Database Features


Learn more about PlantConnectome and its novel utilities.


Composition of PlantConnectome



PlantConnectome was constructed by surveying numerous journals (shown in the pie chart to the right) using GPT.

Unifying 71,136 plant studies, PlantConnectome can be used to study genes, metabolites, tissues, and other biological entities, illuminating 4,819,469 relationships altogether.

Searching PlantConnectome

PlantConnectome offers three search options:


Term Searches

Search by keywords and gene IDs:

  • CESA1
  • AT4G32410
  • Proline

Author Search

Finds and displays publications by author.

Pubmed ID Search
Displays publications of interest by Pubmed ID.

Search Results

All search queries with hits return six results:


Size of Network and Number of Papers
A sample entity-relationship graph

The number of abstracts and full-texts in the database containing the search query is shown for reference.

GPT-Based Extracted and Generated Entity Definitions
A sample entity-relationship graph

A collection of functions associated with the search query is displayed.

Edge Basis and Species
A sample entity-relationship graph

Upon clicking an edge, the experimental evidences and species for a particular relationship is displayed.

Entity Relationship Graph
network graph

This directed graph summarizes the various entities in the database sharing relationships with the search query. Each node (i.e., colored shapes) and edge (i.e., colored arrows) on the graph represents an entity and a relationship shared between two entities, respectively. The colored shapes and colored arrows represents different entity types and relationship types.

This graph is also interactive; the user can alter its appearance via several options and filter the graph based on entity type and relationship type.

Text Summary
Text-summary of search results

A text summary of the entity-relationship graph is shown for reference and the corresponding PMID for each relationship is stated. Text summary changes dynamically with visibility of the graph.

Entity Relationship Table
A sample entity-relationship graph
A table summary of the node-edge interactions in the Knowledge Network graph is also shown, which is fully sortable, downloadable as a TSV file, and has hyperlinked Pubmed IDs.