Difference between revisions of "Web Services REST API"
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| Line 10: | Line 10: | ||
'''Organism Search''' | '''Organism Search''' | ||
<pre> | <pre> | ||
| − | curl | + | curl https://genomevolution.org/coge/api/v1/organisms/search/col-0 |
{ | { | ||
"organisms": | "organisms": | ||
| Line 25: | Line 25: | ||
'''Organism Fetch''' | '''Organism Fetch''' | ||
<pre> | <pre> | ||
| − | curl | + | curl https://genomevolution.org/coge/api/v1/organisms/1 |
{ | { | ||
"id": 1, | "id": 1, | ||
| Line 36: | Line 36: | ||
'''Genome Fetch''' | '''Genome Fetch''' | ||
<pre> | <pre> | ||
| − | curl | + | curl https://genomevolution.org/coge/api/v1/genomes/16911 |
{ | { | ||
"id": 16911 | "id": 16911 | ||
| Line 55: | Line 55: | ||
'''Experiment Add''' | '''Experiment Add''' | ||
<pre> | <pre> | ||
| − | curl -H "Content-Type: application/json" -X PUT --data @experiment_add.json " | + | 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: | Here is a sample JSON request body for experiment_add.json: | ||
Revision as of 11:00, 17 July 2015
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:
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!
