Clarify text embeddings

README.md

@@ -69,6 +69,12 @@ dataset/
         ...
         image_set_63.tar.gz
 embeddings/
+    biocap/
+        txt_emb_species.json
+        txt_emb_species.npy
+    bioclip/
+        txt_emb_species.json
+        txt_emb_species.npy
     txt_emb_species.json
     txt_emb_species.npy
 metadata/
@@ -88,7 +94,7 @@ visuals/
     phyla_ToL_tree.png
 ```
 
-The `embeddings/` directory contains the [BioCLIP](https://huggingface.co/imageomics/bioclip) text embeddings for all images in the TreeOfLife-10M dataset.
+[BioCLIP](https://huggingface.co/imageomics/bioclip) and [BioCAP](https://huggingface.co/imageomics/biocap) text embeddings for TreeOfLife-10M images are provided under `embeddings/<model-name>/`. The BioCLIP text embeddigns are duplicated in the `embeddings/` to maintain [`pybioclip`](http://github.com/Imageomics/pybioclip) functionality for versions 2.1.1 and earlier, which do not incorporate BioCAP as a "Tree of Life Model".
 
 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.
@@ -314,7 +320,7 @@ This dataset (the compilation) has been marked as dedicated to the public domain
 }
 ```
 
-Note that this version is updated from [Revision ffa2a31](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/tree/ffa2a318a1396f2f9e456ba171d3b5b5d8b4f051). This updated version resolves taxonomic alignment issues discovered in the first version. The taxonomic resolution was completed using [TaxonoPy](https://github.com/Imageomics/TaxonoPy), which was developed for [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M).
+Note that this version is updated from [Revision ffa2a31](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/tree/ffa2a318a1396f2f9e456ba171d3b5b5d8b4f051). This updated version resolves taxonomic alignment issues discovered in the first version. The taxonomic resolution was completed using [TaxonoPy](https://github.com/Imageomics/TaxonoPy), which was developed for [TreeOfLife-200M](https://huggingface.co/datasets/imageomics/TreeOfLife-200M). Additionally, it adds the [BioCAP](https://huggingface.co/imageomics/biocap) text embeddings.
 
 [Revision 69ca82e](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/tree/69ca82e7481dcae0764f7c5452ea32b3a41cf620) is the version used for the original BioCLIP model training ([BioCLIP Revision 7b4abf1](https://huggingface.co/imageomics/bioclip/tree/7b4abf1f6ee747c15de00c7d28a5e62990b5dabc)), presented in the paper. There are **no substantial differences to the dataset itself between that and Revision ffa2a31**; Revision ffa2a31 simply added extra [files](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/commit/5f1c0c80a94da39b7e84024d34f9b936db9f7ae1) and [instructions](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/commit/343c36b9b362494065ac427ac1da989b834b22cf) required for reproducibility of the dataset, as well as the [BioCLIP text embeddings](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/commit/4e719078e4cab104a0b631c0fd724ba9ee02411b) (from BioCLIP Revision 7b4abf1).
 
@@ -374,4 +380,4 @@ year = {2026}
 
 ### Contributions
 
-The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
+The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.