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Knowledge extraction and semantic annotation of text from the Encyclopedia of Life
Thessen, A.E.; Parr, C.S. (2014). Knowledge extraction and semantic annotation of text from the Encyclopedia of Life. PLoS One 9(3): e89550. dx.doi.org/10.1371/journal.pone.0089550
In: PLoS One. Public Library of Science: San Francisco. ISSN 1932-6203, more
Peer reviewed article  

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  • Thessen, A.E.
  • Parr, C.S.

Abstract
    Numerous digitization and ontological initiatives have focused on translating biological knowledge from narrative text to machine-readable formats. In this paper, we describe two workflows for knowledge extraction and semantic annotation of text data objects featured in an online biodiversity aggregator, the Encyclopedia of Life. One workflow tags text with DBpedia URIs based on keywords. Another workflow finds taxon names in text using GNRD for the purpose of building a species association network. Both workflows work well: the annotation workflow has an F1 Score of 0.941 and the association algorithm has an F1 Score of 0.885. Existing text annotators such as Terminizer and DBpedia Spotlight performed well, but require some optimization to be useful in the ecology and evolution domain. Important future work includes scaling up and improving accuracy through the use of distributional semantics.

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