Specification Guide

The normative specification lives in docs/spec. ProcessCore is the small shared model. Decorations specialize or extend it for ISA, Workflow Run, and Datamap use cases without changing the core requirements.

ProcessCore

flowchart LR
    Dataset --processes--> LabProcess
    Dataset --hasPart--> Data
    Dataset --hasPart--> Dataset
    LabProcess --inputs--> Material
    LabProcess --outputs--> Data
    LabProcess --executesProtocol--> LabProtocol
    LabProcess --parameterValue--> PropertyValue
    LabProtocol --parameters--> FormalParameter
    PropertyValue --instanceOf--> FormalParameter

Core entities:

Entity	Source
Dataset	Dataset
LabProcess	LabProcess
LabProtocol	LabProtocol
Material	Material
Data	Data
PropertyValue	PropertyValue
FormalParameter	FormalParameter
DefinedTerm	DefinedTerm

Decorations

Decorations add domain-specific meaning through additionalType, specialized properties, and decoration-specific entities.

Decoration	Purpose	Source
ISA	Investigation, Study, Assay, Source, Sample, and ISA property value roles	ISA
Workflow Run	Workflow and Run datasets, workflow protocols, and workflow invocations	Workflow Run
Datamap	Datamap datasets and DataContext annotations for file fragments	Datamap

Naming Notes

The current core vocabulary uses LabProcess and LabProtocol, not the older placeholder names Process and Protocol.

For process I/O, the current core and YAML schema names are:

inputs
outputs
executesProtocol
parameterValue
additionalProperty

Some legacy/profile-shaped examples and upstream references use RO-Crate or Bioschemas names such as object, result, and executesLabProtocol. See Examples and schemas for how those files are treated.

Querying

The query use cases are described in Querying. The implementation exposes Path as a returned value object, while traversal and query operations are attached to the model types in src/ProcessCore/Graph.fs.