International chemical identifier for reactions (RInChI)

Grethe, Guenter; Blanke, Gerd; Kraut, Hans; Goodman, Jonathan M.

doi:10.1186/s13321-018-0277-8

“…6 + 1 (is a center and bond broken) 7 9 8 + 1 (is a center and bond made) 9 10 6 + 4 (bond is both broken and its order changes) A 11 10 + 1 (is a center, bond broken and order changes) B 12 8 + 4 (bond is both made and its order changes) C 13 12 + 1 (is a center, bond made and order changes) D Table S7: Bond change status encoding -1 will be increased to 0 10 will be reduced to 4 11 will be reduced to 5 12 will be reduced to 8 13 will be reduced to 9…”

Section: Resultsmentioning

confidence: 99%

“…The Reaction International Chemical Identifier (RInChI) [10], an application of InChI [11,12] was recently developed with the objective to offer a unique reaction identifier, which can help to organize and validate reaction databases. [10] Besides the formats specifically designed to describe reaction transforms and allow easy data exchange, other more versatile formats have been developed in order to try to offer more flexibility and be utilized in different contexts related to reactions. In 1986, Fujita proposed the Imaginary Transition State (ITS) format, which aggregates reactants and products inside a pseudo-molecule in which the bond changes of a reaction are annotated.…”

Section: Introductionmentioning

confidence: 99%

ReactionCode: a new versatile format for searching, analysis, classification, transform, and encoding/decoding of reactions

Delannée¹,

Nicklaus²

2020

Preprint

0

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In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis and data exchange. A lot of efforts have been made on molecule formats but only few for reactions where the endeavors have been made mostly by companies leading to proprietary formats. Here, we developed a new open-source format which allows to encode and decode a reaction into multi-layers machine readable code, which aggregates reactants and products into a condensed graph of reaction (CGR). This format is flexible and can be used in a context of reaction similarity searching and classification. It is also designed for database organization, machine learning applications and as a new transform reaction language.

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“…An ontology for the periodic table in relation to catalytic materials was recently proposed . Moving forward, an ontology for the structure of the molecule‐surface interface could be developed and integrated with a recently proposed ontology for chemical reactions …”

Section: Machine Learning Conceptsmentioning

confidence: 99%

Machine Learning for Computational Heterogeneous Catalysis

Lamoureux

¹

,

Winther

²

,

Torres

³

et al. 2019

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Big data and artificial intelligence has revolutionized science in almost every field – from economics to physics. In the area of materials science and computational heterogeneous catalysis, this revolution has led to the development of scientific data repositories, as well as data mining and machine learning tools to investigate the vast materials space. The goal of using these tools is to establish a deeper understanding of the relations between materials properties and activity, selectivity and stability – the important figures of merit in catalysis. Based on these insights, catalyst design principles can be established, which hopefully lead us to discover highly efficient catalysts to solve pressing issues for a sustainable future and the synthesis of highly functional materials, chemicals and pharmaceuticals. The inherent complexity of catalytic reactions quests for machine learning methods to efficiently navigate through the high‐dimensional hyper‐surfaces in structure optimization problems to determine relevant chemical structures and transition states. In this review, we show how cutting edge data infrastructures and machine learning methods are being used to address problems in computational heterogeneous catalysis.

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“…6 + 1 (is a center and bond broken) 7 9 8 + 1 (is a center and bond made) 9 10 6 + 4 (bond is both broken and its order changes) A 11 10 + 1 (is a center, bond broken and order changes) B 12 8 + 4 (bond is both made and its order changes) C 13 12 + 1 (is a center, bond made and order changes) D Table S7: Bond change status encoding -1 will be increased to 0 10 will be reduced to 4 11 will be reduced to 5 12 will be reduced to 8 13 will be reduced to 9…”

Section: Evolutionmentioning

confidence: 99%

“…The Reaction International Chemical Identifier (RInChI) [11], an application of InChI [12,13] was recently developed with the objective to offer a unique reaction identifier, which can help to organize and validate reaction databases. [11] Besides the formats specifically designed to describe reaction transforms and allow easy data exchange, other more versatile formats have been developed in order to try to offer more flexibility and be utilized in different contexts related to reactions. In 1986, Fujita proposed the Imaginary Transition State (ITS) format, which aggregates reactants and products inside a pseudo-molecule in which the bond changes of a reaction are annotated.…”

Section: Introductionmentioning

confidence: 99%

ReactionCode: Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding

Delannée¹,

Nicklaus²

2020

Preprint

View full text Add to dashboard Cite

In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis and data exchange. A lot of efforts have been made on molecule formats but only few for reactions where the endeavors have been made mostly by companies leading to proprietary formats. Here, we developed a new open-source format which allows to encode and decode a reaction into multi-layers machine readable code, which aggregates reactants and products into a condensed graph of reaction (CGR). This format is flexible and can be used in a context of reaction similarity searching and classification. It is also designed for database organization, machine learning applications and as a new transform reaction language.

show abstract

International chemical identifier for reactions (RInChI)

Cited by 48 publications

References 5 publications

ReactionCode: a new versatile format for searching, analysis, classification, transform, and encoding/decoding of reactions

ReactionCode: a new versatile format for searching, analysis, classification, transform, and encoding/decoding of reactions

Machine Learning for Computational Heterogeneous Catalysis

ReactionCode: Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding

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