Introduction to Darwin Core


Teaching: 0 min
Exercises: 90 min
  • 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?

  • 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.


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?


 |-- 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.


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!


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

  1. SAMPLE_DATE (example data: 09-MAR-21 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)


  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


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.

Darwin Core Term Definition Comment Example
occurrenceID An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. To construct a globally unique identifier for each occurrence you can usually concatenate station + date + scientific name (or something similar) but you’ll need to check this is unique for each row in your data. It is preferred to use the fields that are least likely to change in the future for this. For ways to check the uniqueness of your occurrenceIDs see the QA / QC section of the workshop. Station_95_Date_09JAN1997:14:35:00.000_Atractosteus_spatula
basisOfRecord The specific nature of the data record. Pick from these controlled vocabulary terms: HumanObservation, MachineObservation, MaterialSample, PreservedSpecimen, LivingSpecimen, FossilSpecimen, MaterialEntity, Event, Taxon, Occurrence, MaterialCitation HumanObservation
scientificName The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the identificationQualifier term. Note that cf., aff., etc. need to be parsed out to the identificationQualifier term. For a more thorough review of identificationQualifier see this paper. Atractosteus spatula
scientificNameID An identifier for the nomenclatural (not taxonomic) details of a scientific name. Must be a WoRMS LSID for sharing to OBIS. Note that the numbers at the end are the AphiaID from WoRMS.
eventDate The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. Must follow ISO 8601. See more information on dates in the Data Cleaning section of the workshop. 2009-02-20T08:40Z
decimalLatitude The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive. For OBIS and GBIF the required geodeticDatum is WGS84. Uncertainty around the geographic center of a Location (e.g. when sampling event was a transect) can be recorded in coordinateUncertaintyInMeters. See more information on coordinates in the Data Cleaning section of the workshop. -41.0983423
decimalLongitude The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive For OBIS and GBIF the required geodeticDatum is WGS84. See more information on coordinates in the Data Cleaning section of the workshop. -121.1761111
occurrenceStatus A statement about the presence or absence of a Taxon at a Location. For OBIS, only valid values are present and absent. present
countryCode The standard code for the country in which the location occurs. Use an ISO 3166-1-alpha-2 country code. Not required for OBIS but GBIF prefers to have this for their system. For international waters, leave blank. US, MX, CA
kingdom The full scientific name of the kingdom in which the taxon is classified. Not required for OBIS but GBIF needs this to disambiguate scientific names that are the same but in different kingdoms. Animalia
geodeticDatum The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based. Must be WGS84 for data shared to OBIS and GBIF but it’s best to state explicitly that it is. WGS84

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.

Darwin Core Term Definition Comment Example
minimumDepthInMeters The lesser depth of a range of depth below the local surface, in meters. There isn’t a single depth value so even if you have a single value you’ll put that in both minimum and maximum depth fields. 0.1
maximumDepthInMeters The greater depth of a range of depth below the local surface, in meters. For observations above sea level consider using minimumDistanceAboveSurfaceInMeters and maximumDistanceAboveSurfaceInMeters 10.5
coordinateUncertaintyInMeters The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term There’s always uncertainty associated with locations. Recording the uncertainty is crucial for downstream analyses. 15
samplingProtocol The names of, references to, or descriptions of the methods or protocols used during an Event.   Bag Seine
taxonRank The taxonomic rank of the most specific name in the scientificName. Also helps with disambiguation of scientific names. Species
organismQuantity A number or enumeration value for the quantity of organisms. OBIS also likes to see this in the Extended Measurement or Fact extension. 2.6
organismQuantityType The type of quantification system used for the quantity of organisms.   Relative Abundance
datasetName The name identifying the data set from which the record was derived.   TPWD HARC Texas Coastal Fisheries Aransas Bag Bay Seine
dataGeneralizations Actions taken to make the shared data less specific or complete than in its original form. Suggests that alternative data of higher quality may be available on request. This veers somewhat into the realm of metadata and will not be applicable to all datasets but if the data were modified such as due to sensitive species then it’s important to note that for future users. Coordinates generalized from original GPS coordinates to the nearest half degree grid cell
informationWithheld Additional information that exists, but that has not been shared in the given record. Also useful if the data have been modified this way for sensitive species or for other reasons. location information not given for endangered species
institutionCode The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.   TPWD

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.


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.