Journal
BIOINFORMATICS
Volume 27, Issue 23, Pages 3306-3312Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr573
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Funding
- National Institutes of Health, National Library of Medicine [LM000002-01]
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Motivation: Research in the biomedical domain can have a major impact through open sharing of the data produced. For this reason, it is important to be able to identify instances of data production and deposition for potential re-use. Herein, we report on the automatic identification of data deposition statements in research articles. Results: We apply machine learning algorithms to sentences extracted from full-text articles in PubMed Central in order to automatically determine whether a given article contains a data deposition statement, and retrieve the specific statements. With an Support Vector Machine classifier using conditional random field determined deposition features, articles containing deposition statements are correctly identified with 81% F-measure. An error analysis shows that almost half of the articles classified as containing a deposition statement by our method but not by the gold standard do indeed contain a deposition statement. In addition, our system was used to process articles in PubMed Central, predicting that a total of 52 932 articles report data deposition, many of which are not currently included in the Secondary Source Identifier [si] field for MEDLINE citations.
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