collections

Relation Engine Document Schemas

Document schemas define a required format for each collection in the database. Schemas use the JSON Schema specification.

Guidelines

• Every schema file should have name, type ("vertex" or "edge"), and schema (JSON schema) fields
• Every JSON schema should have a "$schema" field
• You can add reusable JSON schema definitions by placing them in the ./definitions directory.

Testing your schema format

Run make test in the root of the repo, which will validate all the schemas in this directory. You can also run make test-schemas or make test-schema <schema-path> to test schemas specifically.

Resources

• Quickly validate JSON schemas: https://www.jsonschemavalidator.net/

Data

Ontologies

• Gene Ontology (GO): go/
• Environmental Ontology (ENVO): envo/

Taxonomies

• Genome Taxonomy Database (GTDB): gtdb/
• Ribosomal Database Project (RDP): rdp/
• SILVA: silva/