EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Text
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| Main Authors: | , , , , , , , , , , |
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| Format: | Preprint |
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2023
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| author | Ahmed, Rafsan Berntsson, Petter Skafte, Alexander Rashed, Salma Kazemi Klang, Marcus Barvesten, Adam Olde, Ola Lindholm, William Arrizabalaga, Antton Lamarca Nugues, Pierre Aits, Sonja |
| author_facet | Ahmed, Rafsan Berntsson, Petter Skafte, Alexander Rashed, Salma Kazemi Klang, Marcus Barvesten, Adam Olde, Ola Lindholm, William Arrizabalaga, Antton Lamarca Nugues, Pierre Aits, Sonja |
| contents | Background Medical and life science research generates millions of publications, and it is a great challenge for researchers to utilize this information in full since its scale and complexity greatly surpasses human reading capabilities. Automated text mining can help extract and connect information spread across this large body of literature, but this technology is not easily accessible to life scientists.
Methods and Results Here, we developed an easy-to-use end-to-end pipeline for deep learning- and dictionary-based named entity recognition (NER) of typical entities found in medical and life science research articles, including diseases, cells, chemicals, genes/proteins, species and others. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. In addition, we provide two accessory scripts which allow processing of files in PubTator format and rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.
Conclusions The NER pipeline we present is applicable in a variety of medical research settings and makes customizable text mining accessible to life scientists. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2304_07805 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Text Ahmed, Rafsan Berntsson, Petter Skafte, Alexander Rashed, Salma Kazemi Klang, Marcus Barvesten, Adam Olde, Ola Lindholm, William Arrizabalaga, Antton Lamarca Nugues, Pierre Aits, Sonja Quantitative Methods Computation and Language 92-04, 92-08, 68T50 J.3; I.2.7; H.3.3 Background Medical and life science research generates millions of publications, and it is a great challenge for researchers to utilize this information in full since its scale and complexity greatly surpasses human reading capabilities. Automated text mining can help extract and connect information spread across this large body of literature, but this technology is not easily accessible to life scientists. Methods and Results Here, we developed an easy-to-use end-to-end pipeline for deep learning- and dictionary-based named entity recognition (NER) of typical entities found in medical and life science research articles, including diseases, cells, chemicals, genes/proteins, species and others. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. In addition, we provide two accessory scripts which allow processing of files in PubTator format and rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19. Conclusions The NER pipeline we present is applicable in a variety of medical research settings and makes customizable text mining accessible to life scientists. |
| title | EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Text |
| topic | Quantitative Methods Computation and Language 92-04, 92-08, 68T50 J.3; I.2.7; H.3.3 |
| url | https://arxiv.org/abs/2304.07805 |