Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Reactome: a knowledgebase of biological pathways.

G Joshi-Tope1, M Gillespie, I Vastrik

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. joshi@cshl.org

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.

Nature communications·2025
Same author

The Physiome Project and Digital Twins.

IEEE reviews in biomedical engineering·2024
Same author

Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs.

Interface focus·2017
Same author

A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine.

Yearbook of medical informatics·2017
Same author

Requirements for the formal representation of pathophysiology mechanisms by clinicians.

Interface focus·2016
Same author

Biophysical constraints on the evolution of tissue structure and function.

The Journal of physiology·2014

Reactome is a database of human biological pathways, organized around reactions grouped into causal chains to form pathways. It includes processes like intermediary metabolism, regulatory pathways, and signal transduction. The database is curated by expert biologists and allows interactive visualization of pathways. Reactome is freely available under open source terms, and human pathways are projected onto other organisms via orthologs. This makes it useful for both human and model organism research. The database supports both qualitative and quantitative data integration.

Area of Science:

  • Systems biology
  • Bioinformatics databases
  • Pathway analysis

Background:

Biological systems involve complex interactions between molecules and processes. While many pathways have been described, a unified framework for organizing and visualizing these processes remains limited. Prior research has shown that pathway databases often lack detailed annotations or fail to integrate diverse biological processes. This gap motivated the development of a comprehensive, curated pathway resource. No prior work had resolved the need for a standardized model to represent both qualitative and quantitative biological data. Existing tools often focus on specific processes, such as metabolism, but lack integration with regulatory and signaling pathways. That uncertainty drove the creation of a database that could unify these diverse processes. The challenge lies in maintaining accuracy while allowing flexible data input and visualization. This uncertainty led to the design of a database that could support both human and model organism research.

Purpose Of The Study:

The aim of this work is to develop a centralized, peer-reviewed database for human biological pathways. The specific problem is the lack of a unified framework for representing diverse biological processes. This study addresses the need for a qualitative and quantitative resource that can integrate metabolism, regulation, and signaling. The motivation is to provide a platform for both expert curation and public access. The study seeks to enable the visualization of biological processes as interactive maps. This approach allows researchers to explore pathways in a structured manner. The goal is to support both human and model organism research through ortholog projections. The purpose is to create a freely available, open-source database for biological pathways.

Keywords:
biological pathwayssystems biologypathway databasebioinformatics

Frequently Asked Questions

Reactome provides a curated, peer-reviewed resource for human biological pathways, including intermediary metabolism, regulatory pathways, and signal transduction.

The basic unit is a reaction, which is grouped into causal chains to form pathways. These are organized into high-level processes such as the cell cycle.

Yes, human pathways are projected onto other organisms via putative orthologs, making Reactome relevant to model organism research.

Expert biologists can use tools for custom data entry and annotation, and interactive process maps allow users to explore pathways visually.

Related Experiment Videos

Main Methods:

The Reactome database is built around the basic unit of a reaction, which is grouped into causal chains to form pathways. A data model was developed to represent diverse biological processes, including intermediary metabolism and signal transduction. Expert biologists use tools for custom data entry and annotation. The database includes high-level processes such as the cell cycle. Visualization tools allow interactive exploration of pathways as process maps. Electronic projections are created by mapping human pathways onto other organisms via orthologs. The database is publicly available under open source terms. This approach ensures both content and software infrastructure are freely accessible.

Main Results:

The Reactome database provides a qualitative framework for representing biological processes in humans. It includes intermediary metabolism, regulatory pathways, and signal transduction. The database allows quantitative data to be superimposed on qualitative structures. Expert curation tools enable accurate data entry and annotation. Interactive process maps allow users to explore pathways visually. Electronic projections of human pathways onto other organisms are regularly created. The database is freely available under open source terms. These features make Reactome a valuable resource for both human and model organism research.

Conclusions:

The authors state that Reactome offers a unified framework for representing diverse biological processes. It supports both qualitative and quantitative data integration. The database includes intermediary metabolism, regulatory pathways, and signal transduction. Interactive tools allow users to explore pathways as process maps. Electronic projections onto other organisms expand its utility for model systems. The open source availability ensures broad accessibility. The database is peer-reviewed and curated by expert biologists. These features make Reactome a valuable resource for biological pathway research.

Yes, the database is publicly available under open source terms, allowing both content and software infrastructure to be freely used and redistributed.

Reactome includes intermediary metabolism, regulatory pathways, signal transduction, and high-level processes such as the cell cycle.