Programmatic Compilation of Chemical Data and Literature from PubChem using MATLAB

Vincent F. Scalfani

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Scientific Computing and Data Management Research Data Management Practices Various Chemistry Research Topics

Abstract

MATLAB live scripts are useful for reproducible programmatic compilation of chemical data and literature. In this article, we use a combination of the PubChem PUG REST Application Programming Interface (API), Structured Data Query (SDQ) agent, and text extraction with MATLAB live scripts that allow programmatic PubChem similarity searching, SMARTS substructure queries, literature searching, compound-based bibliometric data compiling, and SDfile data extraction. All MATLAB live scripts are openly available and adaptable with minimal modification to the script code. We discuss how these live scripts can increase scientific reproducibility and be integrated into chemistry and chemical engineering education.

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References

2018Why Jupyter is data scientists’ computational notebook of choice 2019pybliometrics: Scriptable bibliometrics using a Python interface to Scopus 2019Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks 2016An inverted classroom approach to educate MATLAB in chemical process control 2014Chemical information for chemists: a primer 2012Stimulation of Ideas through Compound‐Based Bibliometrics: Counting and Mapping Chemical Compounds for Analyzing Research Topics in Chemistry, Physics, and Materials Science 2019Substance-Based Bibliometrics: Identifying Research Gaps by Counting and Analyzing Substances

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