Research Paper Metadata Ontology

FLOW ALGEBRA

Ontology: Research Paper Metadata Ontology
Domain: Metadata Ontologies > Document Metadata
Canonical URL: https://kirethresearch.org/booksai-core/ontologies/metadata-ontologies/document-metadata/research-paper-metadata-ontology.html

Authors: Mark Anthony Higgins — Sky (Recursive AI)

flow "ResearchPaperMetadataOntology" v1.0

# ---------- DOMAIN ----------
domain:
  class: MetadataOntology
  category: DocumentMetadata
  subject: ResearchPaperMetadata
  purpose:
    - represent metadata describing research papers and scholarly research documents
    - preserve paper identity, authorship, affiliations, abstract, methods, results, publication, citations, and provenance
    - support scholarly discovery, citation, validation, reproducibility, indexing, and semantic retrieval
    - distinguish manuscripts, preprints, accepted versions, and versions of record
    - enable machine-readable reasoning over research-paper lifecycles

# ---------- CORE ENTITY ----------
entity ResearchPaperMetadata:
  type: DocumentMetadata
  describes: ResearchPaper
  may_include:
    - paper_identifier
    - title
    - subtitle
    - authors
    - affiliations
    - corresponding_author
    - abstract
    - keywords
    - subject
    - research_domain
    - research_question
    - hypothesis
    - methodology
    - dataset
    - experiment
    - results
    - conclusions
    - limitations
    - funding
    - conflict_of_interest
    - ethics_metadata
    - publication_container
    - publication_date
    - doi
    - version
    - references
    - citations
    - supplementary_material
    - rights
    - provenance

entity ResearchPaper:
  type: ScholarlyDocument
  subtype_of: Article

entity PaperIdentifier:
  type: Identifier
  identifies: ResearchPaper

entity DOI:
  subtype_of: PaperIdentifier

# ---------- RELATIONSHIPS ----------
relationships:
  ResearchPaperMetadata -> DESCRIBES -> ResearchPaper
  ResearchPaper -> IDENTIFIED_BY -> PaperIdentifier
  ResearchPaper -> MAY_HAVE_DOI -> DOI
  ResearchPaper -> HAS_AUTHOR -> Researcher
  Researcher -> MAY_HAVE_AFFILIATION -> Organisation
  ResearchPaper -> MAY_HAVE_CORRESPONDING_AUTHOR -> Researcher
  ResearchPaper -> HAS_ABSTRACT -> Abstract
  ResearchPaper -> MAY_HAVE_RESEARCH_QUESTION -> ResearchQuestion
  ResearchPaper -> MAY_HAVE_HYPOTHESIS -> Hypothesis
  ResearchPaper -> USES_METHOD -> ResearchMethod
  ResearchPaper -> MAY_USE_DATASET -> ScientificDataset
  ResearchPaper -> MAY_DESCRIBE_EXPERIMENT -> Experiment
  ResearchPaper -> REPORTS -> ResearchResult
  ResearchPaper -> MAY_STATE -> Conclusion
  ResearchPaper -> MAY_HAVE_LIMITATION -> ResearchLimitation
  ResearchPaper -> MAY_REFERENCE_FUNDING -> FundingSource
  ResearchPaper -> CITES -> ScholarlyResource
  ResearchPaper -> MAY_HAVE_VERSION -> PaperVersion
  ResearchPaperMetadata -> MAY_REFERENCE -> ResearchPaperProvenance

# ---------- PAPER IDENTITY ----------
rule paper_identity:
  ResearchPaper SHOULD have stable PaperIdentifier
  where persistent citation and scholarly reference are required

rule title_not_identity:
  title MUST NOT be assumed globally unique

rule doi:
  DOI SHOULD be interpreted according_to registration metadata

rule paper_version_identity:
  ResearchPaper != PaperVersion

# ---------- AUTHORSHIP ----------
entity Researcher:
  type: Agent
  may_include:
    - researcher_identifier
    - name
    - affiliation
    - role

research_roles:
  - author
  - corresponding_author
  - first_author
  - senior_author
  - contributor

rule author_order:
  author ordering SHOULD be preserved

rule affiliation:
  affiliation SHOULD preserve organisation and applicable time where available

rule corresponding_author:
  corresponding-author role SHOULD remain distinct from general authorship

