Pubmed plugin v0.1

Release Notes

Hi all,

I'm quite new to programming (as you will notice from the coding in this plugin) but I would like to make this plugin available to all of you in order for me to receive some feedback and learn coding a bit faster :-)).

A small introduction might be in order: scientific literature is indexed by NCBI and is searchable through the pubmed website ( Therefore, this plugin is more interesting for scientists that wish to show their latest scientific publications on their profile page. In the widget you can enter an author name and additional search term. After receicing the XML from the NCBI server the data is parsed and the selected number of articles are displayed on the profile page. The MESH terms that are associated with the articles are stored as metadata in a seperate object in order for users to search for other scientists in their institution with that MESH term/substance. In addition, the MESH terms can be made visible in a tag cumulus by using the tag_cumulus plugin from Pedro Prez. (

As a reminder: please consider the current posted plugin more as a proof of principle rather then a finished plugin. I am asking all of you more experienced coders to give me some feedback to improve the quality. I am still struggling with security issues, like filtering the user input.


  • Your code looks of fine quality ;-) This could be interesting. Pity PubMed relates to only BioMed and LifeSciences. If other discplines had similar repositories, your PlugIn could be expanded to also cater for those. I'm working with a certain European university to build an educational research repository based Elgg-Site for one of their departments and they are interested in serving multiple discplines. If you can point to or describe the "security issues" parts of the code I might be tempted to study that. Or better send me PM re: that.

  • m_welkers,

    Please expand this plugin to include other disciplines. I'm interested in your plugin. I have a project that can take advantage of your plugin.

    Thank you.



  • PubMed **only caters for BioMed and LifeSciences...
    We are trying to look for "..similar sites (like Pubmed) for ***other ***disciplines... so we can take a look at it ? " Perhaps you, Vantel, can help us out here and we can expand PubMed into becoming something much bigger. How much spare and free time would you have available to help with some research in this area ?

  • Wow, this is exciting!  Wish I could help with this.  This will be awesome!

  • Having a look... can you suggest some edit parameters to test? 

    Pubmed name 1 = ?

  • @Tom

    You can try 'Montagnier' (one of the two nobel prize winners for identifying the HIV virus) and additional term 'HIV'.

  • ok, try "Rosenfeldt"  and "blood"  ;)

  • typo ;-(

    should be "After simply reading the code earlier..."


    Welkers is away for several until after new year hits us, so please nobody post anything heavy until after about 5 days. BTW - We are working on some sql injection security protect code to ensure PubMed does not get hacked / attacked via this PlugIn and some other issues Welkers has mentioned. I like this PlugIn.. Just up on my road for Elggucational websites.

  • What about EBSCOhost?  I only look for physics papers, I might be in a bubble, but they seem to cover a lot of disciplines.

  • @aj

    thanks for this - i will check it out.. ;-)


  • Hi - just posted a lot of details but the site timed me out and I lost them.

    Anyway - PubMed supports the Open Archive Initiative's Protocol for Metadata Harvesting - which is used by a lot of Journal and Conference Management Software - such as that from the Public Knowledge Project - and Library catalog systems.

    Does your module use this protocol? If it does, it would be able to access a load of academic data sources.

    And EBSCO suck. It is the part of the great academic publishing scam. Open Source is for more than software.

    "Funding for all the academics involved in the research, review and editing comes from you and me, the taxpayer. However, most of the research is published by a small circle of corporate publishers, most of whom are based in Britain and the US. These companies then charge the same Australian taxpayer-funded institutions ridiculous amounts of money for subscriptions to academic journals to which the publishers' contribution hardly exceeds the provision of the paper on which they are printed."

    (I used to work at an Academic Library in Cambodia. I was interviewed by someone writing a paper I can't afford to read)

  • @Don Robertson

    Thank you for your comment,  however I didn't use the OAI-PMH protocol to find metadata but the basic NCBI E-utilities. In short, the user input is transformed into a basic Pubmed search for the author -->  "Doe, John"[Author] (and additional search term if needed/desired) and the XML that is returned is parsed. The Mesh terms and substances from each paper are stored in a separate Elgg object as metadata and connected to that specific user, with the intention of making it searchable by other users. At each pageload that metadata is updated. I do not download the entire paper (when available though Open Access) and anything more than this basic data.


  • Category: Widgets
  • License: GNU General Public License (GPL) version 2
  • Updated: 2014-11-17
  • Downloads: 1150
  • Recommendations: 0

Other Projects

View dr's plugins