Schema¶
The BioSim schema defines a shared metadata model for biomolecular simulation data. It provides a consistent structure for describing simulation setup, execution context, system composition, observables, topology, trajectory, and related computational details.
Why this schema exists¶
Different simulation engines expose similar concepts using different names and formats. This schema provides a canonical vocabulary so metadata can be:
compared across engines
validated consistently
transformed into downstream artefacts for extraction and web forms
reused by other BioSimDR tools
How the schema is organized¶
The schema uses a top-level SimulationMetadata model and is split into
domain-focused component files (for example settings, stages, observables,
topology, and trajectory). This keeps the structure modular while preserving
one coherent metadata object.
The autogenerated LinkML pages below are the authoritative reference for all classes, slots, enums, and types.
How to read the autogenerated reference¶
Use the pages under linkml/index to inspect:
classes: object structure and nested fields
slots: field-level definitions and constraints
enums: controlled vocabularies
types: scalar and custom value types
Autogenerated Reference