Darwin Core, GBIF, and OBIS Reference Guide
Reference Guide: Darwin Core, the Unified GBIF Data Model, and OBIS
This guide introduces the Darwin Core (DwC) standard and its role in supporting data interoperability and publication for Fisheries and Oceans Canada (DFO). It also provides an overview of the Unified GBIF Data Model and the Ocean Biodiversity Information System (OBIS). The focus is on how commonly used fields in DFO fisheries datasets map to Darwin Core terms, enabling integration across internal and external systems.
What is Darwin Core?
Darwin Core is a biodiversity data standard maintained by Biodiversity Information Standards (TDWG). It provides a stable, referenceable set of terms designed to facilitate sharing information about biological diversity — particularly the occurrence of taxa in nature, along with associated metadata like location, time, method, and taxonomy.
Darwin Core is intentionally broad, supporting data from natural history collections, ecological surveys, tagging programs, and more.
Darwin Core as a Translation Layer
In the DFO Pacific Region, diverse data formats and schemas are used across programs, divisions, and systems. Darwin Core provides a common data standard that enables these internal formats to be mapped to:
- Other DFO systems
- National open data platforms
- International biodiversity repositories (e.g., GBIF, OBIS)
By treating Darwin Core as a semantic translation layer, we can harmonize our internal datasets for interoperability, discoverability, and reuse, without requiring all groups to adopt the same database design.
The Unified GBIF Data Model
The GBIF Unified Data Model extends Darwin Core to support complex biodiversity datasets, including:
- Events (e.g., sampling campaigns, cruises, transects)
- Occurrences (e.g., individual specimens, observations)
- Measurements or Facts (e.g., biological measurements, environmental conditions)
This model aligns with DFO data practices that involve nested relationships between surveys, gear deployments, catches, and individual biological samples.
OBIS: Ocean Biodiversity Information System
OBIS builds on Darwin Core and the GBIF model to support marine biodiversity data. It uses a Darwin Core Archive format with specific extensions for:
- Sampling Effort
- Environmental Parameters
- Taxonomic Verification
OBIS is the global node for marine biodiversity under the UN Ocean Decade and is highly relevant for DFO’s coastal and offshore research.
Mapping DFO Fisheries Data to Darwin Core
Below are examples of how commonly used columns in DFO data systems align with Darwin Core terms.
| DFO Field / Concept | Darwin Core Term | Notes |
|---|---|---|
Species_Code or Species_Name |
scientificName |
Can be resolved via WoRMS or NCBI |
Sample_ID |
occurrenceID |
A globally unique identifier for the specimen or observation |
Catch_Date |
eventDate |
Ideally formatted as ISO 8601 |
Survey_Name |
eventID |
Use hierarchical eventIDs for nested events (e.g., cruise → tow → sample) |
Latitude, Longitude |
decimalLatitude, decimalLongitude |
Use WGS84 datum |
Depth_m |
minimumDepthInMeters, maximumDepthInMeters |
Use both where applicable |
Sex, Maturity, Length, Weight |
measurementType, measurementValue, measurementUnit |
Recorded under the MeasurementOrFact extension |
Gear_Type |
samplingProtocol |
Use consistent terminology for methods |
Area_Code, Subarea |
locationID, locality |
Align to spatial standards like NAFO/DFO zones |
Data_Source, Project_Name |
datasetName, recordedBy |
Identify project or responsible team |
Toward Controlled Vocabularies and Ontologies
DFO’s long-term goal is to develop controlled vocabularies and ontology modules that align with:
- Darwin Core term values
- The NERC Vocabulary Server (NVS) for environmental parameters
- World Register of Marine Species (WoRMS) for taxonomic resolution
- CF Conventions for oceanographic and climate data
- The Salmon Ontology developed by NCEAS
These efforts will allow for semantic alignment, improving both machine-readability and clarity for analysts and stakeholders.
Next Steps
- We are actively building a DFO metadata crosswalk using Darwin Core as the central translation layer
- Look for updates on term definitions, controlled value lists, and validation tools
- Join our discussions on standardizing data fields and contributing to the controlled vocabulary development
For questions, feedback, or help mapping your dataset, contact the Data Stewardship Unit.
Darwin Core is not a database format. It’s a lingua franca for biodiversity data. Use it to describe, translate, and publish your data — not to force everything into the same structure.