[ensembl-dev] List endpoint for assemblies by species only returns a single assembly

[Kieron Taylor]

Hi Kurt,

I believe this is a leakage of our internal understanding, combined with poor wording that makes it confusing.

In the human example you can see five "coord_system_versions". This means we have assembly mappings from the latest to the previous ones listed. These additional assemblies are generally only available in the context of the newest assembly, rather than in isolation. The exception to this is the long time favourite GRCh37/hg19, and we provide a data freeze of that assembly via the grch37.rest.ensembl.org service.

Due to complicated historic reasons, organisms like Pseuodmoniae are bundled up differently, such as Pseudomonas_aeruginosa_gca_000705235 : 
http://rest.ensembl.org/info/assembly/Pseudomonas_aeruginosa_gca_000705235?content-type=application/json

Here you can see one assembly named "pseuodomonas" attached to the "species".

If you want to see what others we have, you need the info/species endpoint, but that is very large for bacteria!

https://rest.ensembl.org/info/species?content-type=application/json&division=EnsemblBacteria

We are aware that this requires rather more insight into Ensembl's historic workings than should be necessary, and we are working to improve matters! I have created a ticket to improve the documentation on the endpoint in question, but it is a much larger job to have the endpoints working the way you would perhaps like them to.


Regards,

Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 19 Dec 2019, at 15:22, Kurt Wheeler <kurt.wheeler91 at gmail.com> wrote:
> 
> Hello,
> 
> I'm confused by this endpoint: http://rest.ensembl.org/documentation/info/assembly_info
> 
> It says that it will "List the currently available assemblies for a species, along with toplevel sequences, chromosomes and cytogenetic bands."
> 
> However the response only has a single assembly, it's not even with a JSON list: []
> 
> Example: http://rest.ensembl.org/info/assembly/PSEUDOMONAS_AERUGINOSA?content-type=application/json
> 
> Is this a bug? It seems like I should be expecting the response to be a list based on the documentation.
> 
> Thanks,
> 
> - Kurt
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