Extracting regulatory gene expression networks from PubMed

Authors:
Jasmin Šarić;Lars J. Jensen;Rossitza Ouzounova;Isabel Rojas;Peer Bork
Affiliations:
EML Research gGmbH, Heidelberg, Germany;EMBL, Heidelberg, Germany;EMBL, Heidelberg, Germany;EML Research gGmbH, Heidelberg, Germany;EMBL, Heidelberg, Germany
Venue:
ACL '04 Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics
Year:
2004

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Abstract

We present an approach using syntacto-semantic rules for the extraction of relational information from biomedical abstracts. The results show that by overcoming the hurdle of technical terminology, high precision results can be achieved. From abstracts related to baker's yeast, we manage to extract a regulatory network comprised of 441 pairwise relations from 58,664 abstracts with an accuracy of 83-90%. To achieve this, we made use of a resource of gene/protein names considerably larger than those used in most other biology related information extraction approaches. This list of names was included in the lexicon of our retrained part-of-speech tagger for use on molecular biology abstracts. For the domain in question an accuracy of 93.6-97.7% was attained on POS-tags. The method is easily adapted to other organisms than yeast, allowing us to extract many more biologically relevant relations.