imageomics/TreeOfLife-200M-Embeddings

TreeOfLife-200M Embeddings

Work in progress — this dataset card is under active development.

239 million BioCLIP 2 embeddings (768-dim, float16) for TreeOfLife-200M images, sorted by taxonomic hierarchy. We recommend using DuckDB to access this dataset.

Query Remotely

Query directly from HuggingFace without downloading anything. DuckDB uses Parquet page indexes to skip irrelevant files, making filtered queries fast over the network.

order and class are SQL reserved words — always quote them as "order" and "class".

Python

import duckdb

con = duckdb.connect()
# Authenticate for higher rate limits (recommended)
con.execute("CREATE SECRET (TYPE HUGGINGFACE, TOKEN 'hf_...')")

glob = "hf://datasets/imageomics/TreeOfLife-200M-Embeddings/bioclip-2_float16/*.parquet"

# Get all embeddings for a species
df = con.sql(f"""
    SELECT uuid, emb
    FROM read_parquet('{glob}')
    WHERE species = 'Danaus plexippus'
""").df()

# Count by taxonomic order
con.sql(f"""
    SELECT "order", COUNT(*) as n
    FROM read_parquet('{glob}')
    WHERE "order" IS NOT NULL
    GROUP BY "order"
    ORDER BY n DESC
    LIMIT 10
""").show()

# Filter by family
con.sql(f"""
    SELECT genus, species, COUNT(*) as n
    FROM read_parquet('{glob}')
    WHERE family = 'Felidae'
    GROUP BY genus, species
    ORDER BY n DESC
    LIMIT 10
""").show()

CLI

# Install DuckDB: https://duckdb.org/docs/installation
# Then query directly from the command line:

duckdb -c "
    SELECT species, COUNT(*) as n
    FROM read_parquet('hf://datasets/imageomics/TreeOfLife-200M-Embeddings/bioclip-2_float16/*.parquet')
    WHERE family = 'Nymphalidae'
    GROUP BY species
    ORDER BY n DESC
    LIMIT 10;
"

Download a Taxonomic Slice

Instead of downloading the full 331 GB dataset, extract only the taxa you need. The sorted data and page indexes ensure only the relevant row groups are fetched over the network.

Python

import duckdb

con = duckdb.connect()
con.execute("CREATE SECRET (TYPE HUGGINGFACE, TOKEN 'hf_...')")

glob = "hf://datasets/imageomics/TreeOfLife-200M-Embeddings/bioclip-2_float16/*.parquet"

# Save a single family to a local file
con.sql(f"""
    COPY (
        SELECT * FROM read_parquet('{glob}')
        WHERE family = 'Felidae'
    ) TO 'felidae.parquet'
""")

# Now query locally — instant
con.sql("SELECT species, COUNT(*) as n FROM 'felidae.parquet' GROUP BY species ORDER BY n DESC").show()

CLI

duckdb -c "
    COPY (
        SELECT * FROM read_parquet('hf://datasets/imageomics/TreeOfLife-200M-Embeddings/bioclip-2_float16/*.parquet')
        WHERE \"order\" = 'Primates'
    ) TO 'primates.parquet';
"

Slice Example	Rows	Size	Time
Species: Danaus plexippus	299,874	913 MB	~1 min*
Family: Felidae	149,890	457 MB	~1 min*
Order: Primates	160,307	489 MB	~1 min*

*First query in a session includes a one-time ~3 min glob resolution overhead: DuckDB expands the *.parquet wildcard by making HTTP requests to HuggingFace to discover all 685 filenames. Subsequent queries in the same session reuse the cached file list.

Download Everything

For full-dataset analytics, download all files first.

huggingface-cli download imageomics/TreeOfLife-200M-Embeddings \
  --repo-type dataset --include "bioclip-2_float16/*" --local-dir ./data

duckdb -c "
    SELECT \"order\", COUNT(*) as n
    FROM read_parquet('./data/bioclip-2_float16/*.parquet')
    WHERE \"order\" IS NOT NULL
    GROUP BY \"order\"
    ORDER BY n DESC
    LIMIT 10;
"

Schema

Column	Type	Description
uuid	string	Unique image identifier
kingdom	string	Taxonomic kingdom
phylum	string	Taxonomic phylum
class	string	Taxonomic class
order	string	Taxonomic order
family	string	Taxonomic family
genus	string	Taxonomic genus
species	string	Taxonomic species
img_type	string	Image source type
basisOfRecord	string	Basis of record
publisher	string	Data publisher
identifier	string	Source URI
emb	fixed_size_list<float16>[768]	BioCLIP 2 embedding

Data Organization

• Sort order: kingdom > phylum > class > order > family > genus > species
• Row groups: 50,000 rows each with column statistics and page indexes
• Compression: ZSTD level 3
• Precision: float16 (lossless cosine similarity vs float32 source)

Configs

Config	Model	Precision	Files	Size	Rows
bioclip-2_float16	BioCLIP 2	float16	685	331 GB	239,580,103