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matentzn committed Apr 1, 2024
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9 changes: 4 additions & 5 deletions docs/reference/core-concepts.md
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## Traits and phenotypes - the Conceptual model
## Traits and phenotypes - the Conceptual model of the uPheno framework

### Overview

Here, we discuss the core concepts of the computational phenotype model underpinning the uPheno effort.

![uPheno model](../images/upheno_model.png)

### Table of contents

- [General characteristic](#characteristics)
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<a id="bearer"></a>

### Bearer of Biological Characteristics
### The Bearer (of Biological Characteristics)

!!! example "Bearer"

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1. **Molecular Structure as a Bearer:**
- **Example:** A DNA molecule can be the bearer of the characteristic 'sequence length'.
- **Explanation:** The length of the DNA sequence is a property of the DNA molecule itself, making the molecule the bearer of this characteristic.
1. **Genetic Trait as a Bearer:**
- **Example:** A fruit fly (Drosophila melanogaster) can be the bearer of a genetic trait like eye color.
- **Explanation:** The organism (fruit fly) carries the genetic information that determines eye color, making it the bearer of this specific trait.

In each example, the **"bearer"** is the entity that has, carries, or exhibits a particular biological characteristic. This concept is fundamental in biology and bioinformatics for linking specific traits, qualities, or features to the entities that possess them, thereby enabling a clearer understanding and categorization of biological diversity and functions.

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4 changes: 2 additions & 2 deletions mkdocs.yaml
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- Using uPheno in Data Analysis: tutorials/analysis.md
- Using uPheno in Curation: tutorials/curation.md
- Reference:
- Core concepts: reference/core-concepts.md
- Phenotype data: reference/phenotype-data.md
- Core concepts of phenotype data: reference/core-concepts.md
- Phenotype data in practice: reference/phenotype-data.md
- Integrating phenotype data with the uPheno framework: reference/data-integration.md
- EQ modelling:
- Overview of EQ modelling: reference/eq.md
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