update MSP & make EvidLines heritable

ga4gh · Nov 7, 2024 · 222073d · 222073d
1 parent b65309d
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diff --git a/.requirements.txt b/.requirements.txt
@@ -2,5 +2,5 @@ pytest
 jsonschema
 referencing
 pyyaml
-ga4gh.gks.metaschema==0.3.0b14
+ga4gh.gks.metaschema==0.3.0b16
 pre-commit
diff --git a/schema/gks-core/def/Activity.rst b/schema/gks-core/def/Activity.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 An action or set of actions performed by an agent, that occurs over a period of time. Activities may use, generate, modify, move, or destroy one or more entities.
@@ -19,46 +17,69 @@ Some Activity attributes are inherited from :ref:`Entity`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - type
+      - 
       - string
       - 1..1
       - The name of the class that is instantiated by a data object representing the Entity.
    *  - label
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - subtype
+      - 
       - :ref:`MappableConcept`
       - 0..1
       - A specific type of activity the Activity instance represents.
    *  - date
+      - 
       - string
       - 0..1
       - The date that the Activity was completed.
    *  - performedBy
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Agent`
       - 0..m
       - An Agent who participated in executing the Activity.
    *  - specifiedBy
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Method`
       - 0..m
       - A method that was followed in performing an Activity, that describes how it was executed.
diff --git a/schema/gks-core/def/Agent.rst b/schema/gks-core/def/Agent.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 An autonomous actor (person, organization, or software agent) that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity.
@@ -19,38 +17,53 @@ Some Agent attributes are inherited from :ref:`Entity`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "Agent".
    *  - name
+      - 
       - string
       - 0..1
       - The given name of the Agent.
    *  - subtype
+      - 
       - string
       - 0..1
       - A specific type of agent the Agent object represents. Must be one of {person, organization, software}.
diff --git a/schema/gks-core/def/Characteristic.rst b/schema/gks-core/def/Characteristic.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 An object holding a name-value pair used to describe a trait or role of an individual member of a StudyGroup.
@@ -19,26 +17,35 @@ Some Characteristic attributes are inherited from :ref:`Element`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - name
+      - 
       - string
       - 1..1
       - The type of the trait  or role described by the trait (e.g. 'ethnicity', 'sex', 'age', 'disease status').
    *  - value
+      - 
       - string
       - 1..1
       - The specific value(s) that the indicated traitor role holds in all population members (e.g. 'east asian', 'female', 'adolescent', 'cancer').
    *  - valueOperator
+      - 
       - boolean
       - 0..1
       - An operation that defines how to logically interpret a set of more than one Characteristic values ('AND', 'OR', 'NOT')
diff --git a/schema/gks-core/def/Code.rst b/schema/gks-core/def/Code.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 Indicates that the value is taken from a set of controlled strings defined elsewhere. Technically, a code is restricted to a string which has at least one character and no leading or trailing whitespace, and where there is no whitespace other than single spaces in the contents.
diff --git a/schema/gks-core/def/Coding.rst b/schema/gks-core/def/Coding.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 A structured representation of a code for a defined concept in a terminology or code system.
@@ -19,30 +17,40 @@ Some Coding attributes are inherited from :ref:`Element`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - label
+      - 
       - string
       - 0..1
       - The human-readable name for the coded concept, as defined by the code system.
    *  - system
+      - 
       - string
       - 1..1
       - The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology).
    *  - systemVersion
+      - 
       - string
       - 0..1
       - Version of the terminology or code system that provided the code.
    *  - code
+      - 
       - :ref:`code`
       - 1..1
       - A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the Sequence Ontology code for 'gene').
diff --git a/schema/gks-core/def/ConceptMapping.rst b/schema/gks-core/def/ConceptMapping.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 A mapping to a concept in a terminology or code system.
@@ -19,22 +17,30 @@ Some ConceptMapping attributes are inherited from :ref:`Element`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - coding
+      - 
       - :ref:`Coding`
       - 1..1
       - A structured representation of a code for a defined concept in a terminology or code system.
    *  - relation
+      - 
       - string
       - 1..1
       - A mapping relation between concepts as defined by the Simple Knowledge Organization System (SKOS).
diff --git a/schema/gks-core/def/Contribution.rst b/schema/gks-core/def/Contribution.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 An action taken by an agent in contributing to the creation, modification, assessment, or deprecation of a particular entity (e.g. a Statement, EvidenceLine, DataSet, Publication, etc.)
@@ -19,50 +17,74 @@ Some Contribution attributes are inherited from :ref:`Activity`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - subtype
+      - 
       - :ref:`MappableConcept`
       - 0..1
       - A specific type of activity the Activity instance represents.
    *  - date
+      - 
       - string
       - 0..1
       - The date that the Activity was completed.
    *  - specifiedBy
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Method`
       - 0..m
       - A method that was followed in performing an Activity, that describes how it was executed.
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "Contribution".
    *  - contributor
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Agent`
       - 1..1
       - The agent that made the contribution.
    *  - activityType
+      - 
       - :ref:`MappableConcept`
       - 0..1
       - The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, data generator, etc. . Values of this property may be framed as activities or as contribution roles (e.g. using terms from the Contribution Role Ontology (CRO)).