Reactome: A Curated Pathway Database

About Plant Reactome

PLANT REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with the Reactome editorial staff and cross-referenced to many bioinformatics databases. These include project databases like Gramene, EnsemblUniProt,  ChEBI small molecule databases, PubMed, and Gene Ontology.

The rationale behind Plant Reactome is to convey the rich information in the visual representations of plant pathways familiar from textbooks and prre-reviewed articles in a detailed, computationally accessible format. The core unit of the Plant Reactome data model is the reaction. 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 Plant Reactome include classical intermediary metabolism, signaling and transcriptional regulation. These will be extended to cell cycle, apoptosis and disease.

Plant Reactome provides an intuitive website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. Visualization of Plant Reactome data is facilitated by the Pathway Browser, a Systems Biology Graphical Notation (SBGN)-based interface, that supports zooming, scrolling and event highlighting.

Pathway Analysis tools analyze user-supplied dataset permitting ID mapping, pathway assignment and over-representation or enrichment analysis. The curated rice pathway data are used to infer orthologous events in several sequenced plant genomes. Species Comparison tool allows users to compare predicted pathways to find reactions and pathways common to a selected set of species.

All data and software are freely available for download. Interaction, reaction and pathway data are provided as downloadable flat, MySQL, BioPAX, SBML and PSI-MITAB files and are also accessible through our Web Services APIs. In order to visulalize the Plant Reactome data in its native form, users may want to browse the software and instructions for local installation of the native Reactome database, website, and data entry tools (curator and author tools) are also available to support independent pathway curation.

Plant Reactome is an all-inclusive resource of plant pathways for basic research, genome analysis, pathway modeling, systems biology and education. If you would like to learn more about Plant Reactome, please refer to the a tutorial published on YouTube, with examples.

The Plant Reactome team thanks users for their comments on the pathway visualization and analysis tools. If you have any feedback or questions, please contact us at the Reactome HelpDesk.