---
# Research Base Ontology — shared research-methodology supertypes (Tier 1)
#
# A MIF-compliant intermediate layer between the domain-neutral generic core
# (mif-base / shared-traits) and the research DOMAIN packs (scientific,
# regenerative-agriculture-research, and future *-research packs). It owns the
# ABSTRACT supertypes that recur across every research domain — an inquiry, a
# procedure, an observation, a proposition, a produced artifact, a scholarly
# output, a funding instrument, an apparatus, a finding — so research domains
# inherit them via `extends` and specialize them with `subtype_of`.
#
# Supertype names are deliberately ABSTRACT and distinct from any leaf pack's
# concrete type names (e.g. `observation`, not `measurement`; `inquiry`, not
# `study`): a base a leaf `extends` must not share entity-type NAMES with that
# leaf, or `subtype_of` resolution across the chain is ambiguous.
#
# Cataloged present-but-NOT-core (core=false): never bound to a topic directly.
#
# See docs/decisions/0003-research-and-agriculture-base-layers.md.
#
# Version: 0.1.0
# Last Updated: 2026-06-30

ontology:
  id: research
  version: "0.1.0"
  description: "Shared research-methodology supertypes — the MIF-compliant intermediate layer the research domains extend"
  extends:
    - mif-base
    - shared-traits
namespaces:
  semantic:
    children:
      research:
        description: "Research artifacts, propositions, outputs, instruments, findings"
        type_hint: semantic
  episodic:
    children:
      inquiries:
        description: "Research inquiries as episodic records"
        type_hint: episodic
  procedural:
    children:
      procedures:
        description: "Research procedures and protocols"
        type_hint: procedural
# Abstract supertypes shared across research domains. Leaf packs specialize these
# via `subtype_of` (e.g. scientific `study` subtype_of `inquiry`, `measurement`
# subtype_of `observation`); subsumption is enforced across the extends chain.
entity_types:
  - name: inquiry
    description: "A unit of research inquiry — the episodic container for a study, investigation, or cohort"
    base: episodic
    traits:
      - cited
      - dated
    schema:
      required:
        - title
      properties:
        title:
          type: string
        design:
          type: string
          description: "Inquiry design (observational, experimental, computational, …)"
        objective:
          type: string
        status:
          type: string
          description: "planned / active / completed / retracted"
  - name: research-procedure
    description: "A method, protocol, or procedure applied in research (and its executions)"
    base: procedural
    traits:
      - cited
      - versioned
    schema:
      required:
        - name
      properties:
        name:
          type: string
        procedure:
          type: string
          description: "What the procedure does, step-wise"
        instrument:
          type: string
          description: "Instrument or platform the procedure uses"
  - name: observation
    description: "A measured or observed datum produced by a procedure"
    base: semantic
    traits:
      - cited
      - dated
    schema:
      required:
        - variable
        - value
      properties:
        variable:
          type: string
        value:
          type: string
        unit:
          type: string
        method_ref:
          type: string
          description: "The procedure that produced this observation"
  - name: proposition
    description: "A falsifiable proposition or hypothesis under test"
    base: semantic
    traits:
      - cited
    schema:
      required:
        - statement
      properties:
        statement:
          type: string
          description: "The falsifiable claim"
        status:
          type: string
          description: "untested / supported / refuted / inconclusive"
  - name: research-artifact
    description: "A produced research data artifact (dataset, distribution, service, catalog, series)"
    base: semantic
    traits:
      - cited
      - versioned
    schema:
      required:
        - title
      properties:
        title:
          type: string
        artifact_kind:
          type: string
          description: "dataset / distribution / service / catalog / series"
        license:
          type: string
  - name: scholarly-output
    description: "A published research output (article, preprint, report, dataset descriptor)"
    base: semantic
    traits:
      - cited
      - documented
    schema:
      required:
        - title
      properties:
        title:
          type: string
        output_type:
          type: string
          description: "journal-article / preprint / report / dataset-descriptor"
        doi:
          type: string
  - name: funding-instrument
    description: "A grant or funding instrument supporting research"
    base: semantic
    traits:
      - cited
      - dated
    schema:
      required:
        - funder
      properties:
        funder:
          type: string
        grant_id:
          type: string
        amount:
          type: string
  - name: apparatus
    description: "A device, platform, or instrument used to produce research data"
    base: semantic
    traits:
      - cited
      - versioned
    schema:
      required:
        - name
      properties:
        name:
          type: string
        apparatus_type:
          type: string
        manufacturer:
          type: string
  - name: research-finding
    description: "A finding or observation-level conclusion — the unit of recorded research knowledge a domain observation specializes"
    base: semantic
    traits:
      - cited
    schema:
      required:
        - statement
      properties:
        statement:
          type: string
          description: "The finding or conclusion"
        evidence:
          type: string
        confidence:
          type: string
          description: "Qualitative confidence in the finding"
traits:
  cited:
    description: "Requires citations/sources"
    requires:
      - citations
  dated:
    description: "Adds an event/observation date"
    fields:
      observed_date:
        type: string
        format: date
  versioned:
    description: "Adds version tracking"
    fields:
      version:
        type: string
        pattern: "^\\d+\\.\\d+\\.\\d+.*$"
  documented:
    description: "Adds a documentation reference"
    fields:
      documentation_url:
        type: string
        format: uri
relationships:
  conducts:
    description: "An inquiry conducts a procedure"
    from:
      - inquiry
    to:
      - research-procedure
    symmetric: false
  produces:
    description: "A procedure produces an observation"
    from:
      - research-procedure
    to:
      - observation
    symmetric: false
  tests:
    description: "An inquiry tests a proposition"
    from:
      - inquiry
    to:
      - proposition
    symmetric: false
  yields:
    description: "An inquiry yields a research artifact"
    from:
      - inquiry
    to:
      - research-artifact
    symmetric: false
  reports-in:
    description: "An inquiry is reported in a scholarly output"
    from:
      - inquiry
    to:
      - scholarly-output
    symmetric: false
  funded-by:
    description: "An inquiry is funded by a funding instrument"
    from:
      - inquiry
    to:
      - funding-instrument
    symmetric: false
discovery:
  enabled: false
  confidence_threshold: 0.8
  patterns:
    - content_pattern: "\\b(study|trial|investigation|experiment)\\b"
      suggest_entity: inquiry
      suggest_namespace: _episodic/inquiries
    - content_pattern: "\\b(hypothesis|we hypothesi[sz]e|proposition)\\b"
      suggest_entity: proposition
      suggest_namespace: _semantic/research
    - content_pattern: "\\b(dataset|data set|data catalog|distribution)\\b"
      suggest_entity: research-artifact
      suggest_namespace: _semantic/research