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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
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Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
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Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
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Radicals, the highly reactive species, gain stability by undergoing three different reactions. The first reaction involves a radical-radical coupling, in which a radical combines with another radical, forming a spin‐paired molecule. The second reaction is between a radical and a spin‐paired molecule, generating a new radical and a new spin‐paired molecule. The third reaction is radical decomposition in a unimolecular reaction, forming a new radical and a spin‐paired...
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Related Experiment Video

Updated: Feb 28, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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A Web Tool for Generating High Quality Machine-readable Biological Pathways

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React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

Helia Mohammadi1,2, Fatemeh Almodaresi3, Gregory F J Hogue1

  • 1Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.

Research Square
|February 27, 2026
PubMed
Summary
This summary is machine-generated.

We created React-to-Me, a conversational AI assistant for exploring Reactome pathways. It uses natural language queries to provide accurate, traceable biological information, enhancing scientific knowledge discovery.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Artificial Intelligence in Science

Background:

  • The Reactome Pathway Knowledgebase offers curated biological pathway data but has accessibility challenges for non-experts due to its complex data model and keyword search.
  • General conversational AI lacks the domain specificity, source transparency, and factual reliability needed for scientific research.

Purpose of the Study:

  • To develop a domain-specific conversational assistant, React-to-Me, for intuitive natural language querying of the Reactome Pathway Knowledgebase.
  • To ensure scientific rigor, source traceability, and factual accuracy in AI-generated responses for biological pathway exploration.

Main Methods:

  • Implemented a hybrid retrieval-augmented generation (RAG) approach combined with constrained language model generation.
  • Integrated semantic vector search with lexical keyword matching for improved contextual grounding and factual precision.
  • Ensured responses are grounded in Reactome content, linked to knowledgebase entries, and defer to trusted external sources when necessary.

Main Results:

  • Computational benchmarking showed hybrid retrieval significantly improved contextual grounding and factual precision over dense-only retrieval.
  • Blinded expert evaluations indicated grounded responses received higher quality ratings, with significant gains in factual accuracy, biological specificity, and mechanistic depth.
  • User surveys reported high satisfaction with ease of use (92%), citation reliability (88%), and factual accuracy (85%).

Conclusions:

  • Domain-specific grounding markedly enhances the reliability and usability of conversational AI for biological knowledge exploration.
  • React-to-Me offers a transparent, scientifically robust interface for accessing and exploring Reactome pathway data.
  • The developed system improves user confidence and facilitates more accurate biological discovery.