Update description for publication of repo (#12)

- Update description for publication of repo (eb5da85c6af1208e8469c667e642269056794225)
- Update licensing section to reflect licensing of images shared in this dataset (f6112527b2cbaf72e5f04847ee80926a882d6f37)
- Add description for two files not previously described (7ef909d9a5df47081dab2368521cf2bcae8383c0)

README.md

@@ -1,13 +1,124 @@
 ---
 language:
 - en
-pretty_name: TreeOfLife10M EDA
+pretty_name: TreeOfLife-10M Exploratory Data Analysis
+description: >-
+  Real-time exploratory data analysis of the TreeOfLife-10M and Rare Species
+  datasets during their creation and refinement. It is not intended for re-use
+  as a dataset, but is shared in the spirit of open-science to provide further
+  insight into the creation of the TreeOfLife-10M dataset and the Rare Species
+  benchmark.
+tags:
+- EDA
+- imageomics
+- biology
+- rare-species
+- plants
+- animals
+- fungi
+- reference
+viewer: false
 ---
-# TreeOfLife10M EDA Repo
+# TreeOfLife-10M EDA Repo
 
-This repo contains the analysis of the TreeOfLife10M dataset as it's being crafted and refined.
+This repo contains the real-time exploratory data analysis of the [TreeOfLife-10M](https://huggingface.co/datasets/imageomics/TreeOfLife-10M) and [Rare Species](https://huggingface.co/datasets/imageomics/rare-species) datasets during their creation and refinement. It is not intended for re-use as a dataset, but is shared in the spirit of open-science to provide further insight into the creation of the TreeOfLife-10M dataset and the Rare Species benchmark.
 
-## Data
+## Dataset Details
+
+### Dataset Description
+
+- **Curated by:** Elizabeth G. Campolongo and Matthew J. Thompson
+- **Homepage:** [BioCLIP Project Page](https://imageomics.github.io/bioclip/)
+- **Repository:** [BioCLIP project repo](https://github.com/Imageomics/BioCLIP)
+- **Paper:** [BioCLIP: A Vision Foundation Model for the Tree of Life](https://arxiv.org/abs/2311.18803)
+
+
+## Dataset Structure
+
+As noted above, this dataset consists primarily of the exploratory data analysis during creation of the [TreeOfLife-10M](https://huggingface.co/datasets/imageomics/TreeOfLife-10M) and [Rare Species](https://huggingface.co/datasets/imageomics/rare-species) datasets. More detailed descriptions of its contents are provided below.
+
+```
+data/
+    taxa_files/
+        sample_images/
+            20507360_64639770_eol-full-size-copy.jpg
+            22255430_64639830_eol-full-size-copy.jpg
+            29906970_65415246_eol-full-size-copy.jpg
+            29907020_65415246_eol-full-size-copy.jpg
+            30038365_65415248_eol-full-size-copy.jpg
+            8757019_49951271_eol-full-size-copy.jpg
+            8757071_49951271_eol-full-size-copy.jpg
+            8757093_49951271_eol-full-size-copy.jpg
+            8757102_49951271_eol-full-size-copy.jpg
+            8791997_49952170_eol-full-size-copy.jpg
+            8792002_49952170_eol-full-size-copy.jpg
+            8922943_49955771_eol-full-size-copy.jpg
+        ToL_hybrids_Arthropoda.csv
+        sample_arthropoda_mislabels.txt
+        README.md    # Hemihomonym description and explanation
+    avg_std_byClass.csv
+    catalog-v1-dev.csv
+    catalog.csv
+    licenses.csv
+    missing_taxa_output.txt
+    predicted-catalog.csv
+    stats_avg_std_byClass.csv
+    taxa_counts.csv
+    tol_hierarchy_test.csv
+eol_realign/
+    data/
+        checksums_media_cargo_archive.csv
+        combined-manifest-licenses.csv
+        combined_manifest.csv
+        combined_manifest_with_checksums.csv
+        eol-cargo-archive_catalog_combined-manifest-checksums_links.csv
+        eol-cargo-archive_combined-manifest-checksums_links.csv
+        full_owner_manifest.csv
+        links_cargo_manifest_IDmismatch.csv
+        links_inner.csv
+        links_manifest_cargo_on_md5.csv
+        mismatched_rarespecies.csv
+        rarespecies_full_manifest.csv
+        rs_links.csv
+    notebooks/
+        catalog-cargo-manifest_test.ipynb
+        links_align_reduced.ipynb
+        links_align_reduced.py
+        links_rs_duplicates.ipynb
+        links_rs_duplicates.py
+        re-gen_rs_catalog.ipynb
+        re-gen_tol_catalog.ipynb
+    scripts/
+        make_licenses.py
+        match_owners.py
+notebooks/
+    BioCLIP_data_viz.ipynb
+    BioCLIP_taxa_viz.ipynb
+    BioCLIP_taxa_viz.py
+    BioCLIP_taxa_viz_bySource.ipynb
+    ToL_EDA.ipynb
+    ToL_catalog_EDA.ipynb
+    ToL_catalog_EDA.py
+    ToL_predicted-catalog_EDA.ipynb
+    ToL_predicted-catalog_EDA.py
+    make_ToL_hybrids_Arthropoda_EDA.ipynb
+    missing_taxa_testGen.ipynb
+rare_species/
+    data/
+        licenses.csv
+        rarespecies-catalog.csv
+        rarespecies_manifest.csv
+visuals/
+    category-v1-visuals/    # "catalog v1" visualizations, don't match published dataset
+    kingdom_ToL_tree.html
+    kingdom_ToL_tree.pdf
+    phyla_ToL_tree.html
+    phyla_ToL_tree.pdf
+requirements.txt    # installation of these packages is sufficient for all code (notebooks & scripts) in this repo
+```
+
+
+### 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. [`v3.3`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/d6b583841aed8c0df314e718735756b76164a933/data/catalog.csv) is the version of the catalog that was used for training [BioCLIP v1](https://doi.org/10.57967/hf/1511) (it has the ~30K images we could not re-align).
@@ -17,10 +128,17 @@ images, and images that have labels.
  - `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.
+ - `missing_taxa_output.txt`: output from the [check taxa script](https://github.com/Imageomics/bioclip/blob/main/scripts/evobio10m/check_taxa.py), record of versions of catalog checked are indicated before the printout (text was copied from the terminal).
  - `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. 
+ - `tol_hierarchy_test.csv`: Subset of `catalog-v1-dev.csv` for testing the [`check_taxa` script](https://github.com/Imageomics/bioclip/blob/main/scripts/evobio10m/check_taxa.py) to ensure the hierarchy is properly filled in after data generation.
+ - `licenses.csv`: licensing information for all images in the catalog. This should match the published [licenses.csv](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/blob/main/metadata/licenses.csv) (SHA256 match), described in the [metadata section of the TreeOfLife-10M Dataset Card](https://huggingface.co/datasets/imageomics/TreeOfLife-10M#metadata-files).
 
