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 and 
providing critical feedback. The idea of standardising WGS data specifically
was raised by Eveline. Christopher critical comments were helpful for
developing the presentation further and making the importance clearer.

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

::: {#refs}
:::