Add text embeddings description (#10)

- Add text embeddings description (ad3b59eb11c3f9ebe1cbf29a86613e2d735c92c6)
- Add link to embeddings description (84d55e8bb6baa8d278b336ebfe0a76e242fad7e3)

README.md

@@ -72,7 +72,7 @@ Image Classification, Zero-shot and few-shot Classification.
             source=gbif/
 ```
 
-The `embeddings/` directory contains the [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) text embeddings for all 190,988,120 images with full taxonomic labels in the TreeOfLife-200M dataset.
+The `embeddings/` directory contains the [BioCLIP 2](https://huggingface.co/imageomics/bioclip-2) text embeddings for all 190,988,120 images with full taxonomic labels in the TreeOfLife-200M dataset. See [`embeddings/README.md`](embeddings/README.md) for more information.
 
 
 To avoid republishing existing datasets or interfering with original data source providers' ability to track use of their data, we provide all metadata here with step-by-step reproduction instructions in the [GitHub repository](https://github.com/Imageomics/TreeOfLife-toolbox/tree/main/docs#treeoflife200m-dataset-download-guide) to download the images and recreate the proper webdataset structure. This process will produce a collection of files named `shard-######.tar` in a `train` folder with which to work.

embeddings/README.md

@@ -0,0 +1,60 @@
+# 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`, `phylum`, `class`, `order`, `family`, `genus`, 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"
+  ],
+]
+```