Extracting Various Classes of Data From Biological Text Using the Concept of Existence Dependency

IEEE J Biomed Health Inform. 2015 Nov;19(6):1918-28. doi: 10.1109/JBHI.2015.2392786. Epub 2015 Jan 19.


One of the key goals of biological natural language processing (NLP) is the automatic information extraction from biomedical publications. Most current constituency and dependency parsers overlook the semantic relationships between the constituents comprising a sentence and may not be well suited for capturing complex long-distance dependences. We propose in this paper a hybrid constituency-dependency parser for biological NLP information extraction called EDCC. EDCC aims at enhancing the state of the art of biological text mining by applying novel linguistic computational techniques that overcome the limitations of current constituency and dependency parsers outlined earlier, as follows: 1) it determines the semantic relationship between each pair of constituents in a sentence using novel semantic rules; and 2) it applies a semantic relationship extraction model that extracts information from different structural forms of constituents in sentences. EDCC can be used to extract different types of data from biological texts for purposes such as protein function prediction, genetic network construction, and protein-protein interaction detection. We evaluated the quality of EDCC by comparing it experimentally with six systems. Results showed marked improvement.

MeSH terms

  • Computational Biology / methods*
  • Data Mining / methods*
  • Databases, Genetic
  • Humans
  • Natural Language Processing*
  • Semantics*