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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

[0.1.0] - 2025-06-20

Added

  • Initial version of the Health-RI Ontology model.
  • Two main packages: Gender and Biology, each with detailed OntoUML constructs.
  • Core classes under Gender:
  • Person with Unassigned Sex at Birth
  • Person with Assigned Sex at Birth, including its specializations:
    • Person with Male Sex at Birth
    • Person with Female Sex at Birth
    • Person with Indeterminate Sex at Birth
  • Sex at Birth Assignment, Healthcare Professional, Birth Notification, and Birth-related Legislation Rule
  • Core classes under Biology:
  • Person, Human Cell, Chromosome, Allosome, Gamete, Diploid Cell, Haploid Cell
  • Allosomal variants (Allosome X, Allosome Y) and karyotypical profiles:
    • Regular Karyotypical Male, Regular Karyotypical Female
    • Variant Karyotypical Male, Variant Karyotypical Female
    • Karyotypically Indeterminate Person
  • Use of OntoUML stereotypes including kind, subkind, role, relator, mode, and relations such as mediation and componentOf.
  • Several generalizations and complete disjoint generalization sets:
  • sex at birth, karyotypical sex, variant karyotypic sex, regular karyotypical sex, allosome type, and others.
  • Two diagrams: Sex at Birth and Chromosomes, illustrating core structural aspects of the model.

[0.2.0] - 2025-06-23

Added

  • New package: Legal Gender Model including:
  • Person with Unassigned Legal Gender
  • Person with Legal Gender, with subtypes:
    • Person with Male Legal Gender
    • Person with Female Legal Gender
    • Person with Other Legal Gender
  • Legal Gender Assignment, Government, and Birth Certificate
  • Generalization set: legal gender (complete, disjoint) under Person with Legal Gender
  • Mediation relations:
  • Between Legal Gender Assignment and its participants (Government and Person)
  • Material relation: formalizes between Birth Certificate and Legal Gender Assignment
  • ComponentOf relations:
  • Birth Certificate composed of Legal Gender Assignment
  • Dependency from the new Legal Gender Model package to the Gender package

Changed

  • Ontology version IRI updated to reflect new release
  • Improvements in naming conventions and organization of existing generalization sets for clarity and consistency

Fixed

  • Minor alignment issues in model layout (diagrams were not affected)

[0.3.0] - 2025-06-24

Added

  • New class: Person with Unassigned Legal Gender or Sex at Birth
  • Introduced as a superclass for both unassigned sex and unassigned legal gender persons.
  • New generalization set: legal gender or sex at birth (complete, disjoint), covering:
  • Person with Unassigned Legal Gender or Sex at Birth
  • Person with Unassigned Legal Gender
  • Person with Unassigned Sex at Birth
  • Mediation relations:
  • Between Birth Notification and Person with Unassigned Legal Gender or Sex at Birth
  • Between Birth Certificate and Person with Unassigned Legal Gender or Sex at Birth

Changed

  • Updated generalization structures to reflect the new shared superclass for unassigned status.
  • Adjusted diagram layout to accommodate new shared superclass and its associated relations.

[0.4.0] - 2025-06-25

Added

  • New class: Person with Assigned Legal Gender or Sex at Birth
  • Serves as a common superclass for Person with Legal Gender and Person with Assigned Sex at Birth
  • New generalization set: assigned legal gender or sex at birth (complete, disjoint), including:
  • Person with Assigned Legal Gender or Sex at Birth
  • Person with Legal Gender
  • Person with Assigned Sex at Birth
  • New mediation relations:
  • Between Birth Notification and Person with Assigned Legal Gender or Sex at Birth
  • Between Birth Certificate and Person with Assigned Legal Gender or Sex at Birth

Changed

  • Generalization structure revised to include new superclass for persons with assigned statuses
  • Layout adjustments in diagrams to reflect new hierarchical relationships

[0.5.1] - 2025-06-30

Added

  • Class: Sex was introduced to the model.

Removed

  • Package: Complementary
  • Classes: Biological Sex Assigner, Biological Sex Assignee, and Biological Sex Assignment
  • Classes: Social Gender and Administrative Gender

Changed

  • Renamed Phenotypic Sex Assignment to Phenotypic Sex Assessment.
  • Renamed Phenotypic Sex Assigner to Phenotypic Sex Assessor.
  • Renamed Phenotypic Sex Assignee to Person with Assessed Phenotypic Sex.

[0.5.2] - 2025-06-30

Added

  • Added detailed descriptions for multiple classes in the ontology, replacing previously null values to improve clarity and documentation quality.

Changed

  • Updated descriptions for:
  • Roles, relators, and categories related to sex and gender assignments and recognitions (e.g., Person with Assigned Sex at Birth, Legal Gender Recognizer, Administrative Gender Recognizer).
  • Core biological concepts such as Chromosome, Allosome, Human Cell, Karyotypical Sex, Phenotypic Sex, and Sex at Birth.
  • Traits and characteristic categories for sexual and visual dimorphic features.
  • High-level categories like Sex and Gender, including Legal, Administrative, and Identity forms.
  • General concepts including Person, Organization, Government, and Document.
  • Improved consistency and clarity across all descriptions to support better understanding in administrative, legal, medical, and ontological contexts.

[0.6.0] - 2025-07-30

Added

  • Introduced new classes to represent administrative gender assignments:
  • Person with Male Administrative Gender
  • Person with Female Administrative Gender
  • Person with Non-binary Administrative Gender
  • Male Administrative Gender, Female Administrative Gender, and Non-binary Administrative Gender
  • Added new generalizations and generalization sets:
  • Generalizations linking Person with Administrative Gender roles to Person
  • Generalizations linking administrative gender phases to the Administrative Gender category
  • Generalization sets:
    • person's administrative genders (complete, not disjoint)
    • administrative gender types (complete, disjoint)
    • administrative gender characterization types (complete, disjoint)
  • Introduced three new characterization relations:
  • Each links one of the Person with X Administrative Gender roles with the corresponding X Administrative Gender phase
  • Added names to several previously unnamed relations, such as "has administrative gender"

Changed

  • Swapped internal OntoUML element IDs to improve structural clarity and align with internal conventions. These changes affect class and generalization identifiers but not their semantic content.
  • Improved the clarity of modeling administrative gender recognition as separate from legal or self-identified gender representations.
  • Reorganized the ontology structure to accommodate the new administrative gender module while preserving backward compatibility.

Fixed

  • Corrected some inconsistencies in generalization references and alignment of identifiers for relations and generalizations across the administrative gender module.

[0.7.0] - 2025-07-30

Changed

  • Reassigned internal OntoUML element identifiers to improve structural consistency and tooling traceability:
  • Multiple id values for classes, generalizations, and relations were systematically rotated or swapped.
  • These changes have no impact on the logical content or semantics of the ontology but support improved internal alignment.

Removed

  • Class: Organization (previously defined as a kind) was removed from the ontology.
  • It included a description as a structured group with roles, responsibilities, and formal authority.
  • If still needed, its usage should be reintroduced in future updates or considered as part of an external reference ontology.

[0.8.0] - 2025-07-30

Added

  • Introduced a new diagnostic module with comprehensive modeling of diagnostic types and roles, including:
  • Healthcare Diagnosis, Clinical Diagnosis, Laboratory Diagnosis, Radiological Diagnosis, Administrative Coding Diagnosis, Epidemiological Diagnosis, Surveillance Diagnosis, Research Diagnosis
  • Diagnosis roles such as Diagnosed Biological Part, Diagnosed Specimen, Diagnosed Group, and Diagnosed Cellular Entity
  • Conclusive Diagnostic Assessment, Concluded Diagnostic Relation, and other related constructs
  • New taxonomy and generalization sets for diagnosis classification, including:
  • healthcare diagnosis types by source, healthcare diagnosis types by focus, healthcare diagnosis types by use, types of diagnosed entities, and cellular entity diagnosis types
  • Introduced Self-diagnosis, External Diagnosis, and Diagnosis Suspicion as distinct classes
  • New diagnostic relation: characterization between diagnosis suspicion and assessed condition
  • Expanded health condition classification with:
  • Traumatic Health Condition, Non-traumatic Health Condition, Risk-based Health Condition, Exposure-based Health Condition, Inherent Health Condition, and Injury
  • Introduced Cellular Entity and its states: Living Cellular Entity, Dead Cellular Entity
  • New generalization sets for animal types, trauma-based health condition types, and cellular entity states

Changed

  • Replaced Animal, Non-Human Animal, Living Animal, and Dead Animal with an updated and more expressive Cellular Entity taxonomy
  • Revised several stereotypes:
  • Changed various subkind and unnamed classes to proper category, roleMixin, or phaseMixin stereotypes
  • Updated Health Condition classes to clarify their nature (e.g., intrinsic vs extrinsic modes)
  • Improved modeling coherence for diagnostic processes, replacing older concepts like Antemortem Diagnosis and Postmortem Diagnosis with more granular and categorized alternatives

Removed

  • Removed the entire Animal classification block including:
  • Animal, Non-Human Animal, Living Animal, Dead Animal
  • Their generalizations and generalization sets (e.g., animal types, animal living state)

[0.9.0] - 2025-07-30

Added

  • New textual descriptions were added to key sections of the ontology and diagrams, improving documentation and understandability:
  • Ontology-level description of sex and gender, distinguishing intrinsic and extrinsic modes and their role in formal assessment or self-identification.
  • Detailed diagram descriptions for:
    • Sex at Birth, Karyotypical Sex, Phenotypic Sex
    • Legal Gender, Administrative Gender, Gender Identity
    • Integrated overview diagram of all sex and gender modes
    • Biological Sex as a conceptual umbrella

Changed

  • Swapped internal identifiers of several classes and generalizations to align with structural or tooling needs. These include:
  • Various class IDs for Person, Gender, Health Condition, and diagnostic modules
  • Generalization and generalization set IDs (e.g., in "healthcare diagnosis types by use", "by focus", etc.)
  • These identifier changes do not affect the semantic content of the model but improve consistency and traceability in tooling pipelines.

Fixed

  • Improved alignment and phrasing in existing class descriptions for Gender and Sex, especially in the documentation layer.

[0.9.1] - 2025-07-30

Changed

  • Updated internal identifiers (id fields) for multiple classes, relations, and generalizations to improve consistency in serialization and downstream processing. These changes do not affect the logical structure or semantics of the ontology.

Fixed

  • Corrected typographic artifacts in textual descriptions for sex and gender constructs that previously used escaped HTML-like formatting (**<<mode>>**, **<<phase>>**, etc.). These are now consistently rendered.
  • Minor cleanup in markdown-style syntax within descriptions, ensuring accurate rendering in downstream documentation tools.