presentation.qmd

---
title: "FAIR data for a better understanding of fungal epidemiology"
author:
  - name: "[Sibbe Bakker](https://orcid.org/0009-0001-0696-1684)"
    affiliation: Genetics
  - name: "Anna Fensel"
    affiliation: AI & Data science
format: 
    revealjs:
        csl: diabetologia.csl
        theme: aspar.scss
        standalone: true
        embed-resources: true
        navigation-mode: vertical
        controls-layout: bottom-right
title-slide-attributes:
    data-background-size: cover
    data-background-image: inclusions/blurred-asper.jpg
    data-background-opacity: "0.5"
date: "2024-01-15"
bibliography: "BibDataBase.bib"
---

# Relivance of fungi {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

::: incremental

* Fungi are a diverse taxa.

* A lot good things
    - Fermentation.
    - Plant health.
    - Nutrient cycling.
* A lot of chaos too
    - Food insecurity.
    - Toxicity of food.
    - Diseases in animals.
:::

## The WHO priority pathogens {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

![The priority fungal pathogens identified by
the WHO [@worldhealthorganizationwhoWHOFungalPriority2022]](
inclusions/who-priorities.png)

::: notes

Highlight what these fungi are, how important are they and where?

:::

---

## A closer look at _A. fumigatus_ {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

<!-- Why are we looking here? Because the genetics department does a lot of
work with it -->

::: columns

::: {.column width="60%"}

* Why? Because the WUR has [expertise]{.alert} on _A. fumigatus_.
* It is [imporant]{.alert} for Dutch public health. <br> _Due to the large tulip sector here._

:::

::: {.column width="40%"}

![Conidia of _A. fumigatus_ [@OneHealthFungal2019]](inclusions/aspergillus-fromNBK54998.jpg)

:::

:::


# The knowledge gap {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

## What we need to do {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

> Being able to track the evolution of fungal pathogens.

## How do we do it? {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

phylogeography.

## Phylogeography using nextstrain {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018]. An example:

![Overview of the spread of west-nile in the USA from 
[nextstrain](https://nextstrain.org/narratives/twenty-years-of-WNV?n=3).
](inclusions/west-nile.png)


## Bridging the gap {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

> This has not yet been done because $\dots$

::: incremental

* Whole genome sequences (WGS) of fungi are [upcoming]{.alert}: [@fanComparativeGenomeSequence2020; @lofgrenPangenomeAspergillusFumigatus2022; @rhodesPopulationGenomicsConfirms2022]

* Existing solutions [don't consider]{.alert} WGS data.

* Standardisation is [not a focus]{.alert} in the _A. fumigatus_ domain.

:::

# Method {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

::: incremental

1. Harmonise [existent]{.alert} metadata.

2. Develop a system for harmonising [new]{.alert} metadata.

3. Analyse [phylogeography]{.alert} of *A. fumigatus*.

4. Generalise the workflow to [other fungi]{.alert}.

:::

::: notes

Why me? I have the domain knowledge and network, and the technical ability
and will power to pull it off.

:::


# Outlook {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

::: incremental

* A new method of data collection.

* Existing solutions, like [globalfungi](https://globalfungi.com/) only focus
on the _ITS_ sequence.

* The solution [could be generalised]{.alert} to plant epidemiology also.

:::

# References {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

## More information {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

* [`sibbe.bakker@wur.nl`](mailto:sibbe.bakker@wur.nl)

* Read my [pre-proposal](https://bookdown.org/sibbe_l_bakker/pre-proposal/)

* I thank Eveline Snelders and Christopher Wandabwa for reviewing my work.

## Cited works {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}

::: {#refs}
:::