The following table contains the known resources that have collaborated and/or integrated with Plant Reactome, through data-sharing or by using the Analysis Service, the Graph Database or any of our widgets (diagram or pathways overview). If your resource is using our services, widgets or content and it is not in the list, please This email address is being protected from spambots. You need JavaScript enabled to view it. and we will add it.
Partners
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.
Content Service
Widgets
Graph Database
Gramene
Reactome is an open-source, manually curated and peer-reviewed pathway database, whose goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.
Platform Collaborator
Curation Support
Reactome
The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.
Ontology Integration
Planteome
The mission of the GO Consortium is to develop an up-to-date, comprehensive, computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems.
Ontology Integration
Gene Ontology Consortium
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
Data Sharing
ChEBI
Expression Atlas is an open science resource that gives users a powerful way to find information about gene and protein expression across species and biological conditions. It aims to help answer questions such as ‘where is a certain gene expressed?’ or ‘how does its expression change in a disease?’.
Expression Widget
Data Sharing
Expression Atlas
The Bio-Analytic Resource for Plant Biology. Web-based tools for visualizing functional genomics and other data (i.e. eFP viewing, next-gen mapping). Most of these tools are designed with the plant researcher in mind but they also create tools for the wider research community.
Content Service
Graph Database
BAR
IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
Data Sharing
Service Registration
IntAct
PubChem is an open chemistry database at the National Institutes of Health (NIH), and mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. They collect information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data.
Embedded Pathway Diagrams Small Molecule Data Integration
PubChem
We acknowledge NASA grant # 80NSSC22K0891 (2022-2024) to Sushma Naithani (Oregon State University) that led to the collaboration between the Plant Reactome and NASAGeneLab for the biocuration of plant gravitropism pathways and cross-listing of the Plant Reactome and its Analysis tools on the NASAGeneLab website to support researchers working on space biology projects.
Embedded Pathway Diagrams
NASA
Ensembl Plants (http://plants.ensembl.org) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species.
Analysis Service
Widgets
Ensembl Plants
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