3rd Call for Submissions for “Medical Information Matters”: Tools for Searching the Biomedical Literature

8 05 2011

It takes some doing to breathe life into Medical Information Matters” (blog carnival about medical  information).
A month ago I wrote a 2nd call for submissions post for this blog carnival. Unfortunately the next host, Martin Fenner, didn’t have time to finish a blog post and has come up with a new (interesting) variation on the theme “A Wish list for better medical information”.

Martin asks you to philosophize, blog and/or comment about “Tools for Searching the Biomedical Literature.

You can base your contribution on a recent (editable) survey of 28 different PubMed derivative tools by Zhiyong Lu (NCBI) [1].

Thus, write your thoughts on the various PubMed derivative tools mentioned here or write about your own favorite 3rd party PubMed tool (included or not).

For details, see Martin’s blog post announcing this upcoming edition. The Blog Carnival FAQs are here.

And if you don’t have time to write about this topic, you may still find the survey useful, as well as the views of others on this topic. So check out Martin’s blog Gobbledygook once in a while to see if the blog edition has been posted.

Note [1]: If you have already submitted a post to the carnival, or would like to write about another theme, we will take care that your post (if relevant)  will be included in this or the next edition. You can always submit here.

Note [2]: Would you like to host “Medical Information Matters” at your blog? Please comment here or write to: laika dot spoetnik at gmail dot com. We need hosts for June, July, August and September (submission deadline first Saturday of every month, posting on the next Tuesday)

  1. Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database. 2011 Jan;2011. doi: http://dx.doi.org/10.1093/database/baq036
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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: