Add links to 2.0 changelog

ChangeLog.md

@@ -1,65 +1,67 @@
 # Change Log  1.6.0-beta (2025-06-06) -> 2.0.0-dev (2026-03-25)
 
-### 1. QEdge Constraints Refactor (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#1-qedge-constraints-refactor))
+### 1. QEdge Constraints Refactor (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#1-qedge-constraints-refactor), [reference doc entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#qedge-))
 - `QEdge.attribute_constraints` and `QEdge.qualifier_constraints`have been removed and replaced with `QEdge.constraints`, which is an object that can contain constraints for `knowledge_level`, `agent_type`, `sources`, `attributes`, and `qualifiers`
 - The new `sources` constraint has ALLOW and DENY constructs with an optional `primary_only` flag
 
-### 2. Add Query.parameters and Response.parameters to contain existing log_level and bypass_cache parameters and add timeout query parameter (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#2-new-queryresponse-parameters))
+### 2. Add Query.parameters and Response.parameters to contain existing log_level and bypass_cache parameters and add timeout query parameter (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#2-new-queryresponse-parameters), [reference doc entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#queryparameters-))
 - Move `Query.log_level` to `Query.parameters.log_level`
 - Move `Query.bypass_cache` to `Query.parameters.bypass_cache`
 - Add `Query.parameters.timeout`
 - Add `Response.parameters` that conveys the same parameters as `Query.parameters`
 - Add HTTP 409 code
 
-### 3. Binding Structure Changes (NodeBinding/EdgeBinding/PathBinding) (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#3-binding-structure-changes-nodeedgepath))
+### 3. Binding Structure Changes (NodeBinding/EdgeBinding/PathBinding) (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#3-binding-structure-changes-nodeedgepath), [PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/546))
 - `<node/edge/path>_bindings` are now minProperties: 1 (i.e. when these fields are present, they MUST contain data)
 - `id` properties renamed to `ids` and is now a list
 - `ids` arrays are minItems: 1 (this property is required)
 - `attributes` property completely removed
 - `query_id` was removed from NodeBinding (obsolete with the current subclassing behavior)
 - Each binding is now an object containing only `ids` (which is a list), instead of a list of objects each with `id` and `attributes`
 
-### 4. KL/AT turned into top-level Edge properties, now required (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#4-klat-turned-into-top-level-edge-properties-now-required))
+### 4. KL/AT turned into top-level Edge properties, now required (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#4-klat-turned-into-top-level-edge-properties-now-required), [PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/536/changes/e21490eca92c7f1bf2df5baa6d3711da30d197f4..9d402d20e3fdee360976857fbdbd57c7f09d1a38))
 - `Edge.knowledge_level` and `Edge.agent_type` are now required `Edge` properties instead of being located within `attributes`
 
-### 5. Add COLLATE option to QNode.set_interpretation enum (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#5-add-collate-option-to-qnodeset_interpretation))
+### 5. Add COLLATE option to QNode.set_interpretation enum (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#5-add-collate-option-to-qnodeset_interpretation), [PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/543/changes))
 
-### 6. null is no longer a valid value in queries and responses (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#6-null-is-no-longer-a-valid-value-in-queries-and-responses))
+### 6. null is no longer a valid value in queries and responses (see [migration guide entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md#6-null-is-no-longer-a-valid-value-in-queries-and-responses), [issue for context](https://github.com/NCATSTranslator/ReasonerAPI/issues/527))
 - Remove `nullable: true/false` designations for all properties. Properties with no data must now be *absent* from TRAPI JSON or an empty array/object if the schema allows, rather than allowed to be present but with a null value. Some field descriptions explicitly state that the empty array/object MUST be used in certain circumstances.
 
-### 7. Many optional properties set to <minItems/minProperties>: 1 
+### 7. Many properties set to <minItems/minProperties>: 1 
 In the following properties, empty lists are no longer permitted to say "no data here". "No data" is now expressed with an absent property:
-- `QueryGraph.nodes`
+- [`QueryGraph.nodes`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#querygraph-): [PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/548)
 - `QueryGraph.edges`
-- `Response.logs`
-- `Message.auxiliary_graphs`
-- `Result.analyses`
-- `Analysis.support_graphs`
-- `QNode.member_ids`
+- [`Response.logs`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#response-)
+- [`Message.auxiliary_graphs`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#message-)
+- [`Result.analyses`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#result-)
+- [`Analysis.support_graphs`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#analysis-)
+- [`QNode.member_ids`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#qnode-)
 - `QNode.constraints`
-- `Edge.qualifiers`
-- `MetaKnowledgeGraph.nodes`
-- `MetaEdge.qualifiers`
-- `MetaQualifier.applicable_values`
-- `RetrievalSource.upstream_resource_ids`
+- [`Edge.qualifiers`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#edge-)
+- [`MetaKnowledgeGraph.nodes`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#metaknowledgegraph-)
+- [`MetaEdge.qualifiers`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#metaedge-)
+- [`MetaQualifier.applicable_values`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#metaqualifier-)
+- [`RetrievalSource.upstream_resource_ids`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#retrievalsource-)
 - `RetrievalSource.source_record_urls`
 
-### 8. Removed AuxiliaryGraph.attributes property
+### 8. Removed AuxiliaryGraph.attributes property ([reference doc entry](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#auxiliarygraph-))
 - It was previously required, but never used and its empty arrays bloated responses. Additional undefined properties are still allowed in AuxiliaryGraph objects.
 
 ### 9. The following properties changed to not-required
-- `Nodes.attributes` (to reduce bloat)
-- `QueryGraph.edges` and `QueryGraph.paths` (to accommodate queries with only nodes) (e.g. "what are the attributes of CURIE:123?")
-- `KnowledgeGraph.edges` (to accommodate queries with only nodes)
-- `Result.analyses` (to accommodate queries with only nodes)
+- [`Nodes.attributes`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#node-) (to reduce bloat)
+- [`QueryGraph.edges`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#querygraph-) and `QueryGraph.paths` (to accommodate queries with only nodes) (e.g. "what are the attributes of CURIE:123?")
+- [`KnowledgeGraph.edges`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#knowledgegraph-) (to accommodate queries with only nodes)
+- [`Result.analyses`](https://github.com/NCATSTranslator/ReasonerAPI/blob/2.0/docs/reference.md#result-) (to accommodate queries with only nodes)
 
-### 10. Analysis is technically allowed to have both edge and path bindings (experimental use)
+### 10. Analysis is technically allowed to have both edge and path bindings (experimental use, [PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/547))
 
-### 11. YAML specification document migrated from OpenAPI 3.0.1 to OpenAPI 3.1.2
+### 11. YAML specification document migrated from OpenAPI 3.0.1 to OpenAPI 3.1.2 ([PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/533))
 - All `example` attributes become `examples` in OpenAPI 3.1.2
 
 ### 12. BaseQueryGraph and BaseAnalysis base classes removed in favor of single QueryGraph and Analysis classes that support both pathfinder and regular queries
 
+[PR](https://github.com/NCATSTranslator/ReasonerAPI/pull/544), but look at 2.0 yaml for up-to-date versions of those sub-schemas. 
+
 =============
 
 

ImplementationGuidance/MigrationGuides/MigrationAndImplementationGuide2-0.md

@@ -434,9 +434,9 @@ Examples:
 * `Message.results` MUST NOT be set to `null` when there is no data. Its description states when it MUST be omitted (when not expected, like a query) VS an empty array (when it is expected and there's no data, like a response).
 
 
-### 7. Many optional properties set to `<minItems/minProperties>: 1`
+### 7. Many properties set to `<minItems/minProperties>: 1`
 
-For many optional array and object properties, `minItems`/`minProperties` was set to 1. This was to reduce bloat (only include the field if there's data). See the Changelog for the full list of changed properties.
+For many array and object properties, `minItems`/`minProperties` was set to 1. This was to reduce bloat (only include the field if there's data). See the Changelog for the full list of changed properties.
 
 
 ### 8. `AuxiliaryGraph.attributes` was removed