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

[Matthieu Muffato]

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 
> <mailto: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
>     <mailto: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
Room  A3-123
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468

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