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

[Ramiro Magno]

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
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