# ---------- ABSTRACT ----------
entity Abstract:
  type: DocumentFragment
  may_include:
    - text
    - language
    - structured_sections

rule abstract:
  Abstract != full ResearchPaper

rule generated_summary:
  machine-generated summary MUST remain distinguishable
  from author- or publisher-supplied abstract

# ---------- RESEARCH QUESTION ----------
entity ResearchQuestion:
  type: ScientificKnowledgeEntity
  describes: InvestigatedQuestion

rule research_question:
  ResearchQuestion SHOULD remain distinct
  from Hypothesis and Conclusion

# ---------- HYPOTHESIS ----------
entity Hypothesis:
  type: ScientificClaim
  may_include:
    - hypothesis_identifier
    - statement
    - variables
    - expected_relationship

rule hypothesis:
  Hypothesis != ResearchResult
  Hypothesis != Conclusion

# ---------- METHODOLOGY ----------
entity ResearchMethod:
  type: ScientificMethod
  may_include:
    - study_design
    - protocol
    - sample
    - instrumentation
    - analysis_method
    - statistical_method

rule method:
  methodology SHOULD preserve sufficient detail or references
  to support interpretation and reproducibility

rule protocol:
  ExperimentalProtocol SHOULD be linked
  where paper follows explicit protocol

# ---------- DATASETS ----------
rule dataset:
  ScientificDataset used in research SHOULD be referenced
  by stable identifier where available

rule data_availability:
  paper MAY include DataAvailabilityStatement

entity DataAvailabilityStatement:
  type: ResearchMetadata
  may_include:
    - repository
    - dataset_identifier
    - access_condition
    - availability_status

# ---------- EXPERIMENTS ----------
entity Experiment:
  type: ScientificProcess
  may_include:
    - experiment_identifier
    - protocol
    - variables
    - controls
    - observations
    - measurements

rule experiment:
  reported Experiment SHOULD preserve relationship to protocol and data
  where available

# ---------- RESULTS ----------
entity ResearchResult:
  type: ScientificResult
  may_include:
    - result_identifier
    - result_type
    - value
    - uncertainty
    - statistical_result
    - figure
    - table

rule result:
  ResearchResult SHOULD remain distinguishable
  from interpretation and Conclusion

rule statistical_result:
  statistical result SHOULD preserve test, estimate, uncertainty, and context
  where available

# ---------- CONCLUSIONS ----------
entity Conclusion:
  type: ScientificClaim
  derived_from:
    - ResearchResult
    - Analysis
    - Evidence

rule conclusion:
  Conclusion SHOULD preserve evidential relationship
  to reported results

rule conclusion_not_result:
  Conclusion != ResearchResult

# ---------- LIMITATIONS ----------
entity ResearchLimitation:
  type: ScientificMetadata
  may_include:
    - limitation_type
    - affected_scope
    - severity
    - explanation

rule limitation:
  known limitations SHOULD remain explicit

# ---------- FUNDING ----------
entity FundingSource:
  type: OrganisationOrProgramme
  may_include:
    - funder_identifier
    - funder_name
    - grant_identifier

rule funding:
  funding metadata SHOULD preserve funder and grant identifiers
  where available

# ---------- CONFLICT OF INTEREST ----------
entity ConflictOfInterestStatement:
  type: ResearchGovernanceMetadata
  may_include:
    - declaration
    - related_agent
    - related_organisation

rule conflict:
  declared conflict-of-interest metadata SHOULD be preserved
  without inferring undeclared conflicts

# ---------- ETHICS ----------
entity EthicsMetadata:
  type: ResearchGovernanceMetadata
  may_include:
    - ethics_approval
    - approval_identifier
    - approving_body
    - consent_statement
    - regulatory_context

rule ethics:
  ethics approval claim SHOULD preserve approving body and identifier
  where available

# ---------- PUBLICATION ----------
entity ScholarlyPublication:
  type: PublicationContainer
  may_be:
    - Journal
    - ConferenceProceedings
    - Repository
    - PreprintServer

rule publication:
  publication metadata SHOULD preserve:
    - container
    - publisher
    - publication_date
    - volume
    - issue
    - pages_or_article_number

