Clarified some file descriptions and updated links now that check_taxa script has been merged in open_clip repo.

README.md

@@ -10,38 +10,32 @@ This repo contains the analysis of the TreeOfLife10M dataset as it's being craft
 ### Data
 
 The `data` folder contains
- - `statistics.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the 
-associated taxa information for the image. This is the file that will be updated, while preserving the `v1-dev-names.csv` file for ease of comparison.
+ - `statistics.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information for the image. This is the file that will be updated, while preserving the `v1-dev-names.csv` file for ease of comparison.
 - `stats_avg_std_byClass.csv`: average and standard distribution of images given by class in `statistics.csv`. This is for both all 
 images, and images that have labels.
 
- - `v1-dev-names.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the 
-associated taxa information for the image.
+ - `v1-dev-names.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information for the image. This file will be maintained for v1 reference, and as such will not be updated.
  - `taxa_counts.csv`: count of distinct lower taxa within each higher taxon from `kingdom` down to 
-`genus`, though the genus count was interrupted and therefore is incomplete.
- - `avg_std_byClass.csv`: average and standard distribution of images given by class. This is for both all 
-images, and images that have labels. Note that kingdoms have not been merged and no standardization has 
-been performed on the taxonomic hierarchy prior to creation of this file.
- - `tol_hierarchy_test.csv`: Subset of `v1-dev-names.csv` for testing the [`check_taxa` script](https://github.com/Imageomics/open_clip/tree/main/scripts/evobio10m) to ensure the hierarchy is properly filled in after data generation. 
+`genus` in `v1-dev-names.csv`, though the genus count was interrupted and therefore is incomplete.
+ - `avg_std_byClass.csv`: average and standard distribution of images in `v1-dev-names.csv` given by class (taxonomic rank). This is for both all images, and images that have labels. Note that kingdoms had not been merged and no standardization was performed on the taxonomic hierarchy prior to creation of this file.
+ - `tol_hierarchy_test.csv`: Subset of `v1-dev-names.csv` for testing the [`check_taxa` script](https://github.com/Imageomics/open_clip/blob/main/scripts/evobio10m/check_taxa.py) to ensure the hierarchy is properly filled in after data generation. 
 
 
 ### Notebooks
 
 The `notebooks` folder contains
- - `ToL_stats_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `statistics.csv`.
+ - `ToL_stats_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `statistics.csv`. To be updated as `statistics.csv` is updated, i.e., as the dateset is updated.
  - `ToL_stats_EDA.py`: py file paired to `ToL_stats_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
 
- - `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `v1-dev-names.csv`, generates 
-`taxa_counts.csv`.
- - `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of 
-visualizations in visuals and some histograms. The treemaps produced in the notebook are interactive.
+ - `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `v1-dev-names.csv`, generates `taxa_counts.csv`.
+ - `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of visualizations in `visuals` folder and some histograms. The treemaps produced in the notebook are interactive.
  - `ToL_EDA.ipynb`: more full EDA of TreeOfLife10M dataset. Explores the labeling inconsistencies for 
-direction of standardization efforts.
- - `missing_taxa_testGen.ipynb`: generates `tol_hierarchy_test.csv` to test `check_taxa` script. Also observes species labeled as `(unidentified)` in EOL data.
+direction of standardization efforts. Maintained for v1 reference, should not be updated.
+ - `missing_taxa_testGen.ipynb`: generates `tol_hierarchy_test.csv` to test [`check_taxa` script](https://github.com/Imageomics/open_clip/blob/main/scripts/evobio10m/check_taxa.py). Also observes species labeled as `(unidentified)` in EOL data.
 
-Note: run `pip install -r requirements.txt` before starting the notebooks.
+**Note:** run `pip install -r requirements.txt` before starting the visualization notebooks.
 
 ### Visuals
 
 Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. 
-There is also one for just the iNat21 data included.
+There is also one for just the iNat21 data included.