diff --git a/docs/reference/phenotype-data.md b/docs/reference/phenotype-data.md
index f0a26c60..4403aa29 100644
--- a/docs/reference/phenotype-data.md
+++ b/docs/reference/phenotype-data.md
@@ -37,8 +37,17 @@ The goals of this document are:
### Different shapes of phenotype data
+Phenotype data comes in many different shapes and forms. In the following, we will describe some of the most common features of such data:
+
+- [Pre-coordinated](#precoordinated)
+- [Post-coordinated](#postcoordinated)
+- [Standardised/non-standardized](#standardized)
+- [Quantitative/qualitative](#qual)
+
+#### Pre-coordinated
+
Pre-coordinated phenotype data is popular in the clinical domain, where a lot of observations are taken by a clinician and recorded as "phenotypic abnormalities" with the goal of eventual diagnosis.
[Phenopackets](http://phenopackets.org/) such as the one below are an emerging standard to capture and sharing disease and phenotype information. Phenotypic features in particular are captured as so called "pre-coordinated phenotype terms" such as "Attenuation of retinal blood vessels" (HP:0007843). "Pre-coordinated" in this context means that the various [aspects of the phenotype term](../reference/core-concepts.md), such as the _bearer_ ("retinal blood vessels") and the _characteristic_ ("Attenuation", or "thinning/narrowing"), and the _modifier_ (in the case of HPO terms, simply _abnormal_), are combined ("coordinated") into a single term.
@@ -299,19 +308,23 @@ Pre-coordinated phenotype data is popular in the clinical domain, where a lot of
}
```
-#### Pre-coordinated
-
-- HPO during clinical phenotyping
-- Mouse phenotypes
+Apart from clinical diagnostics, pre-coordinated phenotype terms are used in many other contexts such as model organism research (e.g. [IMPC](https://www.mousephenotype.org/)) or the curation of [Genome Wide Association Studies](https://www.ebi.ac.uk/gwas/)).
#### Post-coordinated
-- Trait + modifier
-- Bearer only
-- Characteristics + modifier + bearer
-- Complex bearers
+Post-coordinated phenotype curation simply means that the different constituents of phenotype (characteristic, bearer, modifier etc) are captured individually.
+This has certain advantages.
+For example, the phenotype space is _enormous_, as you can measure variations in many observable charactertics from chemical entities present in the blood, the microbiome to a host of morphological and developmental abnormalities. Instead of having individual (controlled vocabulary) terms for `increased level of X`, `decreased level X`, `abnormal level of X`, `increased level of X in blood` for thousands of chemical compounds synthesized by the human body, you just have "increased level", "blood" and all the chemical compounds.
+
+There are at least three flavours of post-coordinated phenotype curation prevalent in the biomedical domain, four if you count quantified phenotypes:
+
+- [Trait + modifier](#traitmodifier)
+- [Bearer only](#beareronly)
+- [Characteristics + modifier + bearer](#charmodbear)
+
+Note that bearers can be arbitrarily complex.
diff --git a/mkdocs.yaml b/mkdocs.yaml
index 9e5ca9a1..ca0441a5 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -1,5 +1,58 @@
site_name: Unified Phenotype Ontology
-theme: readthedocs
+theme:
+ name: material
+ icon:
+ edit: material/pencil
+ features:
+ - content.action.edit
+ - navigation.tabs
+ - navigation.sections
+ - toc.integrate
+ - navigation.top
+ - search.suggest
+ - search.highlight
+ - content.tabs.link
+ - content.code.annotation
+ - content.code.copy
+ - content.code.select
+plugins:
+ - search
+markdown_extensions:
+ - toc:
+ permalink: true
+ - pymdownx.superfences:
+ custom_fences:
+ - name: mermaid
+ class: mermaid
+ format: !!python/name:pymdownx.superfences.fence_div_format
+ - pymdownx.inlinehilite
+ - pymdownx.snippets
+ - pymdownx.tabbed
+ - pymdownx.critic
+ - pymdownx.caret
+ - pymdownx.details
+ - pymdownx.keys
+ - pymdownx.mark
+ - pymdownx.tilde
+ - attr_list
+ - md_in_html
+ - pymdownx.highlight:
+ anchor_linenums: true
+ - admonition
+ - pymdownx.arithmatex:
+ generic: true
+ - footnotes
+ - attr_list
+ - md_in_html
+ - tables
+
+extra_javascript:
+ - https://unpkg.com/mermaid@8.5.1/dist/mermaid.min.js
+
+site_url: https://obophenotype.github.io/upheno/
+repo_url: https://github.com/obophenotype/upheno/
+edit_uri: edit/master/docs/
+
nav:
- Getting started: index.md
- Cite: cite.md