update embeddings to include species with empty intermediate levels (#11)

- update embeddings to include species with empty intermediate levels (fe486eed6b6831df351396b25d2efb7d0542ba16)
- Update null value filtering approach (9ca9539b8a562ef2ebfa54b202f7fc6e0a53eb66)


Co-authored-by: Jianyang Gu <[email protected]>

embeddings/README.md

@@ -5,7 +5,7 @@
 ## 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`, `phylum`, `class`, `order`, `family`, `genus`, or `species` are `null`.
+* **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.
 

embeddings/txt_emb_species.json

@@ -1,3 +1,3 @@
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+size 84688926

embeddings/txt_emb_species.npy

@@ -1,3 +1,3 @@
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+size 2664821888