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http://dx.doi.org/10.5808/GI.2020.18.2.e13

Using the PubAnnotation ecosystem to perform agile text mining on Genomics & Informatics: a tutorial review  

Nam, Hee-Jo (Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University)
Yamada, Ryota (Fuku Corporation)
Park, Hyun-Seok (Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University)
Publication Information
Genomics & Informatics / v.18, no.2, 2020 , pp. 13.1-13.6 More about this Journal
Abstract
The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publications based on PMCID. Thus, this review aims to provide a tutorial overview of practicing the iterative task of named entity recognition with the PubAnnotation/PubDictionaries/TextAE ecosystem. We also describe developing a conversion tool between the Genia tagger output and the JSON format of PubAnnotation during the hackathon.
Keywords
named entity recognition; natural language processing; text mining;
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