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

[Ramiro Magno]

Hi Helen,

thank you for the information.

All the best,

Ramiro

On Thu, 2 Jan 2020 at 16:13, Helen Schuilenburg <helens at ebi.ac.uk> wrote:

> 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> 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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