eDNA Data Management Course

Foundations

Overview

Replace this text with a brief, welcoming introduction to the lesson. Describe the problem or workflow it addresses and why it is relevant to biodiversity data practitioners.

Learning outcomes

By the end of this lesson, you will be able to:

Outcome one — use an active verb (e.g. construct, apply, interpret).
Outcome two.
Outcome three.
Outcome four.
Outcome five.

Prerequisites

Before starting this lesson, you should be comfortable with:

Item one (link to resource if possible)
Item two

If you are new to R, we recommend working through the Introduction to R episode in the setup materials first.

Episodes

#	Episode	Description	Time
1	Introduction to eDNA & Biodiversity Data	One sentence description.	~60 min
2	OBIS & Darwin Core: What They Are and Why They Matter	One sentence description.	~60 min
3	Data Standards for eDNA: DwC-A, MIxS, and the DNA Derived Data Extension	One sentence description.	~60 min
4	Structuring Your First eDNA Dataset	One sentence description.	~60 min
5	Metadata: Field Sampling, Protocols, and Documentation	One sentence description.	~60 min

Setup

Before the first episode, please complete the Setup instructions. These cover software installation, package installation, and downloading the example dataset.

How to use these materials

These materials can be used for self-paced study or as part of an instructor-led workshop.

Self-paced: Work through each episode in order. Exercises marked 🧪 are for your own practice; there is no submission required.
Instructor-led: Your instructor will guide the pace. Exercises will be worked through together or in small groups.

Tip boxes, challenge boxes, and key-point summaries appear throughout. Take time to read them — they highlight common mistakes and the most important concepts.

Acknowledgements

This lesson was developed for the Ocean Biodiversity Information System (OBIS) training programme.

Lesson design follows the pedagogical framework of The Carpentries, whose Curriculum Development Handbook informed the structure of these materials. Content is original and independent; this is not an official Carpentries lesson.

Maintained by OBIS. Licensed CC BY 4.0.

This lesson was last rendered on 2026-04-14.

--- title: "{{< var lesson.title >}}" subtitle: "{{< var lesson.subtitle >}}" ---  ![](figures/banner.png){fig-alt="A descriptive alt text for the banner image." width=100%} ## Overview  Replace this text with a brief, welcoming introduction to the lesson. Describe the problem or workflow it addresses and why it is relevant to biodiversity data practitioners. ## Learning outcomes By the end of this lesson, you will be able to: - Outcome one — use an active verb (e.g. *construct*, *apply*, *interpret*). - Outcome two. - Outcome three. - Outcome four. - Outcome five. ## Prerequisites ::: {.callout-important icon=false} ## Prerequisites Before starting this lesson, you should be comfortable with: - Item one (link to resource if possible) - Item two If you are new to R, we recommend working through the [Introduction to R episode](setup.qmd) in the setup materials first. ::: ## Episodes ```{r} #| label: episode-table #| echo: false #| results: asis files <- sort(list.files("episodes", pattern = "\\.qmd$", full.names = FALSE)) rows <- lapply(seq_along(files), function(i) { path <- file.path("episodes", files[i]) lines <- readLines(path, n = 20) get_field <- function(field) { line <- grep(paste0("^", field, ":"), lines, value = TRUE)[1] if (is.na(line)) return("NA") trimws(gsub(paste0("^", field, ":\\s*[\"']?|[\"']?$"), "", line)) } data.frame( `#` = i, Episode = sprintf("[%s](%s)", get_field("title"), path), Description = get_field("description"), Time = get_field("time"), check.names = FALSE ) }) knitr::kable(do.call(rbind, rows)) ``` ## Setup Before the first episode, please complete the [Setup instructions](setup.qmd). These cover software installation, package installation, and downloading the example dataset. ## How to use these materials These materials can be used for **self-paced study** or as part of an **instructor-led workshop**. - **Self-paced:** Work through each episode in order. Exercises marked 🧪 are for your own practice; there is no submission required. - **Instructor-led:** Your instructor will guide the pace. Exercises will be worked through together or in small groups. Tip boxes, challenge boxes, and key-point summaries appear throughout. Take time to read them — they highlight common mistakes and the most important concepts. ## Acknowledgements This lesson was developed for the [Ocean Biodiversity Information System (OBIS)](https://obis.org) training programme. Lesson design follows the pedagogical framework of [The Carpentries](https://carpentries.org), whose [Curriculum Development Handbook](https://cdh.carpentries.org) informed the structure of these materials. Content is original and independent; this is not an official Carpentries lesson. Maintained by {{< var maintainer.name >}}. Licensed {{< var license >}}. --- *This lesson was last rendered on `r Sys.Date()`.*