GBIF Occurrence Annotation System

A system for rule-based annotation and quality control of GBIF occurrence data. This monorepo contains the backend service, R package, and web UI for creating, managing, and applying annotation rules to GBIF mediated occurrence records.

Authentication is required to use the annotation system. You can create a GBIF account at GBIF.org. You use your GBIF username and password to authenticate API requests.

Repository Structure

This is a monorepo containing three main components:

occurrence-annotation/
├── backend-service/     # Spring Boot REST API service
├── r-package/gbifrules/ # R package for programmatic access
└── ui/                  # React web application

Web UI

Visit https://labs.gbif.org/annotations/ to start creating annotation rules through the web interface.

UI Documentation

Backend Service

A Spring Boot REST API that provides the core annotation functionality.

The REST API is available at https://labs.gbif.org/occurrence/experimental/annotation/

Example: Create a Rule

curl -X POST "https://labs.gbif.org/occurrence/experimental/annotation/rule" \
  -H "Content-Type: application/json" \
  -u "username:password" \
  -d '{
    "projectId": 123,
    "title": "Suspicious coastal records",
    "body": "Marine species found far inland",
    "wkt": "POLYGON((-60 -5, -50 -5, -50 5, -60 5, -60 -5))",
    "taxonKeys": [2435098],
    "basisOfRecord": ["HUMAN_OBSERVATION"]
  }'

Full API Documentation

R Package (gbifrules)

An R package providing an interface to the GBIF rule-based annotation API.

• Define rules programmatically
• Create and manage projects
• Clean GBIF downloads

Installation and Usage

# Install from GitHub
# install.packages("pak")
pak::pak("gbif/occurrence-annotation/r-package/gbifrules")

# Load the package
library(gbifrules)

# Set your GBIF credentials in .Renviron
usethis::edit_r_environ()
# Add these lines to your .Renviron file:
# GBIF_USER=your_username
# GBIF_PWD=your_password
# Then restart R for changes to take effect

# Create an annotation rule
rule <- make_rule(
  taxonKey = 2431950,  
  wkt = "POLYGON((-10 35, 10 35, 10 45, -10 45, -10 35))",
  annotation = "SUSPICIOUS"
)

# Get existing rules
rules <- get_rule(taxonKey = 2431950)

# Clean a GBIF download using rgbif
library(rgbif)
d <- occ_download_get('0004693-260120142942310') %>%
  occ_download_import()

clean_download(d)

Documentation |

Related Resources

• GBIF.org - Global Biodiversity Information Facility
• GBIF API Documentation
• rgbif R Package - Access GBIF data in R