[ensembl-dev] JSON schema information

[Anja Thormann]

Dear Alejandro,

thank you for the clarification. We don’t have a formal description of all fields and data types that are returned by VEP available at the moment. But we are aiming to update our documentation for release 103 (planned for early next year). In the meantime maybe you could take a look at a similar request https://github.com/Ensembl/ensembl-vep/issues/658 <https://github.com/Ensembl/ensembl-vep/issues/658> and maybe some of the work that was done by the user can also help you with your work.

Best regards,
Anja

> On 26 Oct 2020, at 16:59, Alejandro Garcia <alejandro.garcia at institutimagine.org> wrote:
> 
> Dear Anja, 
> I've been watching that webpage before, unfortunately is not enough for my purpose. I'm looking for some more detailed and explicit explanation, for example, the different fields that are mandatory or optional, the data type (integer, string, list...). With the example present in the webpage you sent me I don't know what are the data types, I cannot be sure what are the fields expected (what are the fields that can vary from one variant to another). Making the development of downstream tools quite difficult. I attached a screenshot I think will represent better what do I need. 
> 
> Thank you very much 
> 
> Kindly, 
> 
> Alejandro G. 
> 
>> On 26/10/2020 16:25 Anja Thormann <anja at ebi.ac.uk> wrote:
>> 
>> 
>> Dear Alejandro,
>> 
>> we describe VEP’s json output format here: https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json <https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#json> I hope the description is detailed enough to help you with the tool integration. Please let me know if you have any more questions.
>> 
>> Kind regards,
>> Anja Thormann 
>> 
>>> On 26 Oct 2020, at 14:30, Alejandro Garcia <alejandro.garcia at institutimagine.org <mailto:alejandro.garcia at institutimagine.org>> wrote:
>>> 
>>> Hello, 
>>> I'm Alejandro Garcia I'm Engineer working in Imagine Institute. 
>>> Currently, I'm working with the docker VEP version 101 provided. I ran the following command to obtain the output in Json format, "./vep -i  input.vcf  -e -v --cache --assembly GRCh38 --json -o output.json --force_overwrite"
>>> I want to use these JSONs as input to handmade tools but I'm facing problems with the JSON structure in terms of possible fields, data types... I looked for more info in VEP website but I only found a simple explanation of the schema. 
>>> 
>>> I would like to know if you have more detailed information about the JSON schema of the output with the different keys that can appear, if they are mandatory or optional, what is the value type of each field.... 
>>> 
>>> I found really interesting the option for outputting in JSON format it would be quite useful to have this information for further integration of VEP with other tools. 
>>> 
>>> Thank you very much 
>>> 
>>> Kind Regards, 
>>> Alejandro G.
>>> _______________________________________________ 
>>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org> 
>>> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org> 
>>> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/> 
>> 
>> _______________________________________________ Dev mailing list Dev at ensembl.org Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org Ensembl Blog: http://www.ensembl.info/
> <json_schema_example.png>_______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20201028/60fc9642/attachment.html>