INGESTION-GUIDE.md

Contents

• Introduction
• Data submission schemas
• Data re-indexing
• Model schemas
• Examples

Introduction

sBeacon comply with the Beacon V2 schema in terms of the API interface for querying. Data submission to sBeacon follows a similar format with few added fields to build the entity relationships.

Data submission schemas

• Submit dataset - please follow the JSON schema at ../shared_resources/schemas/submit-dataset-schema-new.json
• Update dataset - please follow the JSON schema at ../shared_resources/schemas/submit-dataset-schema-update.json

Data re-indexing

Changes or unavailability of ontology services will require re-indexing upon the service availability. This can be achieved using the /index endpoint using POST requests. The payload assumes the following format with defaults as indicated. The minimal payload can have an empty object ({}).

{
    "reIndexTables": true, // default = true
    "reIndexOntologyTerms": true // default = false
}

Complete indexing (true for all above parameters) must be done, at least once for successful operation of sBeacon. This is automatically carried out on the first data submission done with index=true in the payload. Please refer to the submission schemas.

Model schemas

• Dataset - ../shared_resources/schemas/dataset-schema.json
• Cohort - ../shared_resources/schemas/cohort-schema.json
• Individual - ../shared_resources/schemas/individual-schema.json
• Biosample - ../shared_resources/schemas/biosample-schema.json
• Run - ../shared_resources/schemas/run-schema.json
• Analysis - ../shared_resources/schemas/analysis-schema.json

Schemas does not apply for genomic variations in the ingestion phase of sBeacon. sBeacon supports standard vcf.gz files and must be accompanied with their index vcf.gz.tbi or vcf.gz.csi files.

Examples

Please refer to USAGE-GUIDE.md to find a complete example to get started.