Access to the Document

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats. Results indicate a good performance for extraction of microorganisms and the relation extraction aspects of the task (with a precision of over 80%), while habitat recognition is only moderate (a precision of about 65%). We also conjecture that pdf-to-text conversion can be quite noisy and this implicitly affects any sentence-based relation extraction algorithms.

DOI: 10.2390/biecoll-jib-2011-184

Kolluru, BalaKrishna ; Nakjang, Sirintra ; Hirt, Robert P. ; Wipat, Anil ; Ananiadou, Sophia  (2011)  Automatic extraction of microorganisms and their habitats from free text using text mining workflows. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 8(2), 2011

Online-Journal: http://journal.imbio.de/article.php?aid=184
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2011/5200

Copyright note