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Research article
ReactionCode: Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding
Marc C. Nicklaus
National Cancer Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4775-7030
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This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Journal of Cheminformatics.
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 ha ve 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.
Keywords
ReactionCode, reaction, encoding, decoding, searching, classification
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CURRENT STATUS: Published
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Posted 28 Sep, 2020
Published
On 03 Dec, 2020
No community comments so far
Review #2 received
Received 16 Oct, 2020
Editorial decision: Minor revision
On 16 Oct, 2020
Reviewer #2 agreed
On 05 Oct, 2020
Review #1 received
Received 02 Oct, 2020
Reviewer #1 agreed
On 26 Sep, 2020
Reviewers invited
Invitations sent on 25 Sep, 2020
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On 23 Sep, 2020
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On 23 Sep, 2020
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This preprint is under consideration at Journal of Cheminformatics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
ReactionCode: Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding
Marc C. Nicklaus
National Cancer Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4775-7030
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 1
Posted 28 Sep, 2020
Published
On 03 Dec, 2020
No community comments so far
Review #2 received
Received 16 Oct, 2020
Editorial decision: Minor revision
On 16 Oct, 2020
Reviewer #2 agreed
On 05 Oct, 2020
Review #1 received
Received 02 Oct, 2020
Reviewer #1 agreed
On 26 Sep, 2020
Reviewers invited
Invitations sent on 25 Sep, 2020
Editor assigned
On 24 Sep, 2020
Submission checks complete
On 23 Sep, 2020
Editor invited
On 23 Sep, 2020
First submitted
On 21 Sep, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Journal of Cheminformatics.
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 ha ve 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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.