API Reference

Overview

The PGDD API provides programmatic access to the data in the Plant Genome Duplication Database. You can use it to retrieve information about genomes, species, gene loci, orthology, and synteny.

All API endpoints are available under the /api/ path. Responses are in JSON format.

Authentication

Currently, the PGDD API is open and does not require authentication. This may change in the future.

Genomes

Retrieve information about available genomes.

GET /api/genomes

Returns a list of all available genomes with their metadata.

Example Response:
[
  {
    "id": 1,
    "name": "Arabidopsis thaliana",
    "species": "Arabidopsis thaliana",
    "version": "TAIR10",
    "description": "Reference assembly for Arabidopsis thaliana"
  },
  ...
]

Locus Search

Search for specific gene loci within the database.

POST /locus/search

Searches for loci based on a search term, species, and search type.

Request Body Parameters:
Parameter Type Description
search_term string The gene symbol, locus ID, or description to search for.
species_id integer The ID of the species to filter by.
search_type string 'exact', 'partial', or 'similar'.
Example Request:
{
  "search_term": "AT1G01010",
  "species_id": 1,
  "search_type": "exact"
}
Example Response:
[
  {
    "locus_id": "AT1G01010",
    "gene_symbol": "ANAC001",
    "description": "NAC domain containing protein 1",
    "chromosome": "Chr1",
    "start_position": 3631,
    "end_position": 5899
  }
]

Orthology

Retrieve orthologous gene groups and relationships.

GET /api/orthogroups

Returns a list of orthogroups, optionally filtered by species.

GET /api/orthologs/<locus_id>

Returns orthologs for a specific locus ID.

Synteny

Access synteny data and block information.

GET /api/synteny-data

Returns syntenic block data between specified genomes.