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The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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 Biomedi-cal Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotat-ing, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnota-tion, 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.
| Original language | English |
|---|---|
| Article number | e13 |
| Pages (from-to) | 1-10 |
| Number of pages | 10 |
| Journal | Genomics and Informatics |
| Volume | 18 |
| Issue number | 2 |
| DOIs | |
| State | Published - 2020 |
Bibliographical note
Funding Information:This work was supported by a National Research Foundation of Korea grant (NRF-2019R1F1A1058858) funded by the Korean government (MSIT).
Publisher Copyright:
© 2020, Korea Genome Organization.
Keywords
- Named entity recognition
- Natural language processing
- Text mining