Add text embeddings description
Browse files- embeddings/README.md +60 -0
embeddings/README.md
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# Text Embeddings
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[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.
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## Taxonomic JSON Construction
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The `JSON` was created from the [TreeOfLife-200M catalog](../catalog.parquet) through the following process:
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* **Null Value Filtering:** Remove records where `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, or `species` are `null`.
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* **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.
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* **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.
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### Structure
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The JSON file is a single top-level array. Each element within this array is itself an array of two elements:
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* **Inner Array (Index 0):** A list of strings representing the full taxonomic path from `kingdom` to `species`.
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* **String (Index 1):** The common name associated with that taxonomic combination.
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#### Example
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```json
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[
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[
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[
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"Plantae",
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"Bryophyta",
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"Bryopsida",
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"Bryales",
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"Bryaceae",
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"Bryum",
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"gracile"
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],
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""
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],
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[
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[
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"Animalia",
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"Chordata",
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"Aves",
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"Passeriformes",
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"Mitrospingidae",
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"Orthogonys",
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"chloricterus"
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],
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"Olive-green tanager"
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],
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[
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[
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"Animalia",
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"Arthropoda",
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"Insecta",
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"Lepidoptera",
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"Lycaenidae",
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"Orthomiella",
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"rantaizana"
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],
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"Chinese Straight-wing Blue"
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],
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]
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```
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