Extracting information of anti-AIDS inhibitor from the biological literature based on ontology

Authors:
Chunyan Zhang;Jin Du;Ruisheng Zhang;Xiaoliang Fan;Yongna Yuan;Ting Ning
Affiliations:
Department of Computer Science, Lanzhou University, Gansu, China;Department of Computer Science, Lanzhou University, Gansu, China;Department of Computer Science, Lanzhou University, Gansu, China and Department of Chemistry and Chemical Engineering, Lanzhou University, Gansu, China;Department of Computer Science, Lanzhou University, Gansu, China;Department of Chemistry and Chemical Engineering, Lanzhou University, Gansu, China;Department of Computer Science, Lanzhou University, Gansu, China
Venue:
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Year:
2007

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Abstract

Nowadays, it is still the primary problem to find the inhibitors of retrovirus, protease and integrase in anti-AIDS drug design. However, the research and experimental results about anti-AIDS inhibitors mainly exist in large numbers of scientific literature, not in readable format for computer. In this paper, we introduce an Ontology-based Information Extraction (OIE) approach to extract anti-AIDS inhibitors from literature. Key to the approach is the construction of anti-AIDS inhibitors ontology, which provides a semantic framework for information extraction, and annotation of corpus. Consequently, this paper primarily focuses on the architecture of OIE, on which we construct the anti-AIDS ontology using Protégé tool and annotate corpus. Finally, we employ a demonstrated application scenario to show how to annotate the PubMed articles based on the ontology we have constructed.