A multi-level text mining method to extract biological relationships.

Mathew Palakal, Matthew Stephens, Snehasis Mukhopadhyay, Rajeev Raje, Simon Rhodes

Research output: Contribution to journalArticle

20 Scopus citations


Accurate and computationally efficient approaches in discovering relationships between biological objects from text documents are important for biologists to develop biological models. This paper presents a novel approach to extract relationships between multiple biological objects that are present in a text document. The approach involves object identification, reference resolution, ontology and synonym discovery, and extracting object-object relationships. Hidden Markov Models (HMMs), dictionaries, and N-Gram models are used to set the framework to tackle the complex task of extracting object-object relationships. Experiments were carried out using a corpus of one thousand Medline abstracts. Intermediate results were obtained for the object identification process, synonym discovery, and finally the relationship extraction. For a corpus of thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81%. The approach is both adaptable and scalable to new problems as opposed to rule-based methods.

Original languageEnglish
Pages (from-to)97-108
Number of pages12
JournalProceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference
StatePublished - 2002

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