Difference between revisions of "Web Services REST API"

Latest revision as of 16:53, 23 March 2017

Our web services let you incorporate CoGe's database of organisms, genomes, and other data sets into your web site or pipeline. You can also run any type of analysis on CoGe.

Documentation

• Interactive documentation: https://genomevolution.org/apidocs
  • Live-test API endpoints using simple web interface
  • A tad out of date and doesn't include all API endpoints
• Specification document: http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
  • Up-to-date documentation of all API endoints
• Embedding CoGe JBrowse in your website
• Automated Testing (Robot Framework): https://geco.iplantcollaborative.org/coge/test/log.html

Examples

Organism Search

curl https://genomevolution.org/coge/api/v1/organisms/search/col-0
{
   "organisms":
      [
         {
            "id": "1",
            "name": "Arabidopsis thaliana Col-0 (thale cress)",    
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis"
         }
      ]
}

Genome Search

curl https://genomevolution.org/coge/api/v1/genomes/search/col-0
[
    {
        "name": "",
        "chromosome_count": 7,
        "sequence_type": {
            "id": "1",
            "description": "unmasked sequence data",
            "name": "unmasked"
        },
        "info": "Arabidopsis thaliana Col-0 (thale cress) (v10.02, id16911): unmasked",
        "description": "",
        "organism": {
            "id": 1,
            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis",
            "name": "Arabidopsis thaliana Col-0 (thale cress)"
        },
        "restricted": false,
        "organism_id": 1,
        "version": "10.02",
        "id": 16911,
        "link": ""
    },
    ...
]

Genome Fetch

curl https://genomevolution.org/coge/api/v1/genomes/16911
{
   "id": 16911
   "name": "",
   "description": "",
   "version": "10.02",
   "link": "",
   "restricted": false,
   "sequence_type": {
      "name": "unmasked",
      "description": "unmasked sequence data"
   },
   "experiments": [31,32,33, ...],
   "metadata": [],
   ...
}

Genome Sequence Download

Full Genome:

curl https://genomevolution.org//coge/api/v1/genomes/16911/sequence

Partial Genome:

https://genomevolution.org/coge/coge/api/v1/genomes/16911/sequence/<chr>?start=<x>&stop=<y>

More examples to be added soon!