Difference between revisions of "Web Services REST API"

Revision as of 18:54, 29 July 2015

CoGe's and EPIC-CoGe's web services API let's you incorporate CoGe's database of organisms, genomes, and data sets into your web site or pipeline.

Here is the full API specification document for CoGe and EPIC-CoGe:
http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc

Below are some examples queries:

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"
         }
      ]
}

Organism Fetch

curl https://genomevolution.org/coge/api/v1/organisms/1
{
   "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"
   “genomes” : [ 16911, ... ]
}

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": [],
}

Experiment Add

curl -H "Content-Type: application/json" -X PUT --data @experiment_add.json "https://genomevolution.org/coge/api/v1/experiments?username=xxx&token=yyy"

Here is a sample JSON request body for experiment_add.json:
{
   "restricted": true,
   "genome_id": 16911,
   "version": "1",
   "name": "DiffExpr1",
   "description": "Expression measurements from tissue X with treatment Y.",
   "source_name": "JGI",
   "items": [
      { "type": "irods", "path": "/iplant/home/coge/coge_data/arabidopsis/experimental_condition1.csv" }
   ]
}

More examples to be added soon!