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Snowball 2.0: Generic Material Data Parser for ChemDataExtractor
[Image: see text] The ever-growing amount of chemical data found in the scientific literature has led to the emergence of data-driven materials discovery. The first step in the pipeline, to automatically extract chemical information from plain text, has been driven by the development of software too...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685441/ https://www.ncbi.nlm.nih.gov/pubmed/37934697 http://dx.doi.org/10.1021/acs.jcim.3c01281 |
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author | Dong, Qingyang Cole, Jacqueline M. |
author_facet | Dong, Qingyang Cole, Jacqueline M. |
author_sort | Dong, Qingyang |
collection | PubMed |
description | [Image: see text] The ever-growing amount of chemical data found in the scientific literature has led to the emergence of data-driven materials discovery. The first step in the pipeline, to automatically extract chemical information from plain text, has been driven by the development of software toolkits such as ChemDataExtractor. Such data extraction processes have created a demand for parsers that efficiently enable text mining. Here, we present Snowball 2.0, a sentence parser based on a semisupervised machine-learning algorithm. It can be used to extract any chemical property without additional training. We validate its precision, recall, and F-score by training and testing a model with sentences of semiconductor band gap information curated from journal articles. Snowball 2.0 builds on two previously developed Snowball algorithms. Evaluation of Snowball 2.0 shows a 15–20% increase in recall with marginally reduced precision over the previous version which has been incorporated into ChemDataExtractor 2.0, giving Snowball 2.0 better performance in most configurations. Snowball 2.0 offers more and better parsing options for ChemDataExtractor, and it is more capable in the pipeline of automated data extraction. Snowball 2.0 also features better generalizability, performance, learning efficiencies, and user-friendliness. |
format | Online Article Text |
id | pubmed-10685441 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-106854412023-11-30 Snowball 2.0: Generic Material Data Parser for ChemDataExtractor Dong, Qingyang Cole, Jacqueline M. J Chem Inf Model [Image: see text] The ever-growing amount of chemical data found in the scientific literature has led to the emergence of data-driven materials discovery. The first step in the pipeline, to automatically extract chemical information from plain text, has been driven by the development of software toolkits such as ChemDataExtractor. Such data extraction processes have created a demand for parsers that efficiently enable text mining. Here, we present Snowball 2.0, a sentence parser based on a semisupervised machine-learning algorithm. It can be used to extract any chemical property without additional training. We validate its precision, recall, and F-score by training and testing a model with sentences of semiconductor band gap information curated from journal articles. Snowball 2.0 builds on two previously developed Snowball algorithms. Evaluation of Snowball 2.0 shows a 15–20% increase in recall with marginally reduced precision over the previous version which has been incorporated into ChemDataExtractor 2.0, giving Snowball 2.0 better performance in most configurations. Snowball 2.0 offers more and better parsing options for ChemDataExtractor, and it is more capable in the pipeline of automated data extraction. Snowball 2.0 also features better generalizability, performance, learning efficiencies, and user-friendliness. American Chemical Society 2023-11-07 /pmc/articles/PMC10685441/ /pubmed/37934697 http://dx.doi.org/10.1021/acs.jcim.3c01281 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Dong, Qingyang Cole, Jacqueline M. Snowball 2.0: Generic Material Data Parser for ChemDataExtractor |
title | Snowball 2.0: Generic
Material Data Parser for ChemDataExtractor |
title_full | Snowball 2.0: Generic
Material Data Parser for ChemDataExtractor |
title_fullStr | Snowball 2.0: Generic
Material Data Parser for ChemDataExtractor |
title_full_unstemmed | Snowball 2.0: Generic
Material Data Parser for ChemDataExtractor |
title_short | Snowball 2.0: Generic
Material Data Parser for ChemDataExtractor |
title_sort | snowball 2.0: generic
material data parser for chemdataextractor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685441/ https://www.ncbi.nlm.nih.gov/pubmed/37934697 http://dx.doi.org/10.1021/acs.jcim.3c01281 |
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