ALESS open data portal

Background

Biodiversity of life refers to the variety of species, as well as their distribution and abundance patterns, found on Earth. It is estimated that more than 1.9 million species of living organisms have been described and cataloged, though scientists believe many more remain undiscovered (Antonelli et al., 2020). Biologists are constantly working to document this diversity, and as computer power has increased, researchers are now able to conduct global assessments of biodiversity, making large-scale information databases available for study and research (Ball-Damerow et al., 2019).

Biodiversity research is crucial for understanding ecosystem health, identifying threatened species, tracking the impacts of climate change, monitoring invasive species, and informing conservation decisions. Open biodiversity data collected over centuries from museums, research institutions, and citizen scientists is now accessible online, enabling new types of research questions to be explored.

References

Antonelli, A., Smith, R. J., Fry, C., Simmonds, M. S., Kersey, P. J., Pritchard, H. W., ... & Qi, Y. D. (2020). State of the World’s Plants and Fungi (Research Report, Royal Botanic Gardens (Kew); Sfumato Foundation).

Ball-Damerow, J. E., Brenskelle, L., Barve, N., Soltis, P. S., Sierwald, P., Bieler, R., ... & Guralnick, R. P. (2019). Research applications of primary biodiversity databases in the digital age. PloS one, 14(9), e0215794.

Data Sources

Global Biodiversity Databases

1. Global Biodiversity Information Facility (GBIF)

https://www.gbif.org/

World's largest biodiversity database
Over 2.8 billion species occurrence records (as of 2024)
Data from over 1.7 million species
Includes:
- Museum specimen records
- Scientific field observations
- Citizen science observations
- Species occurrence location and date
- Taxonomic information
Data from 300+ years of biological exploration
Free and open access to all data
How to use: Search by species, location, or dataset → Filter results → Download CSV
Data format: CSV or Darwin Core Archive (more detailed)
Good for: Species distribution, occurrence over time, biodiversity patterns

2. iNaturalist

https://www.inaturalist.org/

Citizen science platform for documenting biodiversity observations
Over 2.1 million species recorded globally
Community-verified species identifications
Each observation includes:
- Photo/audio of organism
- Location (GPS coordinates)
- Date and time
- Species identification (verified by community)
Mobile app available for field observations
Research-grade observations automatically shared with GBIF
Good for: Recent biodiversity data, local species observations, citizen science projects

3. GBIF Species Occurrences on AWS

https://registry.opendata.aws/gbif/

Periodic snapshots of GBIF data in cloud-accessible format
Useful for large-scale data analysis
Data in Parquet format (efficient for big data)
Good for: Advanced analysis of very large datasets

Taxonomic and Conservation Status

4. Catalogue of Life

https://www.catalogueoflife.org/

Comprehensive checklist of world's species
Taxonomic hierarchy and names
Links to GBIF occurrence data
Good for: Understanding species taxonomy and classification

5. IUCN Red List of Threatened Species

https://www.iucnredlist.org/

Global conservation status of species
Categories: Extinct, Critically Endangered, Endangered, Vulnerable, etc.
Searchable database with species assessments
Can download species lists by region or threat status
Good for: Conservation research, threatened species analysis

Regional and National Databases

6. Atlas of Living Australia

https://www.ala.org.au/

Australia-specific biodiversity data
Over 100 million occurrence records
Interactive maps and tools
Good for: Australian biodiversity studies

7. eBird (for bird observations)

https://ebird.org/

Global database of bird observations
Real-time data from birdwatchers worldwide
Detailed occurrence and abundance data
Data feeds into GBIF
Good for: Bird distribution and migration studies

Japan-Specific Data

8. National Institute for Environmental Studies (NIES) Biodiversity Center

http://www.biodic.go.jp/english/

Japanese biodiversity information
National surveys and monitoring data
Species lists and distribution in Japan
Good for: Biodiversity in Japan

9. J-IBIS (Japan Integrated Biodiversity Information System)

https://www.biodic.go.jp/J-IBIS_en.html

Database of Japanese species
Distribution maps and occurrence data
Good for: Researching species in Japan

Example research questions

To answer some of these questions, you might need to find other data to combine with biodiversity datasets (e.g., climate data, habitat types, land use changes, pollution levels, protected area locations, elevation data).

