Update Reproduction Info (#6)

- Add information about naming metadata (804f8152cfd84cd02352d1f7b5b2264b145838c6)
- Clarify reproduction instructions (2226e0b738b5be5e7df9b25a2118fb3dd20af864)

README.md

@@ -65,6 +65,10 @@ English, Latin
         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
@@ -74,7 +78,7 @@ English, Latin
 ```
 
 Each `image_set` is approximately 30GB and contains 100 thousand images, each named `<treeoflife_id>.jpg`. 
-We cannot reproduce the `iNat21` data, but after downloading it and BIOSCAN-1M, one can follow the directions from step 6 of [docs/imageomics/treeoflife10m.md](https://github.com/Imageomics/bioclip/blob/main/docs/imageomics/treeoflife10m.md) in the BioCLIP GitHub repo to combine them with the EOL data into the proper webdataset structure. This will produce a collection of files named `shard-######.tar` in a `train`, `val`, and `train_small` folder with which to work.
+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.
 
 Inside each shard is a collection of images (named `<treeoflife_id>.jpg`), for which each has the following files:
 ```
@@ -135,6 +139,9 @@ Note that the `species` column occasionally has entries such as "sp. ___(get ex)
 | Taxonomic | _Animalia Chordata Aves Passeriformes Corvidae Pica hudsonia_ |
 
 
+`naming/`: these files provide the taxonomic name lookup for each data source in the reconstruction of the dataset.
+
+
 `species_level_taxonomy_chains.csv`: CSV with the ITIS taxonomic hierarchy, indicated as follows:
   - `hierarchy_string_tsn`: string of Taxonomic Serial Numbers (TSN)* for the names of the ranks provided from highest to lowest, connected by dashes (eg., `202422-846491-660046-846497-846508-846553-954935-5549-5550`).
   - `hierarchy_string_names`: string of the names of the ranks provided from highest to lowest, connected by arrows (eg., `Plantae->Biliphyta->Rhodophyta->Cyanidiophytina->Cyanidiophyceae->Cyanidiales->Cyanidiaceae->Cyanidium->Cyanidium caldarium`).