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