the Republicans dropped a demand to cut funding for Planned Parenthood (Guardian). But no one knows whether the aversion is definitive.

This post isn’t meant to dive deep into the US political debate. It is just meant to reflect on the possibility that one of those federal databases, on which we rely, is wiped away overnight, thereby seriously affecting our usual workflows.

Some consequences when PubMed (and MEDLINE?)  would disappear:

  • Many Doctors can no longer search efficiently for medical information (only brows medical journals,  “Google” or look up outdated info).
  • The same is true for many scientists. Look at FlutesUD remarks about the references for her thesis.
  • The disappearance of Pubmed would especially affect rural areas and third world countries.
  • EBM would become difficult to practice:
    • The comprehensive search of PubMed, obligatory for systematic reviews, has to be skipped.
    • It would become almost impossible to do a critical appraised topic (i.e. interns are often used to search/have only access to PubMed)
    • CENTRAL (the largest database of controlled trials) can no longer retrieve its records from PubMed.
  • Librarians can delete many tutorials, e-learning materials and -even- classes.
  • Perhaps many librarians can even say goodbye to their jobs?
  • MYNCBI Saved searches and alerts are gone.
  • MYNCBI Saved papers (collections) are no more.
  • 3rd party Pubmed tools (Novoseek, GoPubMed, HubMed) would also cease to exist.
  • Commercially available MEDLINE sources will be affected as well.
  • By the way clinical.trials.gov, TOXNET etc would also stop. Another hit for librarians, doctors and patients.

For many, disappearance of PubMed is a relative “minor” event compared to the shutdown of other services like the NASA, or healtcare institutions. The near-disappearance of PubMed made me realize how fragile this excellent service is on which we -librarians, physicians, medical students and scientists- rely. On the other hand, it also made me realize how thankful we should be that such a database is available to us for free (yes, even for people outside the US).

Note: (Per 2011-04-14)

I have changed the title from “PubMed’s Sudden Death averted” to “PubMed’s Shutdown averted”, because Death is permanent and it was unknown if the shutdown, if any, would be permanent.

I have also changed some words in the text (blue), thus changed disappearance to “shutdown” for the same reasons as mentioned above.

On the other hand I’ve added some tweets which clearly indicate that the shutdown was not “nothing to worry about”.

The tweets mentioned are not from official resources. And this is what this post is partly about. The panic that results if there is a lack of reliable information. Other main points: (2) the importance of PubMed for biomedical information and (3) that PubMed’s permanent (free) existence is not granted.

Nikki D at Eagledawg describes the event (lack of info and panic) very clearly in her post: Pubmed. Keep Calm and Carry On?

More Info:

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Implementing Twitter in a Health Sciences Library

23 11 2010

Twitter describes itself as “a service for friends, family, and co-workers to communicate and stay connected through the exchange of quick, frequent answers to one simple question: What are you doing?” [2].

The “answers” are equally simple, because the tweet (that what is being “said”) must fit in 140 characters. The tweet does not only contain plain text, but can contain short-URL’s which link to webpages, figures and videos.

However, tweets have evolved to more than everyday experiences, and take the shape of shared links to interesting content on the web, conversations around hot topics (using hashtags (#), like #cochrane OR #ev2010 (conference evidence2010)), photos, videos, music, and real-time accounts of a newsworthy event [2]. Furthermore, Twitter is now also used by institutions and companies  for branding, marketing and costumer service. This also applies to libraries, with public libraries leading the way. Health science libraries started twittering  in 2009 and as of 2010 there were (only) 24 of them. In addition, the National Library of Medicine (NLM) and most of the regional National Network of Libraries of Medicine (NN/LMs) have a Twitter presence.  I follow @NLM_LHC and @NLM newsroom, for instance.

The NYU Health Sciences Libraries (NYUHSL) began using Twitter in June 2009. The team, consisting of the Director, the Emerging Technologies Librarian and the Web Services Librarian of the NYUHSL, described their experience with the implementation of Twitter in the latest Medical Reference Services Quarterly [1]

The main aim of their Twitter account was to disseminate topics similar to what was posted on their Web site: news about facilities, resources, handy tidbits, services offered, downtime, events, and staff, as well as breaking news.

What was their approach and what were their main experiences?

