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:

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

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26 05 2010
Tweets that mention Ten Years of PubMed Central: a Good Thing that’s Only Going to Get Better. « Laika's MedLibLog -- Topsy.com

[...] This post was mentioned on Twitter by Laika (Jacqueline), Body In Mind. Body In Mind said: 10 Years of PubMed Central: a good Thing that’s Only Going 2 Get Better. OA & Google Knol http://is.gd/cpbXH from @laikas [...]

2 06 2010
Health 2.0 News: iPad, I-Patients, Wii and computer viruses « ScienceRoll

[...] Ten Years of PubMed Central: a Good Thing that’s Only Going to Get Better: It’s interesting to see the major differences and the directions Pubmed is being developed in. [...]

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