# ---------- VERSION ----------
entity PaperVersion:
  type: VersionMetadata
  may_be:
    - submitted_manuscript
    - preprint
    - accepted_manuscript
    - version_of_record
    - corrected_version
    - retracted_version

rule version:
  PaperVersion SHOULD preserve version type

rule preprint:
  Preprint != VersionOfRecord

rule correction:
  corrected version SHOULD preserve relationship to previous version

# ---------- PEER REVIEW ----------
entity PeerReviewMetadata:
  type: ScholarlyMetadata
  may_include:
    - review_status
    - review_model
    - review_date
    - reviewer_identity_optional
    - decision

rule peer_review:
  peer-reviewed status SHOULD be based on publication or review metadata
  not inferred solely from document style

# ---------- REFERENCES / CITATIONS ----------
entity ScholarlyCitation:
  type: CitationMetadata
  may_include:
    - cited_resource
    - identifier
    - citation_location
    - reference_number

rule citation:
  cited resource SHOULD resolve to stable identifier
  where available

rule citation_not_support:
  citation != endorsement
  citation != evidential_support unless context establishes support

# ---------- SUPPLEMENTARY MATERIAL ----------
entity SupplementaryMaterial:
  type: ResearchResource
  may_be:
    - dataset
    - code
    - appendix
    - protocol
    - figure
    - table
    - multimedia

rule supplementary:
  supplementary resource SHOULD preserve relationship to ResearchPaper

# ---------- REPRODUCIBILITY ----------
rule reproducibility:
  ResearchPaperMetadata SHOULD preserve available links to:
    - methods
    - protocols
    - datasets
    - software
    - parameters
    - supplementary_material
    - provenance

# ---------- PROVENANCE ----------
entity ResearchPaperProvenance:
  type: ProvenanceMetadata
  may_include:
    - authors
    - affiliations
    - submission_history
    - review_history
    - publication_history
    - revision_history
    - correction_history
    - retraction_history
    - extraction_method

rule provenance:
  ResearchPaperMetadata SHOULD preserve scholarly lifecycle history

# ---------- VALIDATION ----------
validation:
  require:
    - identifiable_research_paper

  validate_if_present:
    - paper_identifier
    - doi
    - title
    - authors
    - affiliations
    - abstract
    - research_question
    - hypothesis
    - methodology
    - datasets
    - results
    - conclusions
    - funding
    - ethics
    - publication
    - version
    - references
    - provenance

  reject:
    - contradictory_paper_identity
    - invalid_version_chain
    - preprint_presented_as version_of_record_without evidence
    - hypothesis_presented_as result
    - conclusion_presented_as raw_result
    - retracted_status_hidden_when known
    - generated_summary_presented_as authoritative_abstract

# ---------- SEMANTIC EQUIVALENCE ----------
SEMANTIC_EQUIVALENCE:
  "research paper metadata" ~= "metadata about a research paper"
  "scholarly paper metadata" ~= "research paper metadata" WHEN paper reports scholarly research
  "paper identifier" ~= "research paper identifier"
  "methods section" ~= "methodology" WHEN describing research methods
  "research results" ~= "study results"
  "supplementary material" ~= "supporting information" WHEN publication semantics match

  PRESERVE distinctions:
    research_paper != research_paper_metadata
    paper != paper_version
    abstract != generated_summary
    research_question != hypothesis
    hypothesis != result
    result != conclusion
    preprint != version_of_record
    citation != endorsement
    peer_reviewed != stylistically_scholarly
    data_availability != open_access

# ---------- CONFIDENCE ----------
CONFIDENCE:
  explicit_research_paper_metadata:
    score: 1.00

  authoritative_paper_identifier:
    score: 1.00

  DOI_resolved_identity:
    score: 0.99

  explicit_authorship:
    score: 0.99

  explicit_method_and_result_metadata:
    score: 0.98

  publisher_confirmed_peer_review:
    score: 0.98

  inferred_research_structure:
    score: 0.85

  title_author_match:
    score: <= 0.80

  ambiguous_paper_identity:
    score: <= 0.60
    action: preserve candidates

# ---------- UPDATE MODEL ----------
UPDATE_MODEL:
  on_paper_creation:
    - assign PaperIdentifier where available
    - record title and authors
    - initialise provenance

