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DrNote: An open medical annotation service
In the context of clinical trials and medical research medical text mining can provide broader insights for various research scenarios by tapping additional text data sources and extracting relevant information that is often exclusively present in unstructured fashion. Although various works for dat...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9931362/ https://www.ncbi.nlm.nih.gov/pubmed/36812581 http://dx.doi.org/10.1371/journal.pdig.0000086 |
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author | Frei, Johann Soto-Rey, Iñaki Kramer, Frank |
author_facet | Frei, Johann Soto-Rey, Iñaki Kramer, Frank |
author_sort | Frei, Johann |
collection | PubMed |
description | In the context of clinical trials and medical research medical text mining can provide broader insights for various research scenarios by tapping additional text data sources and extracting relevant information that is often exclusively present in unstructured fashion. Although various works for data like electronic health reports are available for English texts, only limited work on tools for non-English text resources has been published that offers immediate practicality in terms of flexibility and initial setup. We introduce DrNote, an open source text annotation service for medical text processing. Our work provides an entire annotation pipeline with its focus on a fast yet effective and easy to use software implementation. Further, the software allows its users to define a custom annotation scope by filtering only for relevant entities that should be included in its knowledge base. The approach is based on OpenTapioca and combines the publicly available datasets from WikiData and Wikipedia, and thus, performs entity linking tasks. In contrast to other related work our service can easily be built upon any language-specific Wikipedia dataset in order to be trained on a specific target language. We provide a public demo instance of our DrNote annotation service at https://drnote.misit-augsburg.de/. |
format | Online Article Text |
id | pubmed-9931362 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-99313622023-02-16 DrNote: An open medical annotation service Frei, Johann Soto-Rey, Iñaki Kramer, Frank PLOS Digit Health Research Article In the context of clinical trials and medical research medical text mining can provide broader insights for various research scenarios by tapping additional text data sources and extracting relevant information that is often exclusively present in unstructured fashion. Although various works for data like electronic health reports are available for English texts, only limited work on tools for non-English text resources has been published that offers immediate practicality in terms of flexibility and initial setup. We introduce DrNote, an open source text annotation service for medical text processing. Our work provides an entire annotation pipeline with its focus on a fast yet effective and easy to use software implementation. Further, the software allows its users to define a custom annotation scope by filtering only for relevant entities that should be included in its knowledge base. The approach is based on OpenTapioca and combines the publicly available datasets from WikiData and Wikipedia, and thus, performs entity linking tasks. In contrast to other related work our service can easily be built upon any language-specific Wikipedia dataset in order to be trained on a specific target language. We provide a public demo instance of our DrNote annotation service at https://drnote.misit-augsburg.de/. Public Library of Science 2022-08-15 /pmc/articles/PMC9931362/ /pubmed/36812581 http://dx.doi.org/10.1371/journal.pdig.0000086 Text en © 2022 Frei et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Frei, Johann Soto-Rey, Iñaki Kramer, Frank DrNote: An open medical annotation service |
title | DrNote: An open medical annotation service |
title_full | DrNote: An open medical annotation service |
title_fullStr | DrNote: An open medical annotation service |
title_full_unstemmed | DrNote: An open medical annotation service |
title_short | DrNote: An open medical annotation service |
title_sort | drnote: an open medical annotation service |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9931362/ https://www.ncbi.nlm.nih.gov/pubmed/36812581 http://dx.doi.org/10.1371/journal.pdig.0000086 |
work_keys_str_mv | AT freijohann drnoteanopenmedicalannotationservice AT sotoreyinaki drnoteanopenmedicalannotationservice AT kramerfrank drnoteanopenmedicalannotationservice |