The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area on...

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Detalles Bibliográficos
Autores principales: Ivanisenko, Timofey V., Demenkov, Pavel S., Kolchanov, Nikolay A., Ivanisenko, Vladimir A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738852/
https://www.ncbi.nlm.nih.gov/pubmed/36499269
http://dx.doi.org/10.3390/ijms232314934
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author Ivanisenko, Timofey V.
Demenkov, Pavel S.
Kolchanov, Nikolay A.
Ivanisenko, Vladimir A.
author_facet Ivanisenko, Timofey V.
Demenkov, Pavel S.
Kolchanov, Nikolay A.
Ivanisenko, Vladimir A.
author_sort Ivanisenko, Timofey V.
collection PubMed
description The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%.
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spelling pubmed-97388522022-12-11 The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition Ivanisenko, Timofey V. Demenkov, Pavel S. Kolchanov, Nikolay A. Ivanisenko, Vladimir A. Int J Mol Sci Article The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%. MDPI 2022-11-29 /pmc/articles/PMC9738852/ /pubmed/36499269 http://dx.doi.org/10.3390/ijms232314934 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ivanisenko, Timofey V.
Demenkov, Pavel S.
Kolchanov, Nikolay A.
Ivanisenko, Vladimir A.
The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title_full The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title_fullStr The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title_full_unstemmed The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title_short The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition
title_sort new version of the anddigest tool with improved ai-based short names recognition
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738852/
https://www.ncbi.nlm.nih.gov/pubmed/36499269
http://dx.doi.org/10.3390/ijms232314934
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