Querying parse tree database of medline text to synthesize user-specific biomolecular networks

Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Scopus citations

Abstract

Curated biological knowledge of interactions and pathways is largely available from various databases, and network synthesis is a popular method to gain insight into the data. However, such data from curated databases presents a single view of the knowledge to the biologists, and it may not be suitable to researchers' specific needs. On the other hand, Medline abstracts are publicly accessible and encode the necessary information to synthesize different kinds of biological networks. In this paper, we propose a new paradigm in synthesizing biomolecular networks by allowing biologists to create their own networks through queries to a specialized database of Medline abstracts. With this approach, users can specify precisely what kind of information they want in the resulting networks. We demonstrate the feasibility of our approach in the synthesis of gene-drug, gene-disease and protein-protein interaction networks. We show that our approach is capable of synthesizing these networks with high precision and even finds relations that have yet to be curated in public databases. In addition, we demonstrate a scenario of recovering a drug-related pathway using our approach.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing 2009, PSB 2009
Pages87-98
Number of pages12
StatePublished - Dec 1 2009
Event14th Pacific Symposium on Biocomputing, PSB 2009 - Kohala Coast, HI, United States
Duration: Jan 5 2009Jan 9 2009

Publication series

NamePacific Symposium on Biocomputing 2009, PSB 2009

Other

Other14th Pacific Symposium on Biocomputing, PSB 2009
CountryUnited States
CityKohala Coast, HI
Period1/5/091/9/09

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

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    Tari, L., Hakenberg, J., Gonzalez, G., & Baral, C. (2009). Querying parse tree database of medline text to synthesize user-specific biomolecular networks. In Pacific Symposium on Biocomputing 2009, PSB 2009 (pp. 87-98). (Pacific Symposium on Biocomputing 2009, PSB 2009).