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NOCTIS: open-source toolkit that turns reaction data into actionable graph networks.

Nataliya Lopanitsyna1, Marta Pasquini2, Marco Stenta2

  • 1Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, AG, Switzerland. nataliya.lopanitsyna@syngenta.com.

Journal of Cheminformatics
|December 5, 2025
PubMed
Summary
This summary is machine-generated.

NOCTIS is a new open-source toolkit for building and analyzing chemical reaction networks. It enables efficient route enumeration and data-driven synthesis planning by representing reactions as graphs.

Keywords:
Chemical reaction networksComputer-aided synthesis designOpen-source softwareReaction data miningSynthesis planningSynthetic route

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Area of Science:

  • Computational Chemistry
  • Chemical Informatics

Background:

  • Chemical reactions form complex networks crucial for synthetic route design.
  • Growing reaction datasets necessitate advanced tools for navigation and analysis.
  • Existing graph-based tools for reaction networks are limited, especially open-source options.

Purpose of the Study:

  • To develop an open-source toolkit, NOCTIS, for constructing and analyzing reaction data as graphs.
  • To provide tools for efficient navigation and mining of large-scale reaction datasets.
  • To facilitate data-driven route design and synthesis planning.

Main Methods:

  • NOCTIS is an open-source Python package utilizing Neo4j technology.
  • It builds Networks of Organic Chemistry (NOCs) from reaction strings.
  • Includes a plugin for exhaustive synthetic route enumeration via graph traversal.
  • Supports parallel processing and export to standard formats like NetworkX and pandas.

Main Results:

  • Demonstrated NOCTIS's route mining capabilities on the MIT USPTO-480k dataset.
  • Analyzed network connectivity and assessed synthetic trees.
  • The toolkit offers a modular and extensible architecture.

Conclusions:

  • NOCTIS provides an open and extensible platform for network-based reaction analysis and route mining.
  • It supports data-driven route design at scale.
  • Future work aims to enhance query capabilities and route extraction efficiency.