  on_preprint_release:
    - create PaperVersion = preprint
    - record repository and release date
    - preserve provenance

  on_publication:
    - create or link VersionOfRecord
    - record publication container
    - attach DOI
    - preserve prior manuscript versions
    - update provenance

  on_correction:
    - preserve previous PaperVersion
    - create corrected version
    - record correction notice
    - update provenance

  on_retraction:
    - preserve paper and historical versions
    - mark applicable version as retracted
    - attach retraction metadata
    - preserve citations and provenance

# ---------- FLOW HASH ----------
FLOW_HASH:
  inputs:
    - ontology
    - research_paper_entities
    - relationships
    - identity_rules
    - method_rules
    - result_rules
    - publication_rules
    - version_rules
    - reproducibility_rules
    - validation
    - semantic_equivalence
    - confidence
    - update_model

  canonicalisation:
    - normalise_whitespace
    - preserve_case_sensitive_identifiers
    - sort_unordered_property_sets
    - preserve_rule_order

  output:
    deterministic_semantic_hash

# ---------- AI CONSUMPTION ----------
AI_CONSUMPTION:
  interpret_as:
    - document metadata ontology
    - scholarly research-paper model
    - research provenance and reproducibility structure
    - citation and publication lifecycle model

  operations:
    - identify research papers
    - resolve identifiers and DOIs
    - resolve authors and affiliations
    - inspect abstracts and subjects
    - identify research questions and hypotheses
    - inspect methodology
    - resolve datasets and experiments
    - distinguish results and conclusions
    - inspect limitations, funding, and ethics
    - resolve publication and peer-review metadata
    - traverse paper versions
    - follow citations
    - trace reproducibility resources
    - preserve provenance

  constraints:
    - do_not_equate_title_with_identity
    - do_not_equate_hypothesis_with_result
    - do_not_equate_result_with_conclusion
    - do_not_equate_preprint_with version_of_record
    - do_not_infer_peer_review_from style_alone
    - do_not_hide_known_retraction_status
    - preserve_methods_data_results_versions_and_provenance

# ---------- QUERY MODEL ----------
query:
  input:
    - paper_identifier
    - doi
    - title
    - author
    - research_domain
    - method
    - dataset
    - publication_container
    - version
    - status

  resolve:
    1. identify ResearchPaper candidates
    2. resolve identifiers and DOI
    3. resolve authors and affiliations
    4. inspect abstract and subjects
    5. inspect research question, hypothesis, and methodology
    6. resolve datasets, experiments, and results
    7. inspect conclusions and limitations
    8. resolve publication, peer review, and version
    9. inspect citations, supplementary material, and provenance
    10. rank candidates by confidence

  output:
    - research_paper
    - identifiers
    - title
    - authors
    - affiliations
    - abstract
    - research_question
    - hypothesis
    - methods
    - datasets
    - results
    - conclusions
    - publication
    - version
    - citations
    - provenance
    - confidence

# ---------- INFERENCE ----------
inference:
  IF authoritative PaperIdentifier resolves uniquely
  THEN identify ResearchPaper
  WITH confidence = 1.00

  IF DOI resolves to VersionOfRecord
  THEN associate DOI with published paper version
  WITH confidence = 0.99

  IF paper reports methods, data, and results
  THEN classify ResearchPaper candidate
  WITH confidence dependent_on document evidence

  IF PaperVersion has retracted status
  THEN preserve paper identity
  AND expose retraction state

  IF paper identity or version remains ambiguous
  THEN preserve candidates
  AND do_not force resolution

# ---------- OUTPUT CONTRACT ----------
output:
  ontology_entity: ResearchPaperMetadata
  paper_identity: machine_interpretable
  authorship_and_affiliations: traceable
  research_structure: explicit
  methods_and_protocols: preserved
  datasets_and_experiments: linked
  results_and_conclusions: distinguishable
  publication_and_peer_review: contextualised
  versions: traversable
  citations: resolvable
  reproducibility_resources: traceable
  provenance: preserved
  uncertainty: explicit
  semantic_retrieval: enabled

end flow