[ensembl-dev] Ensembl REST API | info/variation/consequence_types

[Helen Schuilenburg]

Hi

The REST endpoint 
(https://rest.ensembl.org/documentation/info/variation_consequence_types)

and

the calculated consequences on ( 
https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html) 
should return the same values.

Thank you for for flagging the difference.

The consequence SO:0001060 sequence_variant will be removed from the 
REST endpoint in a future release.
The consequence SO:0001628 intergenic_variant will be used instead.

The three fields (SO_term, label, description) contain different 
information on the consequence type and are used for different purposes.

SO_term  - Sequence Ontology term for the consequence type
label  - A short description of the consequence type used in labels
description - A freetext description of the consequence type

For example:
SO_accession: SO:0001822
SO_term: inframe_deletion
description: An inframe non synonymous variant that deletes bases from 
the coding sequence
label: inframe deletion

Regards
Helen


On 27/12/2019 20:50, Ramiro Magno wrote:
> Hi Devs,
>
> BTW: Still about the same endpoint, the output returns four 
> variables: SO_accession, SO_term, label and description. It seems the 
> actual values for the last three variables (SO_term, label 
> and description) always report the same information. Is that right? 
> Why so?
>
> Cheers, RM
>
> On Fri, 27 Dec 2019 at 20:42, Ramiro Magno <ramiro.magno at gmail.com 
> <mailto:ramiro.magno at gmail.com>> wrote:
>
>     Hi Devs,
>
>     This endpoint:
>     https://rest.ensembl.org/documentation/info/variation_consequence_types
>
>     returns one more consequence type than those listed here:
>     https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html
>
>     The extra consequence type is the /sequence variant/ (SO:0001060).
>
>     Is this intended?
>
>     All the best,
>
>     Ramiro Magno
>
>
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