-## Rare Species 
+#### Taxa Files
+
+This subfolder of `data/` explores instances of hemihomonyms (taxa in different kingdoms with matching Genus-species) in the dataset. One thought is that this may be part of the reason we had so many misclassifications into _Arthropoda_. 
+There is a notebook that partially explores this (`notebooks/make_ToL_hybrids_Arthropoda_EDA.ipynb`) and two associated files (`data/taxa_files/ToL_hybrids_Arthropoda.csv` and `data/taxa_files/sample_arthropoda_mislabels.txt` which is a list of filenames for the sample images in `data/taxa_files/sample_images/`). More details are provided in the [taxa_files README](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/taxa_files/README.md). This discovery lead to the re-resolution of the TreeOfLife-10M taxonomy from the original published dataset ([TreeOfLife-10M (Revision 69ca82e), DOI: 10.57967/hf/1972](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/tree/69ca82e7481dcae0764f7c5452ea32b3a41cf620), the reproducibility + embeddings update to the original is [Revision ffa2a31, DOI: 10.57967/hf/7542](https://huggingface.co/datasets/imageomics/TreeOfLife-10M/tree/ffa2a318a1396f2f9e456ba171d3b5b5d8b4f051)).
+
+### Rare Species 
 All these files were generated in `eol_realign/notebooks/re-gen_rs_catalog.ipynb`.
  - `licenses.csv`: Licensing information for all rarespecies images (includes MD5s and links to catalog and manifest on `rarespecies_id`).
  - `rarespecies_manifest.csv`: Full manifest information for all images included in rarespecies catalog (may have some extra info from realign).
@@ -28,12 +146,12 @@ All these files were generated in `eol_realign/notebooks/re-gen_rs_catalog.ipynb
 For evaluation, Lisa generated a `metadata.csv` that cut the `rarespecies-catalog.csv` down to just the taxonomic columns with index, changing `class` to `cls`, `common` to `common_name`, and creating a `filepath` column (`"2024-03-20/" + <eol_content_id> + "_" + <eol_page_id> + "_eol-full-size-copy.jpg"`), with a `class` column indicating the `sciName` (though this could use a different ID depending on the evaluation).
 
 
-## EOL Re-align
+### EOL Re-align
 
   More detail on the background of this process can be found in the `links_align_reduced` and `links_rs_duplicates` notebooks, as well as [PR #5](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions/5).
   
  * **Data:**
-    More information on all the datacan be found in the `links_align_reduced` and `links_rs_duplicates` notebooks. Just those of primary import and potential continued use are listed here.
+    More information on all the data can be found in the `links_align_reduced` and `links_rs_duplicates` notebooks. Just those of primary import and potential continued use are listed here.
 
     - `checksums_media_cargo_archive.csv`: MD5 of all EOL images in our cargo archive.
     - `full_owner_manifset.csv`: Record of all images from EOL that could potentially be used in the TreeOfLife-10M dataset, this has all the non-taxonomic EOL metadata for the EOL images included in the TreeOfLife-10M catalog (12,330,062 entries, gets reduced down during catalog re-generation), with MD5s aligned to `filename` (`<eol_content_id>_<eol_page_id>_eol-full-size-copy.jpg`).
@@ -54,7 +172,7 @@ For evaluation, Lisa generated a `metadata.csv` that cut the `rarespecies-catalo
      - `make_licenses.py`: Adds license URLs to make the full manifest and license file.
      - `match_owners.py`: Adds extra licensing information toward making the full manifest. Uses `eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv`, makes `eol_realign/data/combined_manifest.csv` for generating final catalog.
 
-## Notebooks
+### 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.
@@ -66,16 +184,86 @@ The `notebooks` folder contains
  - `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.
+ - `make_ToL_hybrids_Arthropoda_EDA.ipynb`:
+ - `missing_taxa_testGen.ipynb`: generates `tol_hierarchy_test.csv` to test [`check_taxa` script](https://github.com