Mining PubMed – another tools available

05 Mar

There are two new tools available that mine semantically PubMed abstracts, e-LiSe and Anne O’Tate. First one was made by my colleagues from Institute of Biochemistry and Biophysics in Warsaw, while the second is from University of Illinois, Chicago. Female-sounding names is not the only thing that makes them look similar, they both provide analogous functionality, like keywords or author names associated with user query.

There’s quite a lot of third party interfaces to PubMed (see David Rothman’s excellent list), so I couldn’t resist to run few queries on both servers and compare them to GoPubmed, which currently wins hands down in terms of features and interface. I wasn’t surprised to see that results overlap significantly, although not completely. Each of servers found valuable keywords other two did not have – that’s understandable, they use different algorithms. I wonder if we will see a meta-server of PubMed data-miners, like there are for protein structure prediction (for example In theory, exhaustive search for meaningful keywords by different methods and then their classification and analysis should work better than any single method, but this is just a guess.


Posted by on March 5, 2008 in bioinformatics, Data mining, PubMed


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5 responses to “Mining PubMed – another tools available

  1. Joan Kureczka

    March 5, 2008 at 18:53

    Are you familiar with NextBio? They have built a google-like search engine capable of searching PubMed and other life sciences data and finding correlations across disciplines. This is already in use by a number of major institutions and pharma/biotech companies.

  2. Pawel Szczesny

    March 5, 2008 at 20:17

    No, I haven’t used NextBio, although the name sounds familiar. But I hope to try – I’ve just applied for a trial account. Thanks a lot!

  3. ChemSpiderMan

    March 11, 2008 at 03:23

    YOu might be interested in the recent integration made between ChemSpider and the Entrez system to access articles on PubMed. Visit for details.

  4. J Kamesh

    March 17, 2009 at 15:23

    I think you can try this one. XTractor Premium ( When it come to semantic search I feel it scores better over others in my opinion. Apart form searching and mining PubMed, it is also a platform for discovery, analysis and modeling of published biomedical facts. You might be interested in the integration made with CytoScape for visualization.

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