Genomics & Informatics

  • 제18권2호
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  • Pages.13.1-13.6
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  • 2020
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  • 1598-866X(pISSN)
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  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
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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)
  • 투고 : 2020.03.25
  • 심사 : 2020.06.01
  • 발행 : 2020.05.28
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초록

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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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참고문헌

  1. Genomics and Informatics archives. Seoul: Korea Genome Organization, 2018. Accessed 2020 Jun 17. Available from: https://genominfo.org/articles/archive.php.
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  5. Kim JD, Wang Y, Fujiwara T, Okuda S, Callahan T, Cohen KB. Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinformatics 2019;35:4372-4380. https://doi.org/10.1093/bioinformatics/btz227
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