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Chemical curation to improve data accuracy: recent development of the 3DMET database

We have developed a three-dimensional structure database of natural metabolites (3DMET). Early development of the 3DMET database relied on content auto-generated from 2D-structures of other chemical databases. From 2009, we began manual curation, obtaining new compounds from published works. In the...

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Detalles Bibliográficos
Autores principales: Maeda, Miki H., Yonezawa, Tomoki, Komaba, Tomomi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Biophysical Society of Japan (BSJ) 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992871/
https://www.ncbi.nlm.nih.gov/pubmed/29892514
http://dx.doi.org/10.2142/biophysico.15.0_87
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author Maeda, Miki H.
Yonezawa, Tomoki
Komaba, Tomomi
author_facet Maeda, Miki H.
Yonezawa, Tomoki
Komaba, Tomomi
author_sort Maeda, Miki H.
collection PubMed
description We have developed a three-dimensional structure database of natural metabolites (3DMET). Early development of the 3DMET database relied on content auto-generated from 2D-structures of other chemical databases. From 2009, we began manual curation, obtaining new compounds from published works. In the process of curation, problems of digitizing 3D-structures from structure drawings of documents were accumulated. As the same as auto-generation, structure drawings should be also payed attention about stereochemistry. Our experiences in manual curation of 3DMET, as described herein, may be useful to others in this field of research and for the development of supporting systems of a chemical structure database. Manual curation is still necessary for proper database entry of the 3D-configurations of chiral atoms, a problem encountered frequently among natural products.
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spelling pubmed-59928712018-06-11 Chemical curation to improve data accuracy: recent development of the 3DMET database Maeda, Miki H. Yonezawa, Tomoki Komaba, Tomomi Biophys Physicobiol Special Issue “Database”: Regular Article We have developed a three-dimensional structure database of natural metabolites (3DMET). Early development of the 3DMET database relied on content auto-generated from 2D-structures of other chemical databases. From 2009, we began manual curation, obtaining new compounds from published works. In the process of curation, problems of digitizing 3D-structures from structure drawings of documents were accumulated. As the same as auto-generation, structure drawings should be also payed attention about stereochemistry. Our experiences in manual curation of 3DMET, as described herein, may be useful to others in this field of research and for the development of supporting systems of a chemical structure database. Manual curation is still necessary for proper database entry of the 3D-configurations of chiral atoms, a problem encountered frequently among natural products. The Biophysical Society of Japan (BSJ) 2018-04-27 /pmc/articles/PMC5992871/ /pubmed/29892514 http://dx.doi.org/10.2142/biophysico.15.0_87 Text en 2018 © The Biophysical Society of Japan This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.
spellingShingle Special Issue “Database”: Regular Article
Maeda, Miki H.
Yonezawa, Tomoki
Komaba, Tomomi
Chemical curation to improve data accuracy: recent development of the 3DMET database
title Chemical curation to improve data accuracy: recent development of the 3DMET database
title_full Chemical curation to improve data accuracy: recent development of the 3DMET database
title_fullStr Chemical curation to improve data accuracy: recent development of the 3DMET database
title_full_unstemmed Chemical curation to improve data accuracy: recent development of the 3DMET database
title_short Chemical curation to improve data accuracy: recent development of the 3DMET database
title_sort chemical curation to improve data accuracy: recent development of the 3dmet database
topic Special Issue “Database”: Regular Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992871/
https://www.ncbi.nlm.nih.gov/pubmed/29892514
http://dx.doi.org/10.2142/biophysico.15.0_87
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