Text Embeddings

BioCLIP 2 text embeddings of TreeOfLife-200M were generated with make_txt_embedding.py, using the txt_emb_species.json to provide the 7-rank Linnean taxonomic names.

Taxonomic JSON Construction

The JSON was created from the TreeOfLife-200M catalog through the following process:

Null Value Filtering: Remove records where kingdom or species are null.
Deduplication: Rows are deduplicated based on the combination of kingdom, phylum, class, order, family, genus, and species. This ensures that each unique taxonomic combination appears exactly once.
- Common Name Handling: Currently, the source metadata often contains multiple common names for a single unique taxonomic combination. During processing, the first common name encountered for a given unique taxonomic combination is retained. We plan future improvements to establish a definitive 1-to-1 mapping or a more comprehensive common name strategy.

Structure

The JSON file is a single top-level array. Each element within this array is itself an array of two elements:

Inner Array (Index 0): A list of strings representing the full taxonomic path from kingdom to species.
String (Index 1): The common name associated with that taxonomic combination.

Example

[
  [
    [
      "Plantae",
      "Bryophyta",
      "Bryopsida",
      "Bryales",
      "Bryaceae",
      "Bryum",
      "gracile"
    ],
      ""
  ],
  [
    [
      "Animalia",
      "Chordata",
      "Aves",
      "Passeriformes",
      "Mitrospingidae",
      "Orthogonys",
      "chloricterus"
    ],
      "Olive-green tanager"
  ],
  [
    [
      "Animalia",
      "Arthropoda",
      "Insecta",
      "Lepidoptera",
      "Lycaenidae",
      "Orthomiella",
      "rantaizana"
    ],
    "Chinese Straight-wing Blue"
  ],
]