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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Biophysical Society of Japan (BSJ)
2018
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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. |
format | Online Article Text |
id | pubmed-5992871 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | The Biophysical Society of Japan (BSJ) |
record_format | MEDLINE/PubMed |
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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