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docs/reference/traits_and_phenotypes.md

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+# Traits and phenotypes - the Conceptual model
+
+

docs/tutorials/curation.md

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+# Using OBA and uPheno in data curation
+
+Authors:
+
+- [James McLaughlin]()
+- [Nicolas Matentzoglu](https://orcid.org/0000-0002-7356-1779)
+
+Last update: 27.03.2024.
+
+## Overview
+
+Phenotyping is, in essence, the process of recording the observable characteristics, or phenotypic profile, of an organism. 
+There are many use cases for doing this task: clinicians have to record a patient's phenotypic profile to facilitate more accurate diagnosis. 
+Researchers have to record phenotypic profiles of model organisms to characterise them to assess interventions (genetic or drug or otherwise). 
+Curators that seek to build a knowledge base which contains associations between phenotypes and other data types need to extract information about phenotypes from often unstructured data sources. 
+
+All of these are different processes, but the essence is the same: a set of observable characteristics has to be recorded using terms from a controlled vocabulary.
+
+There are different schools about how to record phenotypes in a structured manner. 
+Quantified phenotypes can be recorded using either a trait in combination with a measurement datum (“head circumference”, “35 cm”) or a qualified term expressing “phenotypic change” (“increased head circumference”). 
+Furthermore, we can express phenotype terms as “pre-coordinated” terms, like “increased head circumference” or a “post-coordinated expression”, like “head”, “circumference”, “increased”). In the following, we will describe the different concepts and categories around phenotype data, and provide an introduction on how to best use them.
+
+## Core concepts
+
+<!-- Add figure with all core components from OBA poster -->
+
+- Phenotypic characteristic
+- Bearer
+- Biological attribute
+- Phenotypic abnormality
+- Disease
+
+### (Phenotypic) Characteristic
+
+"Characteristics" or "qualities" refer to an inherent or distinguishing characteristic or attribute of something or someone.
+It represents a feature that defines the nature of an object, organism, or entity and can be used to describe, compare, and categorize different things.
+Characteristics can be either qualitative (such as color, texture, or taste) or quantitative (such as height, weight, or age).
+
+Some of the most widely use qualities can be seen in the following tables
+
+| quality | description | example |
+| ------- | ----------- | ------- |
+| Length ([PATO:0000051](http://purl.obolibrary.org/obo/PATO_0000051)) | A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. | |
+| Mass ([PATO:0000128](http://purl.obolibrary.org/obo/PATO_0000128)) | A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. | |
+| Level ([PATO:0000128](http://purl.obolibrary.org/obo/PATO_0000128)) | A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. | |
+| Morphology ([PATO:0000051](http://purl.obolibrary.org/obo/PATO_0000051)) | A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. | |
+
+
+
+### Biological Trait
+
+### Phenotypic abnormality
+
+- Nature of "comparators" in the notion of a phenotypic abnormality.
+- In database curation you are effectively de-contextualising the phenotype term, which means you loose the original comparator.
+- normal changed wildtype comparator
+
+### Disease
+
+## Important relationships wrt to phenotype data
+
+- inheres in / characteristic of
+- bearer of
+
+## Examples of phenotype data
+
+1. gene to phenotype associations
+1. gene to disease assocations
+1. phenotype - phenotype semantic similarity
+1. Quantified trait data (QTL etc)
+
+## Types of phenotype data
+
+- Precoordinated phenotype
+- Post-coordinated phenotype
+- Attribute-measurement
+