Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review
The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2020-06-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-2-e13.pdf |
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| Summary: | The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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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| ISSN: | 2234-0742 |