# Tree of Life 10M EDA Repo

This repo contains the analysis of the TreeOfLife10M dataset as it's being crafted and refined.

### Data

The `data` folder contains
 - `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.
 - `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.

### Notebooks

The `notebooks` folder contains
 - `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.
 - `ToL_EDA.ipynb`: more full EDA of TreeOfLife10M dataset. Explores the labeling inconsistencies for 
direction of standardization efforts.

Note: run `pip install -r requirements.txt` before starting the 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.