Difference between revisions of "Web Services REST API"

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==CoGe Web Services RESTful API==
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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.
  
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CoGe's web services API let's you incorporate CoGe's database of organisms, genomes, and data sets into your web site or pipeline. 
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==Documentation==
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* Interactive documentation:  https://genomevolution.org/apidocs
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Here is our draft API specification document:<br>
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** Live-test API endpoints using simple web interface
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http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
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** A tad out of date and doesn't include all API endpoints
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* Specification document: http://docs.google.com/document/d/1GXOPIVvyTwoGR2IRjDNmdd2nj_6d8db7jx9hG8RxTDc
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** Up-to-date documentation of all API endoints
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Below are some examples queries ...
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* [[Embedding CoGe JBrowse in your website]]
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* Automated Testing ([http://robotframework.org/ Robot Framework]): https://geco.iplantcollaborative.org/coge/test/log.html
  
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==Examples==
  
 
'''Organism Search'''
 
'''Organism Search'''
 
<pre>
 
<pre>
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curl http://genomevolution.org/coge/api/v1/organisms/search/col-0
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curl https://genomevolution.org/coge/api/v1/organisms/search/col-0
 
{
 
{
 
   "organisms":
 
   "organisms":
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</pre>
 
</pre>
  
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'''Organism Fetch'''
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'''Genome Search'''
 
<pre>
 
<pre>
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curl http://genomevolution.org/coge/api/v1/organisms/1
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curl https://genomevolution.org/coge/api/v1/genomes/search/col-0
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{
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[
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  "id": 1,
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    {
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  "name": "Arabidopsis thaliana Col-0 (thale cress)",
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        "name": "",
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  "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis"
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        "chromosome_count": 7,
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  “genomes” : [ 16911, ... ]
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        "sequence_type": {
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}
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            "id": "1",
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            "description": "unmasked sequence data",
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            "name": "unmasked"
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        },
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        "info": "Arabidopsis thaliana Col-0 (thale cress) (v10.02, id16911): unmasked",
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        "description": "",
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        "organism": {
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            "id": 1,
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            "description": "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis",
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            "name": "Arabidopsis thaliana Col-0 (thale cress)"
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        },
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        "restricted": false,
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        "organism_id": 1,
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        "version": "10.02",
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        "id": 16911,
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        "link": ""
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    },
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    ...
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]
 
</pre>
 
</pre>
  
 
'''Genome Fetch'''
 
'''Genome Fetch'''
 
<pre>
 
<pre>
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curl http://genomevolution.org/coge/api/v1/genomes/16911
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curl https://genomevolution.org/coge/api/v1/genomes/16911
 
{
 
{
 
   "id": 16911
 
   "id": 16911
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   "experiments": [31,32,33, ...],
 
   "experiments": [31,32,33, ...],
 
   "metadata": [],
 
   "metadata": [],
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  ...
 
}
 
}
 
</pre>
 
</pre>
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'''Genome Sequence Download'''
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Full Genome:
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<pre>curl https://genomevolution.org//coge/api/v1/genomes/16911/sequence</pre>
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Partial Genome:
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<pre>https://genomevolution.org/coge/coge/api/v1/genomes/16911/sequence/<chr>?start=<x>&stop=<y></pre>
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 +
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More examples to be added soon!

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

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!

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