ghga-de · anandhi-iyappan · Nov 8, 2024 · Nov 8, 2024 · Nov 8, 2024
diff --git a/docs/schema_markdown/Individual_geographical_region_term.md b/docs/schema_markdown/Individual_geographical_region_term.md
@@ -2,7 +2,7 @@
 # Slot: geographical_region_term
 
 
-The geographical region where the Individual is located.
+The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
 
 URI: [GHGA:Individual_geographical_region_term](https://w3id.org/GHGA/Individual_geographical_region_term)
 

diff --git a/docs/schema_markdown/Individual_sex.md b/docs/schema_markdown/Individual_sex.md
@@ -2,7 +2,7 @@
 # Slot: sex
 
 
-The genotypic sex of the Individual (e.g., female).
+The biological sex of the Individual (e.g., female).
 
 URI: [GHGA:Individual_sex](https://w3id.org/GHGA/Individual_sex)
 

diff --git a/docs/schema_markdown/Ontology.md b/docs/schema_markdown/Ontology.md
@@ -32,7 +32,7 @@ URI: [GHGA:ontology](https://w3id.org/GHGA/ontology)
  * [diagnosis_ids](diagnosis_ids.md) - One or more diagnoses that the entity is associated with at the time of retrieval from the organism. The diagnosis is captured using a code from ICD-10 (WHO version). Please restrict the ICD code to the chapter letter and two digits for the main diagnosis (e.g., E10, C01).
  * [diagnosis_terms](diagnosis_terms.md) - The ICD-10 terms corresponding to the ICD-10 codes (e.g., Type 1 diabetes mellitus, Malignant neoplasm of base of tongue).
  * [geographical_region_id](geographical_region_id.md) - The geographical region where the Individual is located.
- * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located.
+ * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
  * [phenotypic_features_ids](phenotypic_features_ids.md) - The corresponding ID to the HPO vocabulary (e.g., HP:0002732, HP:0012735, HP:0002615).
  * [phenotypic_features_terms](phenotypic_features_terms.md) - The phenotypic feature concepts that the entity is associated with at the time of retrieval from the organism. The Phenotypic Feature is captured using a concept from the Human Phenotype Ontology (e.g., Lymph node hypoplasia, Cough, Hypotension).
 

diff --git a/docs/schema_markdown/geographical_region_term.md b/docs/schema_markdown/geographical_region_term.md
@@ -2,7 +2,7 @@
 # Slot: geographical_region_term
 
 
-The geographical region where the Individual is located.
+The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
 
 URI: [GHGA:geographical_region_term](https://w3id.org/GHGA/geographical_region_term)
 

diff --git a/docs/schema_markdown/index.md b/docs/schema_markdown/index.md
@@ -164,7 +164,7 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi
      * [ResearchDataFile➞format](ResearchDataFile_format.md) - The file format of the Research Data File (e.g., FASTQ, uBAM, FASTA).
  * [geographical_region_id](geographical_region_id.md) - The geographical region where the Individual is located.
      * [Individual➞geographical_region_id](Individual_geographical_region_id.md)
- * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located.
+ * [geographical_region_term](geographical_region_term.md) - The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
      * [Individual➞geographical_region_term](Individual_geographical_region_term.md)
  * [included_in_submission](included_in_submission.md) - Whether a File is included in the Submission or not.
      * [File➞included_in_submission](File_included_in_submission.md)
@@ -238,7 +238,7 @@ The submission centric metadata schema for the German Human Genome-Phenome Archi
      * [ExperimentMethod➞sequencing_layout](ExperimentMethod_sequencing_layout.md)
  * [sequencing_read_length](sequencing_read_length.md) - Length of sequencing reads (e.g., long or short or actual number of the read length).
      * [ExperimentMethod➞sequencing_read_length](ExperimentMethod_sequencing_read_length.md)
- * [sex](sex.md) - The genotypic sex of the Individual (e.g., female).
+ * [sex](sex.md) - The biological sex of the Individual (e.g., female).
      * [Individual➞sex](Individual_sex.md)
  * [software_versions](software_versions.md) - key/value pairs where key corresponds to a software name and value corresponds to a version descriptor (e.g., `salmon` = '1.3.0', `trim-galore` = '0.6.6', `bedtools` = '2.29.2').
      * [AnalysisMethod➞software_versions](AnalysisMethod_software_versions.md)

diff --git a/docs/schema_markdown/individual.md b/docs/schema_markdown/individual.md
@@ -1,23 +1,77 @@
 
-# Slot: individual
+# Class: Individual
 
 
-The Individual associated with an entity.
+An Individual is a Person who is participating in a Study.
 
-URI: [GHGA:individual](https://w3id.org/GHGA/individual)
+URI: [GHGA:Individual](https://w3id.org/GHGA/Individual)
 
 
-## Domain and Range
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[IndividualSupportingFile],[IndividualSupportingFile]-%20individual%201..1>[Individual&#124;phenotypic_features_terms:string%20*;phenotypic_features_ids:string%20*;diagnosis_ids:string%20*;diagnosis_terms:string%20*;sex:IndividualSexEnum;geographical_region_term:string%20%3F;geographical_region_id:string%20%3F;ancestry_terms:string%20*;ancestry_ids:string%20*;alias:string],[Sample]-%20individual%201..1>[Individual],[Submission]++-%20individuals%201..*>[Individual],[Sample]-%20individual(i)%200..1>[Individual],[IndividualSupportingFile]-%20individual(i)%200..1>[Individual],[Submission]-%20individuals(i)%200..*>[Individual],[Individual]uses%20-.->[IdentifiedByAliasMixin],[IdentifiedByAliasMixin])](https://yuml.me/diagram/nofunky;dir:TB/class/[Submission],[Sample],[IndividualSupportingFile],[IndividualSupportingFile]-%20individual%201..1>[Individual&#124;phenotypic_features_terms:string%20*;phenotypic_features_ids:string%20*;diagnosis_ids:string%20*;diagnosis_terms:string%20*;sex:IndividualSexEnum;geographical_region_term:string%20%3F;geographical_region_id:string%20%3F;ancestry_terms:string%20*;ancestry_ids:string%20*;alias:string],[Sample]-%20individual%201..1>[Individual],[Submission]++-%20individuals%201..*>[Individual],[Sample]-%20individual(i)%200..1>[Individual],[IndividualSupportingFile]-%20individual(i)%200..1>[Individual],[Submission]-%20individuals(i)%200..*>[Individual],[Individual]uses%20-.->[IdentifiedByAliasMixin],[IdentifiedByAliasMixin])
 
-None &#8594;  <sub>0..1</sub> [Individual](Individual.md)
+## Uses Mixin
 
-## Parents
+ *  mixin: [IdentifiedByAliasMixin](IdentifiedByAliasMixin.md)
 
+## Referenced by Class
 
-## Children
+ *  **[IndividualSupportingFile](IndividualSupportingFile.md)** *[IndividualSupportingFile➞individual](IndividualSupportingFile_individual.md)*  <sub>1..1</sub>  **[Individual](Individual.md)**
+ *  **[Sample](Sample.md)** *[Sample➞individual](Sample_individual.md)*  <sub>1..1</sub>  **[Individual](Individual.md)**
+ *  **[Submission](Submission.md)** *[Submission➞individuals](Submission_individuals.md)*  <sub>1..\*</sub>  **[Individual](Individual.md)**
+ *  **None** *[individual](individual.md)*  <sub>0..1</sub>  **[Individual](Individual.md)**
+ *  **None** *[individuals](individuals.md)*  <sub>0..\*</sub>  **[Individual](Individual.md)**
 
- *  [IndividualSupportingFile➞individual](IndividualSupportingFile_individual.md)
- *  [Sample➞individual](Sample_individual.md)
+## Attributes
 
-## Used by
+
+### Own
+
+ * [Individual➞phenotypic_features_terms](Individual_phenotypic_features_terms.md)  <sub>0..\*</sub>
+     * Description: The phenotypic feature concepts that the entity is associated with at the time of retrieval from the organism. The Phenotypic Feature is captured using a concept from the Human Phenotype Ontology (e.g., Lymph node hypoplasia, Cough, Hypotension).
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞phenotypic_features_ids](Individual_phenotypic_features_ids.md)  <sub>0..\*</sub>
+     * Description: The corresponding ID to the HPO vocabulary (e.g., HP:0002732, HP:0012735, HP:0002615).
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞diagnosis_ids](Individual_diagnosis_ids.md)  <sub>0..\*</sub>
+     * Description: One or more diagnoses that the entity is associated with at the time of retrieval from the organism. The diagnosis is captured using a code from ICD-10 (WHO version). Please restrict the ICD code to the chapter letter and two digits for the main diagnosis (e.g., E10, C01).
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞diagnosis_terms](Individual_diagnosis_terms.md)  <sub>0..\*</sub>
+     * Description: The ICD-10 terms corresponding to the ICD-10 codes (e.g., Type 1 diabetes mellitus, Malignant neoplasm of base of tongue).
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞sex](Individual_sex.md)  <sub>1..1</sub>
+     * Description: The biological sex of the Individual (e.g., female).
+     * Range: [IndividualSexEnum](IndividualSexEnum.md)
+ * [Individual➞geographical_region_term](Individual_geographical_region_term.md)  <sub>0..1</sub>
+     * Description: The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞geographical_region_id](Individual_geographical_region_id.md)  <sub>0..1</sub>
+     * Description: The geographical region where the Individual is located.
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞ancestry_terms](Individual_ancestry_terms.md)  <sub>0..\*</sub>
+     * Description: A person's descent or lineage from a population.
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+ * [Individual➞ancestry_ids](Individual_ancestry_ids.md)  <sub>0..\*</sub>
+     * Description: A person's descent or lineage from a population.
+     * Range: [String](types/String.md)
+     * in subsets: (ontology)
+
+### Mixed in from IdentifiedByAliasMixin:
+
+ * [IdentifiedByAliasMixin➞alias](IdentifiedByAliasMixin_alias.md)  <sub>1..1</sub>
+     * Description: The alias for an entity at the time of submission.
+     * Range: [String](types/String.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | subject |
+|  | | patient |
 
diff --git a/docs/schema_markdown/sex.md b/docs/schema_markdown/sex.md
@@ -2,7 +2,7 @@
 # Slot: sex
 
 
-The genotypic sex of the Individual (e.g., female).
+The biological sex of the Individual (e.g., female).
 
 URI: [GHGA:sex](https://w3id.org/GHGA/sex)
 

diff --git a/spreadsheets/ghga_submission_full.xlsx b/spreadsheets/ghga_submission_full.xlsx
diff --git a/src/schema/submission.yaml b/src/schema/submission.yaml
@@ -1301,7 +1301,7 @@ slots:
 
   geographical_region_term:
     description: >-
-      The geographical region where the Individual is located.
+      The geographical region where the Individual is located. The geographical region is captured using a concept from the NCIT "country" class (NCIT:C25464) (e.g., Austria, Germany, Italy).
     in_subset:
       - ontology
     # range: GeographicalRegionEnum
@@ -1315,7 +1315,7 @@ slots:
 
   sex:
     description: >-
-      The genotypic sex of the Individual (e.g., female).
+      The biological sex of the Individual (e.g., female).
     range: IndividualSexEnum
 
   biospecimen_age_at_sampling: