Web Services REST API

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 our draft API specification document:
http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc

Below are some examples queries (authentication not required) ...

Organism Search

curl http://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 http://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 http://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 "http://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!