---
language:
- en
pretty_name: TreeOfLife10M EDA
---
# TreeOfLife10M EDA Repo

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

### Data

The `data` folder contains
 - `catalog.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 `catalog-v1-dev.csv` file for ease of comparison.
- `stats_avg_std_byClass.csv`: average and standard distribution of images given by class in `catalog.csv`. This is for both all 
images, and images that have labels.
- `predicted-catalog.csv`: the metadata and identifiers for all entries expected in the dataset, prior to webdataset creation. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information. In version 3.3 (first time it was generated), it showed 27K more entries than in the webdataset and they all had full taxonomic rank filled.

 - `catalog-v1-dev.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` in `catalog-v1-dev.csv`, though the genus count was interrupted and therefore is incomplete.
 - `avg_std_byClass.csv`: average and standard distribution of images in `catalog-v1-dev.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 `catalog-v1-dev.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_catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `catalog.csv`. To be updated as `catalog.csv` is updated, i.e., as the dataset is updated.
 - `ToL_catalog_EDA.py`: py file paired to `ToL_catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
 - `ToL_predicted-catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `predicted-catalog.csv`. To be updated as `predicted-catalog.csv` is updated, i.e., as the dataset is updated.
 - `ToL_predicted-catalog_EDA.py`: py file paired to `ToL_predicted-catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
- `BioCLIP_taxa_viz.ipynb`: generates data visualizations, in particular, the generation of treemaps in `visuals` folder; also includes a histogram of kingdoms. The treemaps produced in the notebook are interactive and `HTML` interactive versions can also be found in [`visuals`](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/visuals).

 - `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `catalog-v1-dev.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. 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 visualization notebooks. EDA notebooks only require `pandas` and `seaborn`.

### Visuals

Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. 
- `category-v1-visuals`: visualizations made for the original `catalog-v1-dev.csv` using `BioCLIP_taxa_viz_bySource.ipynb`.
There is also one for just the iNat21 data included.
- `kingdom_ToL_tree.html`: interactive treemap from `kingdom` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.
- `kingdom_ToL_tree.pdf`: static treemap from `kingdom` to `family`to demonstrate the distribution of the data. 2:1 aspect ratio.
- `phyla_ToL_tree.html`: interactive treemap from `phylum` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.
- `kingdom_ToL_tree.pdf`: static treemap from `phylum` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.