[ensembl-dev] Unable to get All Annotations in REST API

[Nuno Agostinho]

Hi Sana,

Our REST API provides ENSP and UniParc protein identifiers when using VEP endpoints:
To return ENSP protein identifiers, include option protein=1 in the URL query
To return UniProt-related protein identifiers (SWISSPROT, TREMBL and UniParc), include option uniprot=1 in the URL query

I will create a ticket to add support for LOEUF plugin in our REST API, but it will not be available until the next Ensembl release (3-4 months from now). In the meantime, you can run VEP locally in your computer to get LOEUF results.

I am sorry for the inconvenience.

Tell me if there is anything else you would like to discuss.

Cheers,
Nuno

> On 16 Jan 2024, at 08:30, e259345 <sana.basharat at metu.edu.tr> wrote:
> 
> Dear Nuno Agostinho,
> 
> Thank you so much for your detailed and prompt reply.
> 
> I've checked the endpoints you mentioned and found most of what I needed in the options part. However, I was not able to find:
> 
> ENSP protein identifiers
> UniParc Accession of protein product
> LOEUF (most important)
> Is it possible for you to add these to the REST API? And if so, what would be the estimated timeline for this?
> 
> Again, thank you for your support.
> 
> Best regards,
> Sana Basharat
> Masters student (Data Informatics)
> Middle East Technical University
> Ankara, Turkiye
> 
> On 2024-01-15 13:35, Nuno Agostinho wrote:
> 
>> Dear Sana,
>>  
>> Thanks for your interest in Ensembl VEP.
>>  
>> First of all, note that we have a special domain for REST requests regarding the GRCh37 assembly: http://grch37.rest.ensembl.org/
>>  
>> To check the documentation for Ensembl VEP endpoints on GRCh37 assembly, please check the VEP section <http://grch37.rest.ensembl.org/#VEP> of that website. The endpoints support similar options, including which VEP plugin results to optionally return (such as SpliceAI, dbscSNV and GO plugins). LOEUF plugin is currently not available via REST, but do tell me if this is something you would like to have and if we are missing any other data that would be useful to you.
>>  
>> Have a great day!
>>  
>> Best regards,
>> Nuno Agostinho
>>  
>> Ensembl
>> EMBL-EBI
>> 
>>> On 14 Jan 2024, at 19:46, e259345 <sana.basharat at metu.edu.tr> wrote:
>>> 
>>> Hello,
>>> 
>>> I'm trying to use Ensembl VEP as part of my Masters thesis project where I'm building a Python package that will annotate my data using Ensembl VEP as well as other tools and then feed it to a model to predict an outcome. I'm using the GrCH37 assembly.
>>> 
>>> Initially, I was using the web version of Ensembl VEP manually to get annotations, but now, I want to use the REST API to integrate the Ensembl VEP annotation part into my code.
>>> 
>>> But upon looking at the Ensembl Rest API endpoints <https://rest.ensembl.org/> and testing them out, I cannot seem to find most of the annotations that the web version was providing me with, namely SpliceAI, ada_score, rf_score, LOEUF, ENSP terms, GO terms and UNIPARC terms. Is it because these are plugins?
>>>  
>>> Can you please let me know if these annotations are provided within the REST API, and if so, which endpoints I can use to get them?
>>> 
>>> Thank you so much for your time and your effort.
>>>  
>>> Best regards,
>>> Sana Basharat
>>> Masters student (Data Informatics)
>>> Middle East Technical University
>>> Ankara, Turkiye
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