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The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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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| Format: | Article |
| Language: | English |
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BioMed Central
2020-06-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-2-e13.pdf |
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| _version_ | 1832569889565442048 |
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| author | Hee-Jo Nam Ryota Yamada Hyun-Seok Park |
| author_facet | Hee-Jo Nam Ryota Yamada Hyun-Seok Park |
| author_sort | Hee-Jo Nam |
| collection | DOAJ |
| description | The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository.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. |
| format | Article |
| id | doaj-art-b997294662494318b7b485753da6df1f |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2020-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-b997294662494318b7b485753da6df1f2025-02-02T19:03:50ZengBioMed CentralGenomics & Informatics2234-07422020-06-01182e1310.5808/GI.2020.18.2.e13610Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial reviewHee-Jo Nam0Ryota Yamada1Hyun-Seok Park2 Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Korea Fuku Corporation, Tokyo 113-0033, Japan Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, KoreaThe 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.http://genominfo.org/upload/pdf/gi-2020-18-2-e13.pdfnamed entity recognitionnatural language processingtext mining |
| spellingShingle | Hee-Jo Nam Ryota Yamada Hyun-Seok Park Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review Genomics & Informatics named entity recognition natural language processing text mining |
| title | Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review |
| title_full | Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review |
| title_fullStr | Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review |
| title_full_unstemmed | Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review |
| title_short | Using the PubAnnotation ecosystem to perform agile text mining on : a tutorial review |
| title_sort | using the pubannotation ecosystem to perform agile text mining on a tutorial review |
| topic | named entity recognition natural language processing text mining |
| url | http://genominfo.org/upload/pdf/gi-2020-18-2-e13.pdf |
| work_keys_str_mv | AT heejonam usingthepubannotationecosystemtoperformagiletextminingonatutorialreview AT ryotayamada usingthepubannotationecosystemtoperformagiletextminingonatutorialreview AT hyunseokpark usingthepubannotationecosystemtoperformagiletextminingonatutorialreview |