Overview

Teaching: 0 min
Exercises: 90 min

Questions

• What is Darwin Core?

• What is a Darwin Core Archive?

• Why do people use Darwin Core for their data?

• What are the required Darwin Core terms for sharing to OBIS?

Objectives

• Understand the purpose of Darwin Core.

• Understand how to map data to Darwin Core.

• Plan for mapping to Darwin Core.

Darwin Core - A global community of data sharing and integration

Darwin Core is a data standard to mobilize and share biodiversity data. Over the years, the Darwin Core standard has expanded to enable exchange and sharing of diverse types of biological observations from citizen scientists, ecological monitoring, eDNA, animal telemetry, taxonomic treatments, and many others. Darwin Core is applicable to any observation of an organism (scientific name, OTU, or other methods of defining a species) at a particular place and time. In Darwin Core this is an occurrence. To learn more about the foundations of Darwin Core read Wieczorek et al. 2012.

Demonstrated Use of Darwin Core

The power of Darwin Core is most evident in the data aggregators that harvest data using that standard. The one we will refer to most frequently in this workshop is the Ocean Biodiversity Information System (learn more about OBIS). Another prominent one is the Global Biodiversity Information Facility (learn more about GBIF). It’s also used by the Atlas of Living Australia, iDigBio, among others.

Darwin Core Archives

Darwin Core Archives are what OBIS and GBIF harvest into their systems. Fortunately the software created and maintained by GBIF, the Integrated Publishing Toolkit, produces Darwin Core Archives for us. Darwin Core Archives are pretty simple. It’s a zipped folder containing the data (one or several files depending on how many extensions you use), an Ecological Metadata Language (EML) XML file, and a meta.xml file that describes what’s in the zipped folder.

Exercise

Challenge: Download this Darwin Core Archive and examine what’s in it. Did you find anything unusual or that you don’t understand what it is?

Solution

 dwca-tpwd_harc_texasaransasbay_bagseine-v2.3
 |-- eml.xml
 |-- event.txt
 |-- extendedmeasurementorfact.txt
 |-- meta.xml
 |-- occurrence.txt

Darwin Core Mapping

Now that we understand a bit more about why Darwin Core was created and how it is used today we can begin the work of mapping data to the standard. The key resource when mapping data to Darwin Core is the Darwin Core Quick Reference Guide. This document provides an easy-to-read reference of the currently recommended terms for the Darwin Core standard. There are a lot of terms there and you won’t use them all for every dataset (or even use them all on any dataset) but as you apply the standard to more datasets you’ll become more familiar with the terms.

Tip

If your raw column headers are Darwin Core terms verbatim then you can skip this step! Next time you plan data collection use the standard DwC term headers!

Exercise

Challenge: Find the matching Darwin Core term for these column headers.

1. SAMPLE_DATE (example data: 09-MAR-21 05.45.00.000000000 PM)
2. lat (example data: 32.6560)
3. depth_m (example data: 6 meters)
4. COMMON_NAME (example data: staghorn coral)
5. percent_cover (example data: 15)
6. COUNT (example data: 2 Females)

Solution

1. eventDate
2. decimalLatitude
3. minimumDepthInMeters and maximumDepthInMeters
4. vernacularName
5. organismQuantity and organismQuantityType
6. This one is tricky- it’s two terms combined and will need to be split. indvidualCount and sex

Tip

To make the mapping step easier on yourself, we recommend starting a mapping document/spreadsheet (or document it as a comment in your script). List out all of your column headers in one column and document the appropriate Dawin Core term(s) in a second column. For example:

my term	DwC term
lat	decimalLatitude
date	eventDate
species	scientificName

What are the required Darwin Core terms for publishing to OBIS?

When doing your mapping some required information may be missing. Below are the Darwin Core terms that are required to share your data to OBIS plus a few that are needed for GBIF.

What other terms should be considered?

While these terms are not required for publishing data to OBIS, they are extremely helpful for downstream users because without them the data are less useful for future analyses. For instance, depth is a crucial piece of information for marine observations, but it is not always included. For the most part the ones listed below are not going to be sitting there in the data, so you’ll have to determine what the values should be and add them in. Really try your hardest to include them if you can.

Other than these specific terms, work through the data that you have and try to crosswalk it to the Darwin Core terms that match best.

Exercise

Challenge: Create some crosswalk notes for your dataset.

Compare your data files to the table(s) above to devise a plan to crosswalk your data columns into the DwC terms.

Key Points

• Darwin Core isn’t difficult to apply, it just takes a little bit of time.

• Using Darwin Core allows datasets from across projects, organizations, and countries to be integrated together.

• Applying certain general principles to the data will make it easier to map to Darwin Core.

• Implementing Darwin Core makes data FAIR-er and means becoming part of a community of people working together to understand species no matter where they work or are based.