Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods
Finding publications that propose alternative methods to animal experiments is an important but time-consuming task since researchers need to perform various queries to literature databases and screen many articles to assess two important aspects: the relevance of the article to the research questio...
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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-e18.pdf |
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| _version_ | 1832570591202246656 |
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| author | Mariana Neves |
| author_facet | Mariana Neves |
| author_sort | Mariana Neves |
| collection | DOAJ |
| description | Finding publications that propose alternative methods to animal experiments is an important but time-consuming task since researchers need to perform various queries to literature databases and screen many articles to assess two important aspects: the relevance of the article to the research question, and whether the article’s proposed approach qualifies to being an alternative method. We are currently developing a Web application to support finding alternative methods to animal experiments. The current (under development) version of the application utilizes external tools and resources for document processing, and relies on the PubAnnotation ecosystem for annotation querying, annotation storage, dictionary-based tagging of cell lines, and annotation visualization. Currently, our two PubAnnotation repositories for discourse elements contain annotations for more than 110k PubMed documents. Further, we created an annotator for cell lines that contain more than 196k terms from Cellosaurus. Finally, we are experimenting with TextAE for annotation visualization and for user feedback. |
| format | Article |
| id | doaj-art-c93f1f0a32564e3e9b427f45958422eb |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2020-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-c93f1f0a32564e3e9b427f45958422eb2025-02-02T15:03:17ZengBioMed CentralGenomics & Informatics2234-07422020-06-01182e1810.5808/GI.2020.18.2.e18603Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methodsMariana NevesFinding publications that propose alternative methods to animal experiments is an important but time-consuming task since researchers need to perform various queries to literature databases and screen many articles to assess two important aspects: the relevance of the article to the research question, and whether the article’s proposed approach qualifies to being an alternative method. We are currently developing a Web application to support finding alternative methods to animal experiments. The current (under development) version of the application utilizes external tools and resources for document processing, and relies on the PubAnnotation ecosystem for annotation querying, annotation storage, dictionary-based tagging of cell lines, and annotation visualization. Currently, our two PubAnnotation repositories for discourse elements contain annotations for more than 110k PubMed documents. Further, we created an annotator for cell lines that contain more than 196k terms from Cellosaurus. Finally, we are experimenting with TextAE for annotation visualization and for user feedback.http://genominfo.org/upload/pdf/gi-2020-18-2-e18.pdfanimal testing alternativesinformation storage and retrievaltext mining |
| spellingShingle | Mariana Neves Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods Genomics & Informatics animal testing alternatives information storage and retrieval text mining |
| title | Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods |
| title_full | Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods |
| title_fullStr | Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods |
| title_full_unstemmed | Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods |
| title_short | Integration of the PubAnnotation ecosystem in the development of a web-based search tool for alternative methods |
| title_sort | integration of the pubannotation ecosystem in the development of a web based search tool for alternative methods |
| topic | animal testing alternatives information storage and retrieval text mining |
| url | http://genominfo.org/upload/pdf/gi-2020-18-2-e18.pdf |
| work_keys_str_mv | AT mariananeves integrationofthepubannotationecosysteminthedevelopmentofawebbasedsearchtoolforalternativemethods |