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01.12.2012 | Proceedings | Sonderheft 1/2012 Open Access

BMC Medical Informatics and Decision Making 1/2012

Discovering context-specific relationships from biological literature by using multi-level context terms

BMC Medical Informatics and Decision Making > Sonderheft 1/2012
Sejoon Lee, Jaejoon Choi, Kyunghyun Park, Min Song, Doheon Lee
Wichtige Hinweise

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

LS and JC designed the method and drafted the manuscript along with MS. KP carried out literature analysis for the validation. MS also critically revised the manuscript for important intellectual context and developed the text mining component. DL supervised the work and gave final approval of the version of the manuscript to be submitted.



The Swanson's ABC model is powerful to infer hidden relationships buried in biological literature. However, the model is inadequate to infer relations with context information. In addition, the model generates a very large amount of candidates from biological text, and it is a semi-automatic, labor-intensive technique requiring human expert's manual input. To tackle these problems, we incorporate context terms to infer relations between AB interactions and BC interactions.


We propose 3 steps to discover meaningful hidden relationships between drugs and diseases: 1) multi-level (gene, drug, disease, symptom) entity recognition, 2) interaction extraction (drug-gene, gene-disease) from literature, 3) context vector based similarity score calculation. Subsequently, we evaluate our hypothesis with the datasets of the "Alzheimer's disease" related 77,711 PubMed abstracts. As golden standards, PharmGKB and CTD databases are used. Evaluation is conducted in 2 ways: first, comparing precision of the proposed method and the previous method and second, analysing top 10 ranked results to examine whether highly ranked interactions are truly meaningful or not.


The results indicate that context-based relation inference achieved better precision than the previous ABC model approach. The literature analysis also shows that interactions inferred by the context-based approach are more meaningful than interactions by the previous ABC model.


We propose a novel interaction inference technique that incorporates context term vectors into the ABC model to discover meaningful hidden relationships. By utilizing multi-level context terms, our model shows better performance than the previous ABC model.
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