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# Text Embeddings
[BioCLIP 2 text embeddings of TreeOfLife-200M](txt_emb_species.npy) were generated with [`make_txt_embedding.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding.py), using the [`txt_emb_species.json`](txt_emb_species.json) to provide the 7-rank Linnean taxonomic names.
## Taxonomic JSON Construction
The `JSON` was created from the [TreeOfLife-200M catalog](../catalog.parquet) 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
```json
[
[
[
"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"
],
]
```
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