BioCLIP 2.5 Huge Training Data Update (catalog & provenance)

dataset/catalog.parquet

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dataset/metadata/provenance.parquet

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embeddings/README.md

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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.
+[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. These text embeddings match to the BioCLIP 2 training dataset, specified by the [catalog parquet from Revision a8f38b4](https://huggingface.co/datasets/imageomics/TreeOfLife-200M/blob/a8f38b4388579862c56ae57d6f094c2ac0e92e12/dataset/catalog.parquet).
 
 ## Taxonomic JSON Construction
 
-The `JSON` was created from the [TreeOfLife-200M catalog](../catalog.parquet) and [`VernacularName.tsv` component of the GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei)  using [`make_txt_embedding_json.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding_json.py) through the following process:
+The `JSON` was created from the [TreeOfLife-200M catalog](../catalog.parquet) (if reproducing the process, be sure to use the correct revision for the intended model) and [`VernacularName.tsv` component of the GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei)  using [`make_txt_embedding_json.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding_json.py) 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 catalog metadata often contains multiple common names for a single unique taxonomic combination. During processing, **the first English common name encountered** for a given unique taxonomic combination is retained. If English is not available, the first option of any language is used. We plan future improvements to establish a definitive 1-to-1 mapping or a more comprehensive common name strategy.