| # 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" | |
| ], | |
| ] | |
| ``` | |