Specification Guide

The normative specification lives in docs/spec. The repository organizes the ARC RDM model into three base profiles: Process Provenance, Semantic Designation, and Administrative. Decoration profiles, including Datamap, add domain-specific refinements. The implementation remains one shared model; profile boundaries are documentation and mapping boundaries, not runtime type boundaries.

Base Profiles

flowchart LR
    Dataset --processes--> Process
    Dataset --dataFiles--> Data
    Dataset --agents--> Agent
    Dataset --citations--> ScholarlyArticle
    Dataset --descriptors--> Descriptor
    Dataset --hasPart--> Dataset
    Process --inputs--> Sample
    Process --"outputs"--> Data
    Process --executesRecipe--> Recipe
    Process --parameterValue--> Annotation
    Recipe --parameters--> FormalParameter
    Recipe --components--> Annotation
    Annotation --instanceOf--> FormalParameter
    Descriptor --describes--> Sample
    Descriptor --describes--> Data
    Descriptor --annotations--> Annotation
    Agent --affiliation--> Organization
    ScholarlyArticle --authors--> Agent

Shared model entities:

Entity	Source
Dataset	Process Provenance, Semantic Designation, Administrative
Process	Process
Recipe	Recipe
Sample	Sample
Data	Data
Descriptor	Descriptor
Annotation	Process Provenance, Semantic Designation
FormalParameter	FormalParameter
DefinedTerm	DefinedTerm
Agent	Agent
Organization	Organization
ScholarlyArticle	ScholarlyArticle

Base profile entry points:

Base Profile	Purpose	Source
Process Provenance	Provenance through datasets, processes, protocols, samples, data, and annotations	Process Provenance
Semantic Designation	Semantic descriptions that connect datasets, samples, and data with bundled annotations	Semantic Designation
Administrative	Dataset metadata, agents, affiliations, citations, licenses, and dates	Administrative

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	Data files, selected fragments, and DataContext descriptors	Datamap

Naming Notes

The Process Provenance vocabulary uses Process and Recipe, not the older placeholder names Process and Protocol.

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

inputs
outputs
executesRecipe
parameterValue
additionalProperty

Some legacy/profile-shaped examples and upstream references use RO-Crate or Bioschemas names such as object and result. 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.