Evaluation of Text Data Mining for Database Curation: Lessons Learned from the KDD Challenge Cup
September 2003
Alexander S. Yeh, The MITRE Corporation
Lynette Hirschman, The MITRE Corporation
Alexander A. Morgan, The MITRE Corporation
ABSTRACT
Motivation: The biological literature is a major repository of
knowledge. Many biological databases draw much of their content from a
careful curation of this literature. However, as the volume of
literature increases, the burden of curation increases. Text mining
may provide useful tools to assist in the curation process. To date,
the lack of standards has made it impossible to determine whether text
mining techniques are sufficiently mature to be useful.
Results: We report on a Challenge Evaluation task that we
created for the Knowledge Discovery and Data Mining (KDD) Challenge
Cup. We provided a training corpus of 862 articles consisting of
journal articles curated in FlyBase, along with the associated lists of
genes and gene products, as well as the relevant data fields from
FlyBase. For the test, we provided a corpus of 213 new
("blind") articles; the 18 participating groups provided systems
that flagged articles for curation, based on whether the article contained
experimental evidence for gene expression products. We report on the
the evaluation results and describe the techniques used by the top performing groups.
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Additional Search Keywords
text mining, evaluation, curation, genomics, data management
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