Evidence map›Paper›PMID 41337644›Full record

ArticleJournal of chemical information and modeling2025

SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis.

Tieu-Long Phan, Marcos E González Laffitte, Klaus Weinbauer, Daniel Merkle, Jakob Lykke Andersen, Rolf Fagerberg, Thomas Gatter, Peter F Stadler

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Tieu-Long PhanBioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics & School for Embedded and Composite Artificial Intelligence (SECAI), Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.ORCID 0000-0002-3532-2064
Marcos E González LaffitteBioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics & School for Embedded and Composite Artificial Intelligence (SECAI), Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Klaus WeinbauerBioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics & School for Embedded and Composite Artificial Intelligence (SECAI), Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Daniel MerkleDepartment of Mathematics and Computer Science, University of Southern Denmark, DK-5230 Odense M, Denmark.ORCID 0000-0001-7792-375X
Jakob Lykke AndersenDepartment of Mathematics and Computer Science, University of Southern Denmark, DK-5230 Odense M, Denmark.ORCID 0000-0002-4165-3732
Rolf FagerbergDepartment of Mathematics and Computer Science, University of Southern Denmark, DK-5230 Odense M, Denmark.ORCID 0000-0003-1004-3314
Thomas GatterBioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics & School for Embedded and Composite Artificial Intelligence (SECAI), Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.ORCID 0000-0001-5567-3016
Peter F StadlerBioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics & School for Embedded and Composite Artificial Intelligence (SECAI), Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Computational modeling of chemical reactions is fundamental to modern synthetic chemistry but is often hindered by a fragmented software ecosystem and the complexity of accurately representing the reaction mechanisms. To address this, we introduce SynKit, an open-source Python library that provides a unified, chemically intuitive framework for reaction informatics. SynKit performs core tasks such as reaction canonicalization and transformation classification, while other functionalities─such as synthetic route construction through rule composition─are supported through integration with external libraries. The newly introduced

Indexed as

Models, ChemicalProgramming LanguagesSoftware

Identifiers

PMID41337644
PMCPMC12728950

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.