applied maturity property to ALL classes

schema/core-im/core-im-source.yaml

@@ -7,6 +7,7 @@ imports:
 
 $defs:
   Entity:
+    maturity: draft
     description: Anything that exists, has existed, or will exist.
     $comment: >-
       Entity is the root class of the 'gks-common' core information model. All common classes that
@@ -60,6 +61,7 @@ $defs:
 
   DomainEntity:
     inherits: Entity
+    maturity: draft
     description: >-
       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.
@@ -77,6 +79,7 @@ $defs:
 
   InformationEntity:
     inherits: Entity
+    maturity: draft
     description: >-
       An abstract (non-physical) entity that is about something. It represents the abstract 'information content'
       conveyed by physical or digital information artifacts like books, web pages, data tables, or photographs.
@@ -375,9 +378,9 @@ $defs:
           modification, or administrative management of a data record or object.
 
   EvidenceLine:
+    type: object
     inherits: InformationEntity
     maturity: draft
-    type: object
     description: >-
       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
@@ -461,6 +464,7 @@ $defs:
 
   Statement:
     inherits: InformationEntity
+    maturity: draft
     description: >-
       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
@@ -655,9 +659,9 @@ $defs:
       - object
 
   DataSet:
+    type: object
     inherits: InformationEntity
     maturity: draft
-    type: object
     description: >-
       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.
@@ -808,9 +812,9 @@ $defs:
         additionalProperties: true
 
   StudyGroup:
+    type: object
     inherits: Entity
     maturity: draft
-    type: object
     description: >-
       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,

schema/core-im/json/DataSet

@@ -2,8 +2,8 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-core-im/1.x/core-im/json/DataSet",
    "title": "DataSet",
-   "maturity": "draft",
    "type": "object",
+   "maturity": "draft",
    "description": "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.",
    "$comment": "Instances of this class represent a specific version of a given dataset. Examples include the gnomAD version 3.1.2 dataset carrying allele population frequencies, or a specific version of a VCF file that describes variations observed in a particular patient and various annotations made on them, or a SIFT dataset of computational predictions functional impact for a set of variants.",
    "properties": {

schema/core-im/json/EvidenceLine

@@ -2,8 +2,8 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-core-im/1.x/core-im/json/EvidenceLine",
    "title": "EvidenceLine",
-   "maturity": "draft",
    "type": "object",
+   "maturity": "draft",
    "description": "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.",
    "$comment": "Evidence Lines are used to capture various pieces of information (i.e. 'evidence items') that are assessed together as an argument for or against some 'target proposition' - to report the direction (supports or disputes) and strength (e.g. strong, moderate, weak) that the argument is determined to make. For example, the various allele counts and population frequency calculations for the BRCA2 c.8023A>G variant in the ExAC database are evidence items that may be collectively assessed to build an EvidenceLine making argument of 'moderate' strength that 'supports' a target proposition that the variant is pathogenic for Breast Cancer.\nEvidence Lines are flexible with respect to the granularity of arguments they support, and the scope of evidence items they can collectively assess. Narrow scoping will bucket available evidence into many, fine-grained Evidence Lines that make the most atomic independently meaningful arguments possible. The ACMG Variant Pathogenicity Interpretation Guidelines are an example of a fairly fine-grained evidence interpretation framework. Broader scoping approaches may organize the same evidence into fewer Evidence Lines that build and assess less atomic arguments based on a wider and more diverse set of evidence items.  For example, CIViC curators assess the strength and direction of evidence items at the level of *all information reported in a publication for a specific study* - which can encompass many different results and evidence types that under more fine-grained interpretation approaches might be split apart and assessed as separate arguments.",
    "properties": {

schema/core-im/json/StudyGroup

@@ -2,8 +2,8 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-core-im/1.x/core-im/json/StudyGroup",
    "title": "StudyGroup",
-   "maturity": "draft",
    "type": "object",
+   "maturity": "draft",
    "description": "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.",
    "$comment": "A Study Group may include all participants in a given study, or specific subsets that are designated based on shared roles or characteristics.",
    "properties": {

schema/data-types/data-types-source.yaml

@@ -87,22 +87,22 @@ $defs:
       - name
       - value
 
-  Code:
+  Code:    
+    type: string
     maturity: draft
     description: >-
       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.
-    type: string
     pattern: '\S+( \S+)*'
     example: ENSG00000139618
 
   IRI:
+    type: string
     maturity: draft
     description: >-
       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>`_.
-    type: string
     format: iri-reference

schema/data-types/json/Code

@@ -2,9 +2,9 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/data-types/json/Code",
    "title": "Code",
+   "type": "string",
    "maturity": "draft",
    "description": "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.",
-   "type": "string",
    "pattern": "\\S+( \\S+)*",
    "example": "ENSG00000139618"
 }

schema/data-types/json/IRI

@@ -2,8 +2,8 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/data-types/json/IRI",
    "title": "IRI",
+   "type": "string",
    "maturity": "draft",
    "description": "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).",
-   "type": "string",
    "format": "iri-reference"
 }

schema/domain-entities/domain-entities-source.yaml

@@ -12,6 +12,7 @@ $defs:
 # Condition related domain entities
   Condition:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
       A disease or other medical disorder.
     oneOf:
@@ -21,10 +22,10 @@ $defs:
 
   TraitSet:
     type: object
+    inherits: Condition
     maturity: draft
     description: >-
       A set of phenotype and/or disease concepts that together constitute a condition.
-    inherits: Condition
     properties:
       type:
         extends: type
@@ -44,8 +45,8 @@ $defs:
 
   Disease:
     type: object
-    maturity: draft
     inherits: Condition
+    maturity: draft
     description: >-
       A particular abnormal condition that negatively affects the structure or function
       of all or part of an organism and is not immediately due to any external injury.
@@ -58,8 +59,8 @@ $defs:
 
   Phenotype:
     type: object
-    maturity: draft
     inherits: Condition
+    maturity: draft
     description: >-
       An observable characteristic or trait of an organism.
     properties:
@@ -71,11 +72,11 @@ $defs:
 
 # Gene related domain entities
   Gene:
+    type: object
     inherits: gks.core-im:DomainEntity
     maturity: draft
     description: >-
       A basic physical and functional unit of heredity.
-    type: object
     properties:
       type:
         type: string
@@ -86,6 +87,7 @@ $defs:
 # Therapeutic Procedures related domain entities
   TherapeuticProcedure:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
       An action or administration of therapeutic agents to produce an effect
       that is intended to alter or stop a pathologic process.
@@ -97,8 +99,8 @@ $defs:
 
   TherapeuticAction:
     type: object
-    maturity: draft
     inherits: TherapeuticProcedure
+    maturity: draft
     description: >-
       A therapeutic action taken that is intended to alter or stop a pathologic
       process.
@@ -111,8 +113,8 @@ $defs:
 
   TherapeuticAgent:
     type: object
-    maturity: draft
     inherits: TherapeuticProcedure
+    maturity: draft
     description: >-
       An administered therapeutic agent that is intended to alter or stop a pathologic
       process.
@@ -125,8 +127,8 @@ $defs:
 
   CombinationTherapy:
     type: object
-    maturity: draft
     inherits: TherapeuticProcedure
+    maturity: draft
     description: >-
       A therapeutic procedure that involves multiple different therapeutic procedures
       performed in combination.
@@ -152,8 +154,8 @@ $defs:
 
   TherapeuticSubstituteGroup:
     type: object
-    maturity: draft
     inherits: TherapeuticProcedure
+    maturity: draft
     description: >-
       A group of therapeutic procedures that may be treated as substitutes for one another.
     properties:

schema/domain-entities/json/Condition

@@ -2,6 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/domain-entities/json/Condition",
    "title": "Condition",
+   "maturity": "draft",
    "description": "A disease or other medical disorder.",
    "oneOf": [
       {

schema/domain-entities/json/Gene

@@ -2,9 +2,9 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/domain-entities/json/Gene",
    "title": "Gene",
+   "type": "object",
    "maturity": "draft",
    "description": "A basic physical and functional unit of heredity.",
-   "type": "object",
    "properties": {
       "id": {
          "type": "string",

schema/domain-entities/json/TherapeuticProcedure

@@ -2,6 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/gks-common/1.x/domain-entities/json/TherapeuticProcedure",
    "title": "TherapeuticProcedure",
+   "maturity": "draft",
    "description": "An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.",
    "oneOf": [
       {