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obophenotype · Mar 30, 2024 · 8fc9889 · 8fc9889
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diff --git a/docs/reference/data-integration.md b/docs/reference/data-integration.md
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 ## Integrating phenotype data using the uPheno framework
 
+### Prerequisites
+
+- [Familiarise yourself with the core concepts](../reference/core-concepts.md)
+- [Familiarise the basics of phenotype data](../reference/phenotype-data.md)
 
 ### Level 1 integration: Data
 
+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).
+
+Integrating all kinds of phenotype data into the "uPheno framework" is a complex process which we will break down in the following.
+
+
 
 ### Level 2 integration: Knowledge
 

diff --git a/docs/reference/phenotype-data.md b/docs/reference/phenotype-data.md
@@ -379,13 +379,13 @@ Examples:
 
 Lets break down the second to last row:
 
-- ZFA:0009290 (glutamatergic neuron)
-- BFO:0000050 (part of): a relation used to connect the hair cell to the structure its part of)
-- ZFA:0000008 (brain)
+- ZFA:0009290 (glutamatergic neuron): The primary entity whose characteristic is being observed
+- BFO:0000050 (part of): a relation used to connect the hair cell to the structure its part of
+- ZFA:0000008 (brain): the location of the primary entity being observed
 - PATO:0040043 (increased proportionality to): the modified characteristic being observed.
-- abnormal (the change modifier)
-- ZFA:0009276 (GABAergic neuron)
-- ZFA:0000008 (brain)
+- abnormal: the change modifier (note: not an ontology term)
+- ZFA:0009276 (GABAergic neuron): the secondary entity being observed in relation to which the characteristic is measured
+- ZFA:0000008 (brain): the location of the secondary entity
 - The interested reader may look at an integrated version of that huge post-coordinated expression [here (brain increased proportionality to glutamatergic neuron GABAergic neuron brain, abnormal - ZP:0141834)](https://www.ebi.ac.uk/ols4/ontologies/zp/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FZP_0141834).
 
 Data was obtained [from ZFIN](https://zfin.org/downloads) (Phenotype of Zebrafish Genes) on the 30.03.2023 and simplified for illustration.