Add BioCLIP embeddings (#9)

- Add BioCLIP embeddings (91501708dc8c2341d0818c1809570520698695c1)
- clarify text embeddings (1e1eb8ed8203ad9bb3ef17d006587f0924cd1110)

.gitattributes

@@ -60,3 +60,4 @@ metadata/** filter=lfs diff=lfs merge=lfs -text
 
 # Full dataset
 dataset/** filter=lfs diff=lfs merge=lfs -text
+embeddings/txt_emb_species.json filter=lfs diff=lfs merge=lfs -text

README.md

@@ -27,14 +27,14 @@ size_categories: 10M<n<100M
 
 ## Dataset Description
 
-<!-- - **Homepage:** -->
+- **Homepage:** https://imageomics.github.io/bioclip/
 - **Repository:** [Imageomics/bioclip](https://github.com/Imageomics/bioclip)
 - **Paper:** BioCLIP: A Vision Foundation Model for the Tree of Life ([arXiv](https://doi.org/10.48550/arXiv.2311.18803))
 <!-- - **Leaderboard:** -->
 
 ### Dataset Summary
 
-With over 10 million images covering 454 thousand taxa in the tree of life, TreeOfLife-10M is the largest-to-date ML-ready dataset of images of biological organisms paired with their associated taxonomic labels. It expands on the foundation established by existing high-quality datasets, such as iNat21 and BIOSCAN-1M, by further incorporating newly curated images from the Encyclopedia of Life (eol.org), which supplies most of TreeOfLife-10M’s data diversity. Every image in TreeOfLife-10M is labeled to the most specific taxonomic level possible, as well as higher taxonomic ranks in the tree of life (see [Text Types](#text-types) for examples of taxonomic ranks and labels). TreeOfLife-10M was generated for the purpose of training [BioCLIP](https://huggingface.co/imageomics/bioclip) and future biology foundation models. 

+With over 10 million images covering 454 thousand taxa in the tree of life, TreeOfLife-10M is the largest-to-date ML-ready dataset of images of biological organisms paired with their associated taxonomic labels. It expands on the foundation established by existing high-quality datasets, such as iNat21 and BIOSCAN-1M, by further incorporating newly curated images from the Encyclopedia of Life (eol.org), which supplies most of TreeOfLife-10M’s data diversity. Every image in TreeOfLife-10M is labeled to the most specific taxonomic level possible, as well as higher taxonomic ranks in the tree of life (see [Text Types](#text-types) for examples of taxonomic ranks and labels). TreeOfLife-10M was generated for the purpose of training [BioCLIP](https://huggingface.co/imageomics/bioclip) and future biology foundation models. 
 
 
 <!--This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1). And further altered to suit Imageomics Institute needs. -->
 
@@ -54,29 +54,34 @@ English, Latin
 ## Dataset Contents
 
 ```
-/dataset/
+dataset/
     EOL/
         image_set_01.tar.gz
         image_set_02.tar.gz
         ...
         image_set_63.tar.gz
-    metadata/
-        catalog.csv
-        species_level_taxonomy_chains.csv
-        taxon.tab
-        licenses.csv
-        naming/
-            bioscan_name_lookup.json
-            eol_name_lookup.json
-            inat21_name_lookup.json
-    visuals/
-        kingodm_ToL_tree.html
-        kingdom_ToL_tree.pdf
-        phyla_ToL_tree.html
-        phyla_ToL_tree.pdf
-        phyla_ToL_tree.png
+embeddings/
+    txt_emb_species.json
+    txt_emb_species.npy
+metadata/
+    catalog.csv
+    species_level_taxonomy_chains.csv
+    taxon.tab
+    licenses.csv
+    naming/
+        bioscan_name_lookup.json
+        eol_name_lookup.json
+        inat21_name_lookup.json
+visuals/
+    kingodm_ToL_tree.html
+    kingdom_ToL_tree.pdf
+    phyla_ToL_tree.html
+    phyla_ToL_tree.pdf
+    phyla_ToL_tree.png
 ```
 
+The `embeddings/` directory contains the [BioCLIP](https://huggingface.co/imageomics/bioclip) text embeddings for all 8,455,243 images with full taxonomic labels in the TreeOfLife-10M dataset.
+
 Each `image_set` is approximately 30GB and contains 100 thousand images, each named `<treeoflife_id>.jpg`. 
 We cannot reproduce the `iNat21` data, but step-by-step [***reproduction instructions***](https://github.com/Imageomics/bioclip/blob/main/docs/imageomics/treeoflife10m.md#reproduce-treeoflife-10m) are provided on the BioCLIP GitHub repository to recreate the proper webdataset structure. This process will produce a collection of files named `shard-######.tar` in a `train`, `val`, and `train_small` folder with which to work.
 

embeddings/txt_emb_species.json

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+oid sha256:844e6fabc06cac072214d566b78f40825b154efa9479eb11285030ca038b2ece
+size 65731052

embeddings/txt_emb_species.npy

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+oid sha256:91ce02dff2433222e3138b8bf7eefa1dd74b30f4d406c16cd3301f66d65ab4ed
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