jrsjrs / agr_schemas

A repository of JSON schemas for incorporating data into AGR.

AGR JSON Schemas

This directory contains JSON schemas used to define data for integration into AGR.

Most recent release:

Schema	Description
basicGeneInfoFile	A file of Basic Gene Information objects. This is the base or "root" schema.
basicGeneInformation	An entry with Gene information from a MOD. Gene set includes: genes, psuedogenes and not-protein coding genes. It does not include engineered foreign genes, transcripts or other features.
dataProvider	An standard set of information regarding data source and taxon ids for the AGR.
crossReference	An crossReference entity (e.g.: NCBIGENE links, UniProt Links, and links back to MODs).
metaData	An standard set of information regarding when and from whom the load was generated.

Validation

The python script "agr_validate.py" can be used to validate a JSON entry against a schema for testing/development purposes. Usage is as follows: agr_validate.py -d test_data.json -s base_schema.json

For the basic Gene info file run ./agr_validate.py -d <gene_file.json> -s basicGeneInfoFile.json and for the disease info file run ./agr_validate.py -d <disease_file.json> -s disease/diseaseMetaDataDefinition.json

Formatting Notes

Please use 2 spaces for indentation.