From Literature to Knowledge: Exploiting PubMed to Answer Biomedical Questions in Natural Language

  • Pinaki Bhaskar
  • Marina Buzzi
  • Filippo GeraciEmail author
  • Marco Pellegrini
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9267)


Researchers, practitioners and the general public strive to be constantly up to date with the latest developments in the subjects of bio-medical research of their interest. Meanwhile the collection of high quality research papers freely available on the Web has increase dramatically in the last few years and this trend is likely to continue. This state of facts brings about opportunities as well as challenges for the construction of effective web-based searching tools. Question/Answering systems based on user interactions in Natural Language have emerged as a promising alternative to traditional keyword based search engines. However this technology still needs to mature in order to fulfill its promises. In this paper we present and test a new graph-based proof-of-concept paradigm for processing the knowledge base and the user queries expressed in natural Language. The user query is mapped as a subgraph matching problem onto the internal graph representation, and thus can handle efficiently also partial matches. Preliminary user-based output quality measurements confirm the viability of our method.


Clinical Decision Support System Question Answering Screen Reader Tandem Repeat Sequence Mean Reciprocal Rank 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We acknowledge the support of the Italian Registry of ccTLD “.it” and the ERCIM ‘Alain Bensoussan’ Fellowship Programme.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Pinaki Bhaskar
    • 1
  • Marina Buzzi
    • 1
  • Filippo Geraci
    • 1
    Email author
  • Marco Pellegrini
    • 1
  1. 1.CNRInstitute for Informatics and TelematicsPisaItaly

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