update embeddings to include species with empty intermediate levels

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 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d0891ca519a72cb310f966094ae4290277b12b98595fd9fb179c0a6623282285
-size 79255292
+oid sha256:db3823284ba6663860f2c86e2cea6ab5592cce44ec31601981a8c64a708d47fd
+size 84688926

embeddings/txt_emb_species.npy

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:8d4fd62e156e773d64e1dced9d39a1a935a93f41fb8c4a01f5e85242701c9b71
-size 2493398144
+oid sha256:1524804eb332b59f0b52457fb88c5f5a6bfff28c515d774023fdcc5335aa4ca3
+size 2664821888