[ensembl-dev] resolving gene identifiers via REST API v5

[mag]

Hi Mihai,

The lookup endpoint will only retrieve information about IDs which are 
present in the current release.
The error message you get means exactly that, the versioned ID you tried 
to retrieve could not be found, as the current version is 
ENSMMUG00000022535.3
http://www.ensembl.org/Macaca_mulatta/Gene/Summary?db=core;g=ENSMMUG00000022535;r=15:108396784-108434646;t=ENSMMUT00000031710

If you are using a mix of current and retired IDs, you might want to 
consider using the archive endpoint
http://rest.ensembl.org/archive/id/ENSMMUG00000022535.2?content-type=application/json

This will find retired IDs as well as return the version of the 
latest/current version and which release the ID you entered was last seen.
However, this will not return additional information about that gene, 
like gene name or description.

Please be aware that genes with identical IDs but different versions are 
not the same gene.
The version increment can be due to a small change of sequence in the 
UTR, some exon shifting or even different protein products.
This means additional annotation attached to one versioned ID might not 
always be relevant to an ID with a different version.


Hope that helps,
Magali

On 26/05/2017 14:40, Mihai Glonț wrote:
> Dear colleagues,
>
> Is there anyone on this list that can answer my query?
>
> If not, sorry for the spam :-) --  a nudge towards a more appropriate
> point of contact would be very much appreciated.
>
> Best wishes,
>
> Mihai.
>
> On 19/05/2017 19:30, Mihai Glonț wrote:
>> Dear Ensembl developers,
>>
>> I am trying to programmatically retrieve basic information (gene name &
>> description) about a set of Ensembl genes.
>>
>> The tool works for most cases, such as ENSMUSG00000021620.4[1], but for
>> accessions like ENSMMUG00000022535.2[2] the request returns status code
>> 400 and the error message is
>>
>>      "No object found for ID ENSMMUG00000022535.2"
>>
>> The client is written in Groovy and Java, but I saw the API behaving in
>> the same way for curl as well, so there's something wrong with my
>> general approach, rather than a programming bug.
>>
>> I noticed that I can work around the problem by stripping the version
>> suffix, but I would really like to avoid this, if possible, since the
>> dataset is generated externally.
>>
>> I'd be grateful to hear if there is a fix for this issue.
>>
>> Best wishes,
>> Mihai.
>>
>> [1] curl "http://rest.ensembl.org/lookup/id/ENSMUSG00000021620.4" -H
>> "Accept: application/json"
>>
>> [2] curl "http://rest.ensembl.org/lookup/id/ENSMMUG00000022535.2" -H
>> "Accept: application/json"
>>
>>
>>
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