Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Summer 1, Summer 2
Description
Task: Investigate the Ensembl API at https://rest.ensembl.org/ to determine if the API will return data that can be used by IGB, such as genomic sequence and gene annotations.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3555 [ 22774 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Comment |
[ Read the documentation, went through a few APIs, and found the below information
*GET info/divisions* Get the list of all Ensembl divisions for which information is available: https://rest.ensembl.org/info/divisions?content-type=application/json *GET info/species* Lists all available species, their aliases, available adaptor groups, and data release. Has to specify a division optional parameter to get the species for that ensemble division. API to get the list of all species: https://rest.ensembl.org/info/species?content-type=application/json Doc: https://rest.ensembl.org/documentation/info/species +Note:+ No version info present in the response *GET info/assembly/:species* API to get the list of chromosomes for a selected species: https://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json Doc: https://rest.ensembl.org/documentation/info/assembly_info +Note:+ response has three array variables - one is top_level_region which has a array of objects, each object has name, length and coord_system, this looks similar to the list of chromosomes with the length and name but the coord_system has different values, two of them are scaffold and chromosome which brings the doubt of whether we consider all of them as chromosomes are not? Also, don’t know what the other two arrays intend to describe. *GET info/genomes/:genome_name* Find information about a given genome API to get more information about the genome: https://rest.ensembl.org/info/genomes/arabidopsis_thaliana?content-type=application/json Doc: https://rest.ensembl.org/documentation/info/info_genome +Note:+ genebuild in the response looks similar to genomeVersionName *GET info/assembly/:species/:region_name* Returns information about the specified top-level sequence region for the given species: https://rest.ensembl.org/info/assembly/homo_sapiens/X?content-type=application/json ] |
| Sprint | Summer 1 [ 195 ] | Summer 1, Summer 2 [ 195, 196 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |