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updated build documentation
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anandhi-iyappan committed Nov 8, 2024
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# 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)

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2 changes: 1 addition & 1 deletion docs/schema_markdown/Individual_sex.md
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# 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)

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2 changes: 1 addition & 1 deletion docs/schema_markdown/Ontology.md
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* [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).

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2 changes: 1 addition & 1 deletion docs/schema_markdown/geographical_region_term.md
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# 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)

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4 changes: 2 additions & 2 deletions docs/schema_markdown/index.md
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* [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)
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* [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)
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74 changes: 64 additions & 10 deletions docs/schema_markdown/individual.md
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# 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|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|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 |

2 changes: 1 addition & 1 deletion docs/schema_markdown/sex.md
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# 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)

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