Difference between revisions of "Web Services REST API"
From CoGepedia
(Created page with 'CoGe's Application Programming Interface: There are two main ways a programmer can interact with CoGe: #Through the web pages via URLs #Through CoGe's database's API ==Linking ...') |
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| − | CoGe's | + | 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| + | ** A tad out of date and doesn't include all API endpoints | ||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 ([http://robotframework.org/ Robot Framework]): https://geco.iplantcollaborative.org/coge/test/log.html | ||
| − | == | + | ==Examples== |
| − | + | '''Organism Search''' | |
| + | <pre> | ||
| + | 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" | ||
| + | } | ||
| + | ] | ||
| + | } | ||
| + | </pre> | ||
| − | + | '''Genome Search''' | |
| + | <pre> | ||
| + | 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": "" | ||
| + | }, | ||
| + | ... | ||
| + | ] | ||
| + | </pre> | ||
| − | + | '''Genome Fetch''' | |
| + | <pre> | ||
| + | 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": [], | ||
| + | ... | ||
| + | } | ||
| + | </pre> | ||
| + | |||
| + | '''Genome Sequence Download''' | ||
| + | |||
| + | Full Genome: | ||
| + | <pre>curl https://genomevolution.org//coge/api/v1/genomes/16911/sequence</pre> | ||
| + | |||
| + | Partial Genome: | ||
| + | <pre>https://genomevolution.org/coge/coge/api/v1/genomes/16911/sequence/<chr>?start=<x>&stop=<y></pre> | ||
| + | |||
| + | |||
| + | 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
- 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!
