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Reaction Data Curation I: Chemical Structures and Transformations Standardization.

Timur R Gimadiev1, Arkadii Lin2, Valentina A Afonina3

  • 1Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021, Sapporo, Japan.

Molecular Informatics
|August 24, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a 4-step protocol for curating chemical reaction data, improving experimental data quality. The protocol was implemented in Python3 and applied to major reaction databases, making curated data publicly available.

Keywords:
PistachioReaxysUSPTObig datachemical reactionsdata cleaning

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Area of Science:

  • Chemistry
  • Chemoinformatics
  • Data Science

Background:

  • High-quality experimental data is crucial for chemical reaction studies.
  • The curation of reaction data lacks extensive discussion in scientific literature.
  • Inconsistent or erroneous reaction data can hinder research reproducibility and discovery.

Purpose of the Study:

  • To propose and implement a standardized protocol for chemical reaction data curation.
  • To enhance the reliability and usability of reaction databases.
  • To make curated reaction datasets accessible for the scientific community.

Main Methods:

  • A 4-step protocol was developed, covering curation of structures, transformations, conditions, and endpoints.
  • The protocol was implemented using Python3 and the CGRTools toolkit.
  • The method was applied to clean three prominent reaction databases: Reaxys, USPTO, and Pistachio.

Main Results:

  • A systematic approach to chemical reaction data cleaning was established.
  • Three major reaction databases were curated, improving data integrity.
  • The curated USPTO database was made publicly available on GitHub.

Conclusions:

  • The proposed 4-step protocol offers a robust method for chemical reaction data curation.
  • Implementing this protocol enhances the quality and utility of chemical reaction datasets.
  • Open access to curated data, like the USPTO database, facilitates further research in reaction-driven studies.