[ensembl-dev] REST API: Missing external_name

[Cinzia Malangone]

Hi Brandon,
Thanks :)
I will use e93.rest.ensemb.org <http://e93.rest.ensemb.org/>

Please let us know when the issue will be fixed. (gwas-info at ebi.ac.uk <mailto:gwas-info at ebi.ac.uk>)
C.

> On 16 Oct 2018, at 14:43, Brandon Walts <bwalts at ebi.ac.uk> wrote:
> 
> Sorry, you are correct that dec2017 maps to release 91, not 93. https://jul2018.rest.ensembl.org/ <https://jul2018.rest.ensembl.org/> is the url for release 93. You can also use e93.rest.ensemb.org (or any other valid release number) which will provide a redirect to the correct date.
> 
> Best regards
> -Brandon
> On 16/10/2018 14:36, Cinzia Malangone wrote:
>> Dear all,
>> Thanks for your reply.
>> 
>> Can you please give me the URL for v.93?
>> 
>> It seems to me that 'https://dec2017.rest.ensembl.org <https://dec2017.rest.ensembl.org/overlap/region/homo_sapiens/6:2739490-2739490?feature=gene&logic_name=refseq_import&db_type=otherfeatures%27%20%20%20%20%20%20%20%20%20%20-H%20%27Content-type:application/json%27%20-H%20%20%20%20%20%20%20%20%20%20%27Accept:application/json>’ is related with v.91
>> 
>> Many thanks
>> Cinzia
>> 
>> 
>>> On 16 Oct 2018, at 13:25, Brandon Walts <bwalts at ebi.ac.uk <mailto:bwalts at ebi.ac.uk>> wrote:
>>> 
>>> Dear Cinzia
>>> 
>>> We have identified an issue with the external name cross references in the release 94 otherfeatures database. We will provide an update once we have a better idea of how this issue should be resolved. In the meantime, we suggest you use the release 93 (dec2017) database to get external names for RefSeq import genes.
>>> 
>>> Best regards
>>> On 15/10/2018 14:08, Cinzia Malangone wrote:
>>>> Dear all,
>>>> I noticed that one of the field that we need disappeared from the JSON response when we try to query the feature endpoint for a gene.
>>>> 
>>>> Eg.
>>>> 
>>>> curl -i 'https://rest.ensembl.org/overlap/region/homo_sapiens/6:2739490-2739490?feature=gene&logic_name=refseq_import&db_type=otherfeatures' -H 'Content-type:application/json' -H 'Accept:application/json <https://rest.ensembl.org/overlap/region/homo_sapiens/6:2739490-2739490?feature=gene&logic_name=refseq_import&db_type=otherfeatures%27%20%20%20%20%20%20%20%20%20%20%20%20%20%20-H%20%27Content-type:application/json%27%20-H%20%20%20%20%20%20%20%20%20%20%20%20%20%20%27Accept:application/json>'
>>>> 
>>>> [{"gene_id":"gene17080","feature_type":"gene","id":"gene17080","source":"BestRefSeq","end":2770330,"start":2663629,"strand":-1,"version":1,"description":"myosin light chain kinase family member4","assembly_name":"GRCh38","biotype":"protein_coding","seq_region_name":"6","logic_name":"refseq_import"}]
>>>> 
>>>> versus
>>>> 
>>>> curl -i 'https://dec2017.rest.ensembl.org/overlap/region/homo_sapiens/6:2739490-2739490?feature=gene&logic_name=refseq_import&db_type=otherfeatures' -H 'Content-type:application/json' -H 'Accept:application/json <https://dec2017.rest.ensembl.org/overlap/region/homo_sapiens/6:2739490-2739490?feature=gene&logic_name=refseq_import&db_type=otherfeatures%27%20%20%20%20%20%20%20%20%20%20-H%20%27Content-type:application/json%27%20-H%20%20%20%20%20%20%20%20%20%20%27Accept:application/json>'
>>>> 
>>>> [{"gene_id":"340156","source":"BestRefSeq","logic_name":"refseq_import","version":1,"feature_type":"gene","external_name":"MYLK4","description":null,"assembly_name":"GRCh38","biotype":"protein_coding","end":2770330,"seq_region_name":"6","strand":-1,"id":"340156","start":2663629}]
>>>> 
>>>> 
>>>> I need to retrieve the external_name, can you explain me why this field is not available anymore and eventually how I can retrieve it?
>>>> 
>>>> Many thanks
>>>> Cinzia
>>>> 
>>>> 
>>>> 
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>> 
>> 
>> 
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