biodiversity-data-guide

Biodiversity Data Guide

Access, analyze, and visualize biodiversity data from global databases including GBIF, iNaturalist, and GenBank for ecological and evolutionary research.

Major Biodiversity Data Sources

Querying GBIF (Species Occurrences)

Python (pygbif)

from pygbif import species as sp
from pygbif import occurrences as occ

# Search for a species by name
name_result = sp.name_backbone(name="Panthera tigris", rank="species")
taxon_key = name_result["usageKey"]
print(f"GBIF taxon key: {taxon_key}")
print(f"Status: {name_result['status']}")
print(f"Kingdom: {name_result['kingdom']}")

# Get occurrence records
results = occ.search(
    taxonKey=taxon_key,
    hasCoordinate=True,       # Only georeferenced records
    country="IN",             # India
    limit=100,
    year="2020,2024",         # Year range
    basisOfRecord="HUMAN_OBSERVATION"
)

print(f"Total records matching: {results['count']}")
for record in results["results"][:5]:
    print(f"  [{record.get('year')}] {record.get('decimalLatitude'):.4f}, "
          f"{record.get('decimalLongitude'):.4f} - {record.get('datasetName', 'N/A')}")

R (rgbif)

library(rgbif)
library(sf)
library(ggplot2)

# Get occurrence data
tiger_key <- name_backbone(name = "Panthera tigris")$usageKey

occurrences <- occ_search(
  taxonKey = tiger_key,
  hasCoordinate = TRUE,
  limit = 500,
  year = "2020,2024",
  basisOfRecord = "HUMAN_OBSERVATION"
)

# Convert to spatial data
occ_df <- occurrences$data
coords <- occ_df[, c("decimalLongitude", "decimalLatitude")]
occ_sf <- st_as_sf(coords, coords = c("decimalLongitude", "decimalLatitude"),
                    crs = 4326)

# Map occurrences
world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")
ggplot() +
  geom_sf(data = world, fill = "grey90") +
  geom_sf(data = occ_sf, color = "red", size = 1, alpha = 0.5) +
  coord_sf(xlim = c(60, 150), ylim = c(-10, 50)) +
  labs(title = "Panthera tigris occurrences (2020-2024)") +
  theme_minimal()
ggsave("tiger_map.pdf", width = 10, height = 6)