Using the PubAnnotation ecosystem to perform agile text mining on Genomics & Informatics: a tutorial review
- Author:
Hee-Jo NAM
1
;
Ryota YAMADA
;
Hyun-Seok PARK
Author Information
- Publication Type:Review article
- From:Genomics & Informatics 2020;18(2):e13-
- CountryRepublic of Korea
- Language:English
- Abstract: The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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.
