Dataset Card for TreeOfLife-10M Vector database

Persistent files for vector Database created with chromadb containing the embeddings for all images in the imageomics/TreeOfLife-10M dataset.

Dataset Details

This dataset contains the generated vector database built using ChromaDb as the backend vector database solution for the entire TreeOfLife-10M dataset.

The rationale behind creating a vector database was to enable blazingly fast nearest neighbor search. The vector database is loaded into memory and for a given query embedding in the same dimension as the vectors in the database, we calculate the inner product (ip) to calculate distances. In this case all vectors are of the same dimension i.e. 512 dims.

The files in this dataset are binaries and cannot be read in raw format. The files in this dataset are intended to be used with chromadb.

Below is an example usage:

import chromadb

client = chromadb.PersistentClient(path=self._collection_dir)

collection = client.get_or_create_collection(
    name="imageomics/TreeOfLife-10M",
    metadata={"hnsw:space": "ip", "hnsw:search_ef": 10},
)
# returns ID of 10 nearest neighbor. If an exact match exists,
# that will be the first returned result with a distance of 0.
collection.query(query_embeddings=[query_embedding], n_results=10)

Dataset Structure

tol_vector_db/
├── 97283350-138c-49b4-a4d4-9b93a33960da/
│   ├── header.bin
│   ├── index_metadata.pickle
│   ├── data_level0.bin
│   ├── link_lists.bin
│   └── length.bin
└── chroma.sqlite3

Dataset Creation

Source Data

imageomics/TreeOfLife-10M dataset was the source for all images in the database. Along with every image in the database we also store the taxonomic information as additional columns in the vector database:

kingdom
phylum
class
order
family
genus
species
common name

The image embedding were generated using the TreeOfLifeClassifier available in the pybioclip library.

Citation

BibTeX: Data

@misc{<ref_code>,
  author = {Sreejith Menon},
  title = {Tree Of Life 10M Vector Database},
  year = {2025},
  url = {https://huggingface.co/datasets/imageomics/tree-of-life-vector-db},
}

Acknowledgements

This work was supported by the Imageomics Institute, which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Speical thanks to:

Matt Thompson

Dataset Card Authors

Sreejith Menon - git in

Dataset Card Contact

Sreejith Menon - git in