How does the distribution of species change over time, and how does that correlate with environmental phenomena?

How does the taxonomic diversity vary between localities?

What is the relationship between climate change and shifts in species distribution?

How do invasive species distributions compare to native species in a region?

Is there a relationship between habitat loss and species richness in different areas?

How has species occurrence changed in urban vs. rural areas over decades?

Tips for Using Biodiversity Data

Getting Started:

Start with GBIF or iNaturalist - both are user-friendly
Choose a specific taxonomic group (e.g., butterflies, trees) or region to focus on
Use filters to limit data by date range, location, or species
Download small datasets first to practice
Be aware that data quality varies - check for verified observations

Understanding the Data:

Occurrence record: Documentation of a species at a specific place and time
Taxonomic rank: Species, genus, family, order, class, phylum, kingdom
Georeferenced: Observations with GPS coordinates (latitude/longitude)
Research-grade: Observations verified by multiple expert identifiers (iNaturalist)
Specimen: Physical preserved sample (museum collection)
Observation: Visual or auditory record without physical specimen

Data Quality Considerations:

Not all areas are equally surveyed - popular areas have more data
Some species are easier to observe and identify than others
Historical data may be less precise (locations, identifications)
Absence of data doesn't mean absence of species
Citizen science data quality varies but research-grade observations are reliable

Making Comparisons:

Compare species richness (number of species) between areas
Track changes in distribution over decades
Compare native vs. invasive species patterns
Look at seasonal or temporal patterns in observations
Consider observation effort (more observers = more records)

Combining Datasets: Biodiversity research often requires combining multiple datasets. For example:

Species occurrences + climate data + elevation
Distribution changes + land use changes + time periods
Species richness + habitat types + protected areas
Invasive species locations + human population density + transport routes

For Your Analysis:

Map species distributions to visualize patterns
Create time series graphs to show changes over years
Compare biodiversity metrics between different regions
Account for sampling bias (some areas better studied than others)
Focus on well-documented species groups for reliable results

Citation: Always cite GBIF data properly:

Example: "GBIF.org (05 October 2025) GBIF Occurrence Download https://doi.org/10.15468/dl.[unique_identifier]"

For iNaturalist: "iNaturalist contributors, iNaturalist (2025). iNaturalist Research-grade Observations. Occurrence dataset https://doi.org/10.15468/ab3s5x accessed via GBIF.org on [date]"

Understanding GBIF Data

What GBIF Contains:

Museum specimens (historical collections)
Scientific research observations
Citizen science records (especially from iNaturalist, eBird)
Biodiversity monitoring programs
Species checklists

Temporal Coverage:

Historical records from 1700s-1800s (museum specimens)
Increasing data from 1900s onward
Massive increase in recent years due to citizen science

Geographic Coverage:

Global, but uneven distribution
More data from North America, Europe, Australia
Increasing coverage in other regions
Urban areas often better documented than remote areas

Major Contributing Platforms:

iNaturalist (citizen science, photos)
eBird (bird observations)
Museum collections worldwide
National biodiversity networks
Research projects and surveys

Useful Additional Data Sources

When studying biodiversity, you might want to combine species data with:

Climate data: Temperature, precipitation, seasonality (WorldClim, climate databases)
Land use: Forest cover, agriculture, urbanization (satellite data, land use maps)
Elevation and topography: Digital elevation models (various sources)
Protected areas: Location of parks and reserves (Protected Planet, WDPA)
Environmental variables: Soil type, water bodies, vegetation (various databases)
Human impact: Population density, roads, infrastructure (census, mapping data)

Questions? Need Help?

GBIF has over 2.8 billion records - use filters to make datasets manageable
Focus on well-studied taxonomic groups (birds, butterflies, trees) for more reliable data
iNaturalist is great for recent local observations
Remember to account for observation bias in your analysis
Some species are harder to identify - use research-grade observations when possible
Consider both presence and absence of data in your interpretations

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