README.md

metadata

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 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.

• 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. 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 familyto 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.