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

[Mihai Glonț]

Many thanks, Magali, that was very useful. -- Mihai.


On 26/05/2017 15:21, mag wrote:
> 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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