[ensembl-dev] Ensembl REST API | Question about Ensembl identifiers

[Ramiro Magno]

Great, thanks!

On Wed, 31 Jul 2019 at 16:45, Matthieu Muffato <muffato at ebi.ac.uk> wrote:
>
> Hi Ramiro
>
> Correct: the archive/id endpoint doesn't know how to retrieve the history of gene-tree and family IDs
>
> Matthieu
>
> On 31/07/2019 16:34, Ramiro Magno wrote:
>
> Hi Thibaut,
>
> Thanks!
>
> So, although all entities are the ones listed in e.g., https://www.ensembl.org/info/genome/stable_ids/prefixes.html, the ones that are retrievable via the endpoint "GET archive/id/:id" are only: gene, transcript, protein and exon. Correct?
>
> For example, if I try to get a gene tree, e.g. ENSGT00390000013823: https://rest.ensembl.org/archive/id/ENSGT00390000013823?content-type=application/json
>
> the server replies with "{"error":"No object found for ENSGT00390000013823"}".
>
> Cheers, RM
>
> On Wed, 31 Jul 2019 at 11:20, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:
>>
>> Hi Ramiro
>>
>> Ensembl ID and stable id are the same id. We will have a look at how we can rephrase the two documents to try to remove the ambiguity.
>>
>> The list of entities is correct in the FAQ and https://www.ensembl.org/info/genome/stable_ids/prefixes.html. The document https://www.ensembl.org/info/genome/stable_ids/index.html refers to the stable ids and versioning of genes, transcripts, proteins and exons, this is why they do not have all the entities.
>>
>> Thanks
>> Thibaut
>>
>> > On 30 Jul 2019, at 16:02, Ramiro Magno <ramiro.magno at gmail.com> wrote:
>> >
>> > Hi Devs,
>> >
>> > I have two questions about Ensembl identifiers:
>> >
>> > (i) Ensembl ID and Stable identifiers are the same concept?
>> > https://www.ensembl.org/Help/Faq?id=488
>> > https://www.ensembl.org/info/genome/stable_ids/index.html
>> >
>> > In one case the version suffix seems to be purposefully left out, so I am not sure if by stable you mean without the id version suffix, and whether you reserve the general expression "Ensembl ID" for the five part identifier.
>> >
>> > (ii) What are the entity types referred by these IDs? Is it just the four entities (gene, transcript, protein and exon) as described here https://www.ensembl.org/info/genome/stable_ids/index.html or are there more entities as hinted here https://www.ensembl.org/Help/Faq?id=488 (e.g., FM, protein family, R, regulatory feature and GT, gene tree)?
>> >
>> > Many thanks!
>> >
>> > Ramiro
>
> --
> Matthieu Muffato, Ph.D.
> Ensembl Compara and TreeFam Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus, Hinxton
> Cambridge, CB10 1SD, United Kingdom
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