The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.

Reactome is maintained by an international multidisciplinary team from OICR, OHSU, EMBL-EBI and NYULMC, with expertise in pathway curation and annotation, software development, and training and outreach, dedicated to providing the research community with openly accessible biological pathway knowledge.

The underlying data is fully downloadable in a number of standard formats including PDF, SBML, Neo4j GraphDB, MySQL, PSI-MITAB, and BioPAX.

Pathway diagrams use a Process Description (PD) Systems Biology Graphical Notation (SBGN)-based style.

Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways.

Examples of biological pathways in Reactome include signal transduction, innate and acquired immune function, transcriptional regulation, programmed cell death and classical intermediary metabolism.

If no experimental verification using human reagents exists, pathways may contain steps manually inferred from non-human experimental details, but only if an expert biologist, named as Author of the pathway, and a second biologist, names as Reviewer, agree that this is a valid inference to make.

Physical entities are cross-referenced to relevant external databases, such as UniProt for proteins and ChEBI for small molecules.

The terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License apply to all software and code, e.g. relating to the functionality of the reactome.org, derived websites and webservices, the Curator Tool, the Functional Interaction application, SQL and Graph Database data dumps, and Pathway Illustrations (Enhanced High-Level Diagrams), Icon Library, Art and Branding Materials.

If multiple columns of numeric data are submitted the overlay tool can display them as separate 'experiments', e.g. timepoints or a disease progression.

Users can also download the current data set or individual pathways and reactions in a variety of formats including PDF, BioPAX, and SBML[5] Reactome also has a ReactomeGSA[6] tool, integrated into the Reactome Analysis Tools that allows comparative pathway analyses of multi-omics datasets, with compatibility with single-cell RNA-seq data.

Reactome also has a ReactomeIDG[7] web portal, since 2023, aimed to place dark proteins in the context of manually curated, highly reliable Reactome pathways, to facilitate the understanding of functions and predicting therapeutic potential of dark or understudied proteins.