  • Claim your name, as soon as you vaguely consider using Twitter!
    In the case of  NYUHSL, their usual library acronym was already taken, so they took a similar name: @NYU_HSL (because of the 140-character limit, it is advisable to use as few characters as possible: this will leave more room when somebody replies to you).
  • They added the library logo as a profile picture and included a link to the library website plus a short “bio”.
  • First the team shared responsibility for posting on Twitter (by logging in into the NYU_HSL account and posting), but this posed coordination problems (like double postings, irregular postings). Therefore it was decided that team members would post according to a schedule. Furthermore there was a 2-week rotation. Any important news was tweeted promptly and interesting news from other Twitter users was occasionally retweeted .
  • Later CoTweet was used. This is a free tool, which -as its name suggests- allows multiple people to communicate through corporate Twitter accounts and stay in sync while doing so. One person is the account owner, who creates and maintains the account and gives other people access to it. The individual members can post to Twitter via the Co_tweet account.  CoTweet uses bit.ly as an URL-shortener, displays some (rudimentary) stats, allows scheduling and archiving of tweets and has some other slick features for corporate Twitter use. (See  this post at News CNET for a comparison between CoTweet and the better known Hootsuite)
  • What I most liked about the paper – besides the description of CoTweet – is the content flow diagram the authors used (adapted below). Posts from their library blog were automatically cross-posted via RSS to Twitter using Twitterfeed, whereas tweets were in their turn automatically posted on Facebook. To this end a Twitter Tab was added to the NYUHSL Facebook fan page. In addition it remained possible to post manually to the different social networking tools and to respond to followers or retweet messages of other users.

  • The team also had to find the right tone for Twitter: the style of tweets is more informal than the style of blog posts. They emphasize the importance of keeping the nuances of different social networking sites in mind when establishing an institutional presence.
  • They promoted Twitter in many ways:
    • A large Twitter mascot (blue bird) with the text: “Follow NYU_HSL on Twitter” was placed on the prominent Web’s site feature bar (see Fig. below). Unfortunately the twitter message only appears when you press “next”. Most users will not do this.
    • Creation of a small poster about Twitter.
    • A word of mouth campaign (in orientation presentations, and a tag line with Twitter account information in e-mail correspondence to students: according to Pew Internet [3] college graduates are among the biggest users of Twitter.
    • description and promotion of the Twitter account in the library’s e-mail newsletter and in blog posts.

And finally, we have to come up with the Key Question: was it all worth the effort?

At the time of writing the NYU-HSL had 66 followers, 27 of which were affiliated with the NYU (others being other libraries and librarians for instance). This is not a very big (target) audience, but I agree with the authors that the definition of success in social media is relative.  There were clear (subjective) benefits, like the low cost, ease of use, low effort to maintain the service on the one hand and the possibility to engage the audience, get user opinions and the opportunity to fix problems quickly on the other hand. Furthermore it’s presence on Twitter enhances the library’s reputation, as the library is making an effort to extend beyond its walls and confirms the role of librarians as technology leaders.

I also agree with the library’s basic principle “to give users as many options as possible to keep current with library news, resources, and services.” In this regard Twitter is a simple and effective method for promotion.

Thus health, medical and other libraries. I would say, if you are not twittering, give it a try and read the reviewed paper [1] for more tips. One of these tips is to connect with other libraries on Twitter as to learn from their experiences.

Credits:  @DrShock dm-ed (direct messaged) me on Twitter to alert me to the paper. Thanks Walter!

References (all assessed 2010-11-23)

  1. Cuddy, C., Graham, J., & Morton-Owens, E. (2010). Implementing Twitter in a Health Sciences Library Medical Reference Services Quarterly, 29 (4), 320-330 DOI: 10.1080/02763869.2010.518915
  2. Mashable http://mashable.com/guidebook/twitter/
  3. Lenhart, A., and Fox, S. ‘‘Twitter and Status Updating.’’ Report: Web 2.0, Social Networking. Pew Internet & American Life Project (February 12, 2009). Pew Internet: http://www.pewinternet.org/Reports/2009/Twitter-and-status-updating.aspx




Ten Years of PubMed Central: a Good Thing that’s Only Going to Get Better.

26 05 2010

PubMed Central (PMC) is a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH’s National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM) (see PMC overview).
PMC is a central repository for biomedical peer reviewed literature in the same way as NCBI’s GenBank is the public archive of DNA sequences. The idea behind it “that giving all users free access to the material in PubMed Central is the best way to ensure the durability and utility of the electronical archive as technology changes over time and to integrate the literature with other information resources at NLM”.
Many journals are already involved, although most of them adhere to restrictions (i.e. availability after 1 year). For list see http://www.ncbi.nlm.nih.gov/pmc/journals/

PMC, the brain child of Harold Varmus, once the Director of the National Institutes of Health, celebrated its 10 year anniversary earlier this year.

