Update data-integration.md

docs/reference/data-integration.md

@@ -9,11 +9,43 @@
 
 Before we get started, let's remind ourselves of the basic structure of phenotype data.
 
-![Core concepts](../images/core_concepts.png)
 
-_Characteristics_ (A) and _bearers_ of characteristics (B) are the core constituents of traits/biological attributes (C). _Phenotypes_ are comprised of trait terms (C) combined with a modifier (D). Species-specific phenotypes (F), including _phenotypic abnormalities_ defined in the Human Phenotype Ontology (HPO) are feature of diseases (G). Measurements (H), such as assays, quantify or qualify (measure) traits (C).
+
+<figure markdown="span">
+  ![Core concepts](../images/core_concepts.png){ width="600" }
+  <figcaption>Figure 1: _Characteristics_ (A) and _bearers_ of characteristics (B) are the core constituents of traits/biological attributes (C). _Phenotypes_ are comprised of trait terms (C) combined with a modifier (D). Species-specific phenotypes (F), including _phenotypic abnormalities_ defined in the Human Phenotype Ontology (HPO) are feature of diseases (G). Measurements (H), such as assays, quantify or qualify (measure) traits (C).</figcaption>
+</figure>
+
+
+
+Phenotype data can be integrated to various degrees into the uPheno framework. The goal of integration is always the same:
+
+Associate phenotype data records with pre-coordinated trait and/or phenotype terms.
+
+!!! note "The goal of integration is always the same:"
+
+    Associate phenotype data records with pre-coordinated trait and/or phenotype terms.
+
+!!! warning
+
+    The question of how to turn phenotype data records into [associations](https://biolink.github.io/biolink-model/association-examples-with-qualifiers/),
+    for example for use in a knowledge graph, is out of scope for this document. We are only concerned with how the phenotype described by the data record
+    can be integrated.
+
+The "uPheno framework" is a loose term that describes a family of techniques and ontologies. In terms of ontologies, it includes (among others):
+
+- The Phenotype And Trait Ontology (PATO) for the representation of general characteristics (the fact that its called "Phenotype and Trait" is a bit misleading, as it contains a lot of characteristics that are widely used also for environmental data, like `weight` and `amount`)
+- The Ontology of Biological Attributes (OBA) for the representation of biological traits
+- The Unified Phenotype Ontology (uPheno) for the representation of phenotypic change
+
+As can be seen in Figure 1 at the top of this document, all of these are interconnected:
+
+1. Biological traits in OBA are a direct extension of the "general" characteristics described in PATO.
+1. Terms describing phenotypic change (such as in)
 
 Integrating all kinds of phenotype data into the "uPheno framework" is a complex process which we will break down in the following.
+We will look at a [range of different kinds of phenotype data](../reference/phenotype-data.md), which is probably not exhaustive.
+