rst remake and link typo

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

@@ -230,7 +230,7 @@ $defs:
         type: string
         pattern: "^10.(\\d+)(\\.\\d+)*/[\\w\\-\\.]+"
         description: >-
-          A `Digital Object Identifier <https://www.doi.org/the-identifier/what-is-a-doi/>_`
+          A `Digital Object Identifier <https://www.doi.org/the-identifier/what-is-a-doi/>`_
           for the document.
       pmid:
         type: integer

schema/core-im/def/Agent.rst

@@ -47,4 +47,4 @@ Some Agent attributes are inherited from :ref:`Entity`.
    *  - subtype
       - string
       - 0..1
-      - A specific type of agent the Agent object represents. Must be one of {person, organization, software}
+      - A specific type of agent the Agent object represents. Must be one of {person, organization, software}.

schema/core-im/def/Contribution.rst

@@ -59,4 +59,4 @@ Some Contribution attributes are inherited from :ref:`Activity`.
    *  - activityType
       - :ref:`Coding`
       - 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).)
+      - 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)).

schema/core-im/def/DataSet.rst

@@ -39,7 +39,7 @@ Some DataSet attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -59,7 +59,7 @@ Some DataSet attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).
    *  - type
       - string
       - 1..1

schema/core-im/def/Document.rst

@@ -39,7 +39,7 @@ Some Document attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -59,7 +59,7 @@ Some Document attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).
    *  - type
       - string
       - 1..1
@@ -79,8 +79,8 @@ Some Document attributes are inherited from :ref:`InformationEntity`.
    *  - doi
       - string
       - 0..1
-      - A `Digital Object Identifier <https://www.doi.org/the-identifier/what-is-a-doi/>_` for the document.
+      - A `Digital Object Identifier <https://www.doi.org/the-identifier/what-is-a-doi/>`_ for the document.
    *  - pmid
       - integer
       - 0..1
-      - A `PubMed unique identifier <https://en.wikipedia.org/wiki/PubMed#PubMed_identifier>`_.
+      - A `PubMed unique identifier <https://en.wikipedia.org/wiki/PubMed#PubMed_identifier>`_ for the document.

schema/core-im/def/EvidenceLine.rst

@@ -39,7 +39,7 @@ Some EvidenceLine attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -59,7 +59,7 @@ Some EvidenceLine attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).
    *  - type
       - string
       - 1..1

schema/core-im/def/InformationEntity.rst

@@ -1,6 +1,6 @@
 **Computational Definition**
 
-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.
+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.
 
 **Information Model**
 
@@ -43,7 +43,7 @@ Some InformationEntity attributes are inherited from :ref:`Entity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -63,4 +63,4 @@ Some InformationEntity attributes are inherited from :ref:`Entity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).

schema/core-im/def/Method.rst

@@ -1,6 +1,6 @@
 **Computational Definition**
 
-A set of instructions that specify how to achieve some objective. These may vary in the level of detail they provide, and in scientific research, these include things like experimental protocols, study designs, data analysis parameters,  curation guidelines, cohort selection criteria, and rule sets.
+A set of instructions that specify how to achieve some objective. 
 
 **Information Model**
 
@@ -39,7 +39,7 @@ Some Method attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -59,16 +59,16 @@ Some Method attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).
    *  - type
       - string
       - 1..1
       - MUST be "Method".
    *  - subtype
       - :ref:`Coding`
       - 0..1
-      - A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol')
+      - A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').
    *  - license
       - string
       - 0..1
-      - A specific license that dictates legal permissions for how a method can be used (by whom, where, for what purposes, with what additional requirements, etc.)
+      - A specific license that dictates legal permissions for how a method can be used (by whom, where, for what purposes, with what additional requirements, etc.).

schema/core-im/def/Statement.rst

@@ -43,7 +43,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -63,7 +63,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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).
    *  - subject
       - object
       - 1..1
@@ -92,7 +92,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
       - string
       - 0..1
       - A natural-language expression of what a Statement asserts to be true.
-   *  - subjectClassification
+   *  - classification
       - :ref:`Coding` | :ref:`IRI`
       - 0..1
       - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.

schema/core-im/def/StudyGroup.rst

@@ -1,6 +1,6 @@
 **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.
+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.
 
 **Information Model**
 

schema/core-im/def/StudyResult.rst

@@ -43,7 +43,7 @@ Some StudyResult attributes are inherited from :ref:`InformationEntity`.
    *  - specifiedBy
       - :ref:`Method` | :ref:`IRI`
       - 0..1
-      - A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).
+      - A specification that describes all or part of the process that led to creation of the Information Entity 
    *  - contributions
       - :ref:`Contribution`
       - 0..m
@@ -59,7 +59,7 @@ Some StudyResult attributes are inherited from :ref:`InformationEntity`.
    *  - recordMetadata
       - :ref:`RecordMetadata`
       - 0..1
-      - Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.
+      - 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:`DomainEntity` | :ref:`Coding` | :ref:`IRI`
       - 0..1

schema/core-im/json/Agent

@@ -49,7 +49,7 @@
       },
       "subtype": {
          "type": "string",
-         "description": "A specific type of agent the Agent object represents. Must be one of {person, organization, software}",
+         "description": "A specific type of agent the Agent object represents. Must be one of {person, organization, software}.",
          "enum": [
             "person",
             "organization",

schema/core-im/json/Contribution

@@ -75,7 +75,7 @@
       },
       "activityType": {
          "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/Coding",
-         "description": "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).)"
+         "description": "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))."
       }
    },
    "required": [

schema/core-im/json/DataSet

@@ -46,8 +46,8 @@
                "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI"
             }
          ],
-         "description": "A specification that describes all or part of the process that led to creation of the Information Entity (e.g. a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification).",
-         "$comment": "Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "description": "A specification that describes all or part of the process that led to creation of the Information Entity ",
+         "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "contributions": {
          "type": "array",
@@ -77,7 +77,7 @@
          "type": "string",
          "format": "datetime",
          "description": "Indicates when the information content expressed in the Information Entity was generated.",
-         "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a written sentence in an article, or json object in a data stream) would live in a RecordMetadata object attached to the Information Entity)."
+         "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a  table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)."
       },
       "derivedFrom": {
          "type": "array",
@@ -108,7 +108,7 @@
       },
       "recordMetadata": {
          "$ref": "/ga4gh/schema/gks-core-im/1.0.0-ballot.2024.08.1/core-im/json/RecordMetadata",
-         "description": "Provenance metadata about a specific concrete encoding/serialization of information (e.g. as a record in a specific data/knowledgebase, or an online digital resource) - as opposed to provenance about the abstract information content a record carries.",
+         "description": "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).",
          "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status."
       },
       "type": {