Genomics Inform.
2020 Jun;18(2):e13. 10.5808/GI.2020.18.2.e13.
Using the PubAnnotation ecosystem to perform agile text mining on Genomics & Informatics: a tutorial review
- Affiliations
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- 1Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Korea
- 2Fuku Corporation, Tokyo 113-0033, Japan
- 3Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul 03760, Korea
- KMID: 2503638
- DOI: http://doi.org/10.5808/GI.2020.18.2.e13
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- The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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.
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