Plant Reactome subscribes to the principles of open-source and open-data. We have continuously supported the major open-data standards, including BioPAX, PSI-MITAB, SBML and SBGN export formats. The Plant Reactome data and source code continues to be publicly accessible under the terms of a Creative Commons Attribution 3.0 Unported License.
The Plant Reactome GitHub repository is accessible here.
The full download page is accessible here.
Access to our most recent data release can be found below.
Identifier mapping files:
Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway:
Mapping files link the source database identifier to all levels of the pathway hierarchy:
- UniProt to All pathways
- ChEBI to All pathways
- ENSEMBL to All pathways
- NCBI to All pathways
- miRBase to All pathways
Mapping files link the source database identifier to all reactions:
- UniProt to All reactions
- ChEBI to All reactions
- ENSEMBL to All reactions
- NCBI to All reaction
- miRBase to All reaction
Physcial Entity (PE) Identifier mapping files:
Lowest level pathway diagram / Subset of the pathway:
All levels of the pathway hierarchy:
- UniProt to All pathways
- ChEBI to All pathways
- ENSEMBL to All pathways
- NCBI to All pathways
- miRBase to All pathways
Database identifier to all reactions:
- UniProt to All reactions
- ChEBI to All reactions
- ENSEMBL to All reactions
- NCBI to All reaction
- miRBase to All reaction
Other Plant Reactome Exports
- All gene products listed by pathway and species: contains curated and projected gene product identifiers grouped by pathway and species (tab-delimited).
- Biopax3 export
- MySQL database dump
- Neo4j 3.4 database archive
- Identifiers Mapping
The mapping files consist of a tab-separated table that indicates which external protein, gene or small molecule identifiers in the source database were mapped to Plant Reactome pathway and reaction annotations. Our goal with distributing three sets of files for each different identifier type is to provide these mapping files link the source database identifier to:
- the lowest level pathway diagram or subset of the pathway
- all level pathway diagrams (filename appended with 'All_Levels’),
- all reaction events.
The columns within the mappings files follow a similar format:
Source database identifier, e.g. UniProt, ENSEMBL, NCBI Gene or ChEBI identifier
- Plant Reactome Pathway Stable identifier
- URL
- Event (Pathway or Reaction) Name
- Evidence Code
- Species
Reactome Web services
- Our ContentService provides outside users with direct access to pathway data in Plant Reactome. The Plant Reactome Diagram Widget and Fireworks Widget are also available for integration into third party websites. For details about these web services, please see this document: Reactome Developer Guide.