For this occasion Dr. Lipman, Director of the NCBI, gave an overview of past and future plans for the NIH’s archive of biomedical research articles. See videotape of the Columbia University Libraries below:

Vodpod videos no longer available.

more about “Ten Years of PubMed Central | Scholar…“, posted with vodpod

The main points raised by David Lipman (appr. time given if you want to learn more about it; the text below is not a transcription, but a summary in my own words):

PAST/PRESENT

  • >7:00. BiomedCental (taken over by Spinger) and PLoS ONE show that Open Access can be a sustaining way in Publishing Science.
  • 13:23 Publisher keeps the copyright. He may stop depositing but the content already deposited remains in PMC.
  • 13:50 PMC is also an obligatory repository for author manuscripts under various funding agencies mandates, like the NIH and the UK welcome trust.
  • 14:31 One of the ideas from the beginning was to crosslink the literature with the underlying molecular and other databases. For instance NCBI is capable of mining out the information in the archived text and connecting it to the compound and the protein structure database.
  • 16:50 There is a back issue digitization for the journals that are participating, enabling to find research that you wouldn’t have easily found otherwise.
  • PMC has become international (not restricted to USA)
  • The PMC archive becomes more useful if it becomes more comprehensive
  • Before PMC you could do a Google Scholar search and find a paper in PubMed, that appeared funded by NIH, but then you had to pay $30 for it in order to get it. That’s hard to explain to the taxpayers (Lipman had a hard time explaining it to his dad who was looking for medical information online). This was the impetus for making the results of NIH-sponsored results freely available.

PRESENT/FUTURE

  • 23:00 Discovery initiative: is the use of tracking tools to find out which changes to the website work for users and which don’t. Thus modifications should lead to alterations in users behavior (statistics is easy with millions of users). Discovery initiative led to development and improvement of sensors, like sensors for disease names, drug names, genes and citations. What is being measured is if people click through (if it isn’t interesting, they usually don’t) and how quickly they find results. Motto: train the machine, not the users.
  • 30:37 We changed the looks of PMC. Planning to make a better presentation on the i-phone and on broad monitors.
  • 31:40. There are almost 2 million articles in PubMed Central, 585 journals fully participate in PMC
  • 32.30 It takes very long to publish a paper, even in Open Access papers. Therefore a lot of people are not publishing little discoveries, which are not important enough to put a lot of time in. Publishing should be almost as easy as writing a blog, but with peer review. This requires a new type of journal, with peer review, but with instant feedback from readers and reviewers and rapid response to comments. The Google Knol authoring system offers a fast and simple authoring system where authors (with a Google profile) can collaborate and compose the article on the server. Uploading of documents and figures is easy, the article updates are simple and fast, there is a simple workflow for moderators. After the paper is accepted you press a button, the paper is immediately available and the next day PMC automatically gets the XML content. There is also a simple Reference Manager included to paste citations.
  • Principle: How you can start a journal with this system (see Figure). Till now: 60 articles in PLOS Currents Influenza. There are also plans for other journals: the CDC is announcing a Systematic Reviews journal, for instance.

QUESTIONS (>39:30):

  • Process by which “KNOL-journal” is considered for inclusion in NLM?
    • Decide: is it in scope?, implicit policy (health peer review being done), who are the people involved, look at a dozen articles.
  • As the content in PMC increases, will it become possible to search in the full text, just like in Google Scholar?
    • Actually the full text is searchable in PMC as apposed to PubMed, but we are not that happy with the full text retrieval. Even with a really good approach, searching full text works just a little bit better than searching PubMed.
      We are incorporating more of the information of PMC into PubMed, and are working on a separate image database with all the figures from books and articles in PMC (with other search possibilities). Subsets of book(chapter)s (like practice guidelines) will get PubMed abstracts and become searchable in PubMed as well.
  • Are there ways to track a full list of our institutions OA articles in PMC (not picking up everything in PubMed)
    • Likely NIH will be contacting offices responsible for research to let them know what articles are out of compliance,  get their assistance in making sure that those get in.
    • Authors can easily update the electornic My Bibliography (in My NCBI in PubMed).
    • Author ID project, involves computational disambiguation. Where you are asked if you are the author of a paper if you didn’t include it. It may also be possible to have automatic reporting to the institutions.
  • What did it took politically to get the appropriation bill passed (PMC initiative)?
    • Congress always pushed more open access, because it was already spending money on the research. Most of the initiative came more from librarians (i.e. small libraries not having sufficient access) and government, than from the NIH.
  • Is there way to narrow down to NIH, free full text papers from PMC?
    • In PubMed, you can filter free full text articles in general via the limits.
  • Are all the articles deposited in PMC submitted the final manuscript?
    • Generally, yes.

HT: @bentoth on Twitter