Add time_reference and timeref_epochset composite types to V_gamma

schemas/V_gamma/CURIE_lookups_meta.json

@@ -3,7 +3,7 @@
     "$id": "https://did-schema.example.org/meta/CURIE_lookups_meta.json",
     "title": "CURIE Registry for DID/NDI V_gamma",
     "description": "Registry mapping CURIE prefixes (used in ontology_term.node values and in field-level _ontology._node annotations) to their authoritative URI base and metadata. Consumer tooling uses this file to expand a CURIE such as 'uberon:0002436' into the full URI 'http://purl.obolibrary.org/obo/UBERON_0002436'. Prefixes are matched case-insensitively; by convention prefixes are written in lowercase inside documents and annotations.",
-    "_format_version": "1.0.0",
+    "_format_version": "1.1.0",
     "_prefixes": {
         "iao": {
             "_label": "Information Artifact Ontology",
@@ -33,6 +33,20 @@
             "_approximate": false,
             "_documentation": "Anatomical ontology for the developing mouse."
         },
+        "mmusdv": {
+            "_label": "Mouse Developmental Stages",
+            "_uri_base": "http://purl.obolibrary.org/obo/MmusDv_",
+            "_uri_style": "obo_underscore",
+            "_approximate": false,
+            "_documentation": "Life-cycle / developmental-stage ontology for Mus musculus. Useful inside ontology_term values and in time_reference values whose referent_kind == 'ontology_stage' (e.g., 'mmusdv:0000037' postnatal stage)."
+        },
+        "hsapdv": {
+            "_label": "Human Developmental Stages",
+            "_uri_base": "http://purl.obolibrary.org/obo/HsapDv_",
+            "_uri_style": "obo_underscore",
+            "_approximate": false,
+            "_documentation": "Life-cycle / developmental-stage ontology for Homo sapiens. Useful for time_reference values whose referent_kind == 'ontology_stage'."
+        },
         "ncit": {
             "_label": "NCI Thesaurus",
             "_uri_base": "http://purl.obolibrary.org/obo/NCIT_",

schemas/V_gamma/did_schema_meta.json

@@ -2,7 +2,7 @@
     "$schema": "http://json-schema.org/draft-07/schema#",
     "$id": "https://did-schema.example.org/V_gamma/did_schema_meta.json",
     "title": "DID/NDI Schema Meta-Schema (V_gamma)",
-    "description": "Validates the structure of DID/NDI schema files for V_gamma. V_gamma introduces named composite types 'duration', 'ontology_term', 'volume', 'mass', 'length', 'voltage', 'current', and 'frequency', and a redesigned field-level '_ontology' annotation shape with keys '_node' (CURIE) and '_name' (label); the CURIE prefix is resolved against CURIE_lookups_meta.json. The six SI-dimensioned types share the same sub-field layout as 'duration' (a canonical-unit double, 'approximate' boolean, 'source_unit' char, 'source_value' double); only the canonical sub-field name and the allowed source units differ. NAMING CONVENTION: property names that are standard JSON Schema keywords (type, $schema, $id, $ref, $defs, properties, required, items, enum, const, pattern, description, etc.) are used as-is. Every property name introduced by this schema system — i.e. not part of the JSON Schema vocabulary — is prefixed with an underscore (_) to distinguish custom extensions from standard vocabulary.",
+    "description": "Validates the structure of DID/NDI schema files for V_gamma. V_gamma introduces named composite types 'duration', 'ontology_term', 'volume', 'mass', 'length', 'voltage', 'current', 'frequency', 'timeref_epochset', and 'time_reference', and a redesigned field-level '_ontology' annotation shape with keys '_node' (CURIE) and '_name' (label); the CURIE prefix is resolved against CURIE_lookups_meta.json. The seven SI-dimensioned types share the same sub-field layout as 'duration' (a canonical-unit double, 'approximate' boolean, 'source_unit' char, 'source_value' double); only the canonical sub-field name and the allowed source units differ. The 'time_reference' type expresses a time value as an offset from a chosen origin (a depended-on document, an acquisition-clock epoch, a UTC wall-clock timestamp, or an ontology-anchored stage); 'timeref_epochset' is the four-tuple sub-composite that names an acquisition-clock origin. NAMING CONVENTION: property names that are standard JSON Schema keywords (type, $schema, $id, $ref, $defs, properties, required, items, enum, const, pattern, description, etc.) are used as-is. Every property name introduced by this schema system — i.e. not part of the JSON Schema vocabulary — is prefixed with an underscore (_) to distinguish custom extensions from standard vocabulary.",
     "type": "object",
     "required": [
         "_classname",
@@ -215,7 +215,9 @@
                         "length",
                         "voltage",
                         "current",
-                        "frequency"
+                        "frequency",
+                        "timeref_epochset",
+                        "time_reference"
                     ],
                     "description": "Data type of the field. Uses the standard JSON Schema keyword 'type'; values are NDI-specific."
                 },

schemas/V_gamma/session_occurrence.json

@@ -0,0 +1,60 @@
+{
+    "_classname": "session_occurrence",
+    "_class_version": "1.0.0",
+    "_maturity_level": "work_in_progress",
+    "_superclasses": [
+        {
+            "_classname": "base",
+            "_schema": "$NDISCHEMAPATH/base/schema.json"
+        }
+    ],
+    "_depends_on": [
+        {
+            "_name": "session_id",
+            "_mustBeNonEmpty": true,
+            "_documentation": "The session document this occurrence describes. Cascading delete: when the session is deleted, this occurrence is deleted too.",
+            "_must_refer_to_document_class": "session"
+        },
+        {
+            "_name": "started_at_referent_id",
+            "_mustBeNonEmpty": false,
+            "_documentation": "Document that anchors started_at when started_at.referent_kind == 'document'. Empty otherwise.",
+            "_must_refer_to_document_class": ""
+        },
+        {
+            "_name": "ended_at_referent_id",
+            "_mustBeNonEmpty": false,
+            "_documentation": "Document that anchors ended_at when ended_at.referent_kind == 'document'. Empty otherwise.",
+            "_must_refer_to_document_class": ""
+        }
+    ],
+    "_file": [],
+    "_fields": [
+        {
+            "_name": "started_at",
+            "type": "time_reference",
+            "_blank_value": null,
+            "_default_value": null,
+            "_mustBeNonEmpty": false,
+            "_mustBeScalar": true,
+            "_mustNotHaveNaN": true,
+            "_queryable": true,
+            "_ontology": null,
+            "_documentation": "When the session started. Optional; leave null when start time is not recorded. Use referent_kind == 'unknown' to assert that the start time is intentionally not knowable rather than merely missing.",
+            "_constraints": {}
+        },
+        {
+            "_name": "ended_at",
+            "type": "time_reference",
+            "_blank_value": null,
+            "_default_value": null,
+            "_mustBeNonEmpty": false,
+            "_mustBeScalar": true,
+            "_mustNotHaveNaN": true,
+            "_queryable": true,
+            "_ontology": null,
+            "_documentation": "When the session ended. Same shape and conventions as started_at.",
+            "_constraints": {}
+        }
+    ]
+}

schemas/V_gamma/subject_birth_event.json

@@ -0,0 +1,35 @@
+{
+    "_classname": "subject_birth_event",
+    "_class_version": "1.0.0",
+    "_maturity_level": "work_in_progress",
+    "_superclasses": [
+        {
+            "_classname": "base",
+            "_schema": "$NDISCHEMAPATH/base/schema.json"
+        }
+    ],
+    "_depends_on": [
+        {
+            "_name": "subject_id",
+            "_mustBeNonEmpty": true,
+            "_documentation": "The subject document whose birth (or birth-equivalent origin) this document records. Cascading delete: when the subject tag document is deleted, this event is deleted too.",
+            "_must_refer_to_document_class": "subject"
+        }
+    ],
+    "_file": [],
+    "_fields": [
+        {
+            "_name": "occurred_at",
+            "type": "time_reference",
+            "_blank_value": null,
+            "_default_value": null,
+            "_mustBeNonEmpty": true,
+            "_mustBeScalar": true,
+            "_mustNotHaveNaN": true,
+            "_queryable": true,
+            "_ontology": null,
+            "_documentation": "When the subject was born, expressed as a time_reference. For wild-caught animals or subjects without recorded DOB, use referent_kind == 'unknown'; for stage-only knowledge use referent_kind == 'ontology_stage' with a developmental-stage CURIE (e.g., 'mmusdv:0000037' postnatal stage). Document-kind references are unusual here but permitted (e.g., birth witnessed during another logged event).",
+            "_constraints": {}
+        }
+    ]
+}

schemas/V_gamma/treatment.json

@@ -1,6 +1,6 @@
 {
     "_classname": "treatment",
-    "_class_version": "2.0.0",
+    "_class_version": "2.1.0",
     "_maturity_level": "work_in_progress",
     "_superclasses": [
         {
@@ -26,6 +26,12 @@
             "_mustBeNonEmpty": false,
             "_documentation": "The document ID of the protocol associated with this treatment.",
             "_must_refer_to_document_class": ""
+        },
+        {
+            "_name": "administered_at_referent_id",
+            "_mustBeNonEmpty": false,
+            "_documentation": "Document whose start, end, or midpoint is the origin for administered_at. Required when administered_at.referent_kind == 'document'; left empty otherwise. Cascading delete: if the referenced document is deleted, this treatment document is deleted too.",
+            "_must_refer_to_document_class": ""
         }
     ],
     "_file": [],
@@ -68,6 +74,19 @@
             "_ontology": null,
             "_documentation": "The character string value associated with the treatment.",
             "_constraints": {}
+        },
+        {
+            "_name": "administered_at",
+            "type": "time_reference",
+            "_blank_value": null,
+            "_default_value": null,
+            "_mustBeNonEmpty": false,
+            "_mustBeScalar": true,
+            "_mustNotHaveNaN": true,
+            "_queryable": true,
+            "_ontology": null,
+            "_documentation": "When the treatment was administered, expressed as a time_reference. Optional — leave null when administration time is not recorded. When referent_kind == 'document', depends_on_name must equal 'administered_at_referent_id'.",
+            "_constraints": {}
         }
     ]
 }