[ensembl-dev] REST API: Missing external_name

[Brandon Walts]

Sorry, you are correct that dec2017 maps to release 91, not 93. 
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
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info: 
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181016/50429889/attachment.html>