Release v5.0.0

Major Updates:

• Add ClinicalTrial Class
  • Note that clinicalStudyDesign and eligibilityCriteria slots have been removed
• Add ParticipantDataFileManifest Class for and add slot participantDataFileManifestLocation to DataFile

Minor Updates

• Add enums to enum_researchDomain:
  • Auditory Perception
  • Embryonic and Fetal Development
  • Neurodevelopmental Disorders
  • Nutritional and Metabolic Diseases
  • Psychiatric Disorders
  • Respiratory Tract Diseases
  • Social Determinants of Health
• Add enums to enum_studyDesign:
  • Trial Readiness Study
  • Technology Development
• Add enums to enum_dataCategory
  • Adherence
  • changed "Sleep Study" to "Sleep"
  • removed "Harmonized" from "Harmonized Demographic/Clinical Data" for use in Study::Expected Data Category (continue to use "Unharmonized Demographic/Clinical Data" for Datasets and DataFiles)
• Add enums to enum_clinicalDataSourceType:
  • Wearable
• Add enums to enum_studyCode:
  • APAP21
  • ASPIRE
  • ARC-DS
  • DS-HPBM
  • EACH-DS
  • HomeGrown
  • MOSAIC-DS
  • TOPS-DS
• Make the following slots multivalued = true:
  • studyWebsite
  • dataType
  • otherRepository
• Add enum_Unknown to range for ageAtFirstParticipantEngagement and ageAtBiospecimenCollection
• Update description of Family ID to specify not required for Proband-only individuals
• Clarify in slot descriptions that Parent and Collection info is required for each Sample, and that each Parent and Collection must also be listed as a Sample
• change title of guidMapped from "GUIDs Mapped?" to "GUID Mapped"

Known Bugs:

Auto-generation of the documentation site for this model is currently broken and still shows the previous release (v4.0.0). A fix is in progress.

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Full Changelog: v4.0.0...v5.0.0

Release v4.0.0

Major Updates:

• Combined multiple schema YAML files into a single file
• Added ER diagram to documentation
• Deprecated custom Pydantic validator in favor of using native LinkML validator

Minor Updates:

• Added new enums to existing ranges (e.g. study codes for new cohorts)
• Added new slots, mostly to Dataset class (e.g. DOI)
• Made existing slots multivalued

What's Changed

• Doc and readme updates by @madanucd in #191
• About and versions pages fix by @madanucd in #192
• excluding previous versions implementation by @madanucd in #193
• doc_template file by @madanucd in #194
• Updated some slot descriptions to be clearer for contributors by @lopierra in #198
• NA and other minor error handling by @madanucd in #199
• add AADSC and OPTimal to enum_studyCode by @lopierra in #201
• Create slack-test.txt by @lopierra in #202
• Handling difference charter encodings and multivalue slot updates by @madanucd in #205
• Proposed changes to Study metadata by @lopierra in #208
• update isHarmonized, add datasetManifestLocation to Dataset by @lopierra in #216
• pydantic model udpates by @madanucd in #217
• 2024 12 30 pl by @lopierra in #239
• Issue 115 235 formating documentation by @madanucd in #262
• Fix erdiagram auto doc by @madanucd in #266
• Pl 2025 05 15 by @lopierra in #269
• add DSpostBFmulti to enum_studyCode by @lopierra in #271
• add Epigenomics to enum_dataCategory by @lopierra in #272
• deprecate custom validator by @madanucd in #273

Full Changelog: v3.0.0...v4.0.0_rc

Release v3.0.0

Highlights:

• Model updates since previous release (v2.2.0):
  • Updated Assay component to include latest Virtual Biorepository model
  • Updated Study component and added new Dataset and DatasetManifest components to support new Study/Dataset pages in Data Hub
  • Inclusion of over 25 new slots
  • 5 new enumerations: EnumClinicalDataSourceType, EnumDataCategory, EnumGuidType, EnumParticipantLifespanStage, EnumResearchDomain
• Validation: Streamlines data cleaning and validation via the command line (CLI), allowing users to specify the data type and file path. The CLI reads, cleans, and validates data using LinkML-defined models for robust validation. For more details, use validate-data --help.
  • Error Reporting and Logging: Summarizes errors by type for quick corrective action and saves validation results for traceability and analysis.

 

What's Changed

• add hasStudy to Condition by @lopierra in #118
• re-generating jsonld and csv from yaml (no changes to model) by @lopierra in #122
• update hakonarson study name; add containerAvailability by @lopierra in #153
• 2024 01 15 updates by @lopierra in #154
• Add new slots and enums to Study; add new class Dataset by @lopierra in #163
• Last updates before major release by @lopierra in #181
• gh pages uml fix by @madanucd in #183
   
  Full Changelog: v2.2.0...v3.0.0_rc1

v2.2.0

This is the final release of the data model for the Spring 2023 INCLUDE Data Hub release

What's Changed

• Domain specific yamls by @putmantime in #81
• Schematic transform refactor by @putmantime in #82
• Updates to Study, Participant, and Assay YAMLs by @lopierra in #89
• updates to Participant & Study, mostly adding enums, meanings & descriptions by @lopierra in #96
• add constant variable that finds the project root by @putmantime in #105
• Pl final march edits by @lopierra in #106
• combine condition+measure source text & age; capitalize HPO, MONDO, MAXO by @lopierra in #111
• add Global to slot names and descriptions for INCLUDE internal IDs by @lopierra in #112
• fixed a couple more capitalizations of ID by @lopierra in #113

Full Changelog: v2.1.0...v2.2.0

Release v2.1.0

• Improvements to the readability of the schema by separating concerns to multiple YAML files
• Refator of the Schematic JSONLD transformer to use the LinkML Schemaview tool and support multiple YAML Files

Release v2.0.0

Initial release. Semantic versioning begins at v2 because this model is replacing previous model in different implementation.