Examples And Schemas

Schemas are derived representations of the markdown specification. The markdown files in docs/spec remain the normative source.

Schema Artifacts

Location	Status
`schemas/sql/`	SQLite-oriented SQL profile with executable DDL and seed data
`schemas/yml/`	JSON Schema draft 2020-12 expressed in YAML for core entities
`schemas/document-db/`	Placeholder for a future document database representation

The YAML schemas describe the current core vocabulary. In particular, LabProcess.yml expects inputs, outputs, and executesProtocol.

Examples

Location	Status
`examples/core/minimal.yml`	Schema-shaped core example intended to match the current YAML schema vocabulary
`examples/isa/`	Legacy/profile-shaped ISA and Datamap examples kept as domain examples
`examples/workflow-run/`	Placeholder for future Workflow Run examples

The current ISA examples are useful profile examples, but they are not currently guaranteed to validate against the strict core YAML schemas. They use some RO-Crate/Bioschemas profile terms such as object, result, executesLabProtocol, propertyValues, and additionalProperties.

Reconciliation Rule

When adding new examples, prefer one of these explicit categories:

Core schema examples that use the current schema vocabulary and should be validatable.
Profile-shaped examples that preserve upstream/profile terminology and are labeled as such.

This avoids mixing schema-valid core examples with legacy/profile examples that intentionally use another vocabulary.

Core Example Shape

id: dataset:demo
type: schema:Dataset
identifier: demo
processes:
  - id: process:extract
    type: bioschemas:LabProcess
    name: Extraction
    inputs:
      - id: material:leaf
        type: bioschemas:Sample
        additionalType: Source
        name: Leaf tissue
    outputs:
      - type: File
        path: raw/extract.tsv
    executesProtocol:
      id: protocol:extraction
      type: bioschemas:LabProtocol
      name: Extraction