lowercase primitive data types (À la FHIR)

ga4gh · Oct 31, 2024 · a4e2170 · a4e2170
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diff --git a/schema/gks-core/def/Activity.rst b/schema/gks-core/def/Activity.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.

diff --git a/schema/gks-core/def/Agent.rst b/schema/gks-core/def/Agent.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.

diff --git a/schema/gks-core/def/Characteristic.rst b/schema/gks-core/def/Characteristic.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.

diff --git a/schema/gks-core/def/Code.rst b/schema/gks-core/def/Code.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.
@@ -43,6 +37,6 @@ Some Coding attributes are inherited from :ref:`Element`.
       - 0..1
       - Version of the terminology or code system that provided the code.
    *  - code
-      - :ref:`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 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.

diff --git a/schema/gks-core/def/Contribution.rst b/schema/gks-core/def/Contribution.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    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.)

diff --git a/schema/gks-core/def/DataSet.rst b/schema/gks-core/def/DataSet.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A collection of related data items or records that are organized together in a common format or structure, to enable their computational manipulation as a unit.
@@ -43,15 +37,15 @@ Some DataSet attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/Document.rst b/schema/gks-core/def/Document.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A collection of information, usually in a text-based or graphic human-readable form, intended to be read and understood together as a whole.
@@ -43,15 +37,15 @@ Some Document attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/DomainEntity.rst b/schema/gks-core/def/DomainEntity.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 An Entity that is specific to a particular biomedical domain such as disease, therapeutics, or genes. Domain Entities are considered as 'concept-level' entities, as opposed to particular instances. e.g. 'Lung Cancer', not 'patient123's lung cancer'. Or 'Erlotinib', not the particular doses given to a patient on a specific occasion.

diff --git a/schema/gks-core/def/Element.rst b/schema/gks-core/def/Element.rst
@@ -1,8 +1,3 @@
-
-.. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 The base definition for all identifiable data objects.

diff --git a/schema/gks-core/def/Entity.rst b/schema/gks-core/def/Entity.rst
@@ -1,8 +1,3 @@
-
-.. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 Anything that exists, has existed, or will exist.

diff --git a/schema/gks-core/def/EvidenceLine.rst b/schema/gks-core/def/EvidenceLine.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 An independent, evidence-based argument that may support or refute the validity of a specific proposition. The strength and direction of this argument is based on an interpretation of one or more pieces of information as evidence for or against the target proposition.
@@ -43,15 +37,15 @@ Some EvidenceLine attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/Extension.rst b/schema/gks-core/def/Extension.rst
@@ -1,8 +1,3 @@
-
-.. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 The Extension class provides entities with a means to include additional attributes that are outside of the specified standard but needed by a given content provider or system implementer. These extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.

diff --git a/schema/gks-core/def/InformationEntity.rst b/schema/gks-core/def/InformationEntity.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 An abstract (non-physical) entity that is about something - representing the underlying 'information content' conveyed by physical or digital information artifacts like books, web pages, data tables, or photographs.
@@ -47,15 +41,15 @@ Some InformationEntity attributes are inherited from :ref:`Entity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/MappableConcept.rst b/schema/gks-core/def/MappableConcept.rst
@@ -1,8 +1,3 @@
-
-.. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A concept label that may be mapped to one or more :ref:`Codings <Coding>`.

diff --git a/schema/gks-core/def/Method.rst b/schema/gks-core/def/Method.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A set of instructions that specify how to achieve some objective.
@@ -43,15 +37,15 @@ Some Method attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/Proposition.rst b/schema/gks-core/def/Proposition.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 The abstract entity representing a possible fact that may be put forth as true, or subjected to an evidence-based assessment, by a Statement. As abstract entities, their identity and existence are independent of space and time, and whether they are ever asserted to be true by some agent. Propositions may be used in two contexts; (1) by Statements that assert them to be true or false, or describe the overall level of confidence/evidence for or against them; (2) by Evidence Lines that report the direction and strength of an evidence-based argument for the Proposition.

diff --git a/schema/gks-core/def/RecordMetadata.rst b/schema/gks-core/def/RecordMetadata.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A reusable structure that encapsulates provenance metadata about a serialized data record or object in a particular dataset (as opposed to provenance about the real world entity this record or object represents).

diff --git a/schema/gks-core/def/Statement.rst b/schema/gks-core/def/Statement.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A claim of purported truth as made by a particular agent, on a particular occasion. Statements may be used to simply put forth a possible fact (i.e. a 'proposition') as true, or to provide a more nuanced assessment of the level of confidence or evidence supporting a particular proposition.
@@ -47,15 +41,15 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored

diff --git a/schema/gks-core/def/StudyGroup.rst b/schema/gks-core/def/StudyGroup.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A collection of individuals or specimens from the same taxonomic class, selected for analysis in a scientific study based on their exhibiting one or more common characteristics  (e.g. species, race, age, gender, disease state, income). May be referred to as a 'cohort' or 'population' in specific research settings.

diff --git a/schema/gks-core/def/StudyResult.rst b/schema/gks-core/def/StudyResult.rst
@@ -1,9 +1,3 @@
-
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 A collection of data items from a single study that pertain to a particular subject or experimental unit in the study, along with optional provenance information describing how these data items were generated.
@@ -47,15 +41,15 @@ Some StudyResult attributes are inherited from :ref:`InformationEntity`.
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - specifiedBy
-      - :ref:`Method` | :ref:`IRI`
+      - :ref:`Method` | :ref:`iriReference`
       - 0..1
       - A specification that describes all or part of the process that led to creation of the Information Entity
    *  - contributions
       - :ref:`Contribution`
       - 0..m
       - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.
    *  - reportedIn
-      - :ref:`Document` | :ref:`IRI`
+      - :ref:`Document` | :ref:`iriReference`
       - 0..m
       - A document in which the the Information Entity is reported.
    *  - dateAuthored
@@ -67,7 +61,7 @@ Some StudyResult attributes are inherited from :ref:`InformationEntity`.
       - 0..1
       - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).
    *  - focus
-      - :ref:`Entity` | :ref:`MappableConcept` | :ref:`IRI`
+      - :ref:`Entity` | :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
       - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD.
    *  - sourceDataSet

diff --git a/schema/gks-core/def/date.rst b/schema/gks-core/def/date.rst
@@ -0,0 +1,3 @@
+**Computational Definition**
+
+A string is valid against this format if it represents a date in the following format: YYYY-MM-DD.
diff --git a/schema/gks-core/def/datetime.rst b/schema/gks-core/def/datetime.rst
@@ -0,0 +1,3 @@
+**Computational Definition**
+
+A string is valid against this format if it represents a date-time in the following format: YYYY:MM::DDThh:mm:ss.sTZD.
diff --git a/schema/gks-core/def/IRI.rst → schema/gks-core/def/iriReference.rst b/schema/gks-core/def/IRI.rst → schema/gks-core/def/iriReference.rst
@@ -1,8 +1,3 @@
-
-.. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-
-
 **Computational Definition**
 
 An IRI Reference (either an IRI or a relative-reference), according to `RFC3986 section 4.1 <https://datatracker.ietf.org/doc/html/rfc3986#section-4.1>`_ and `RFC3987 section 2.1 <https://datatracker.ietf.org/doc/html/rfc3987#section-2.1>`_. MAY be a JSON Pointer as an IRI fragment, as described by `RFC6901 section 6 <https://datatracker.ietf.org/doc/html/rfc6901#section-6>`_.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		Computational Definition

		A string is valid against this format if it represents a date in the following format: YYYY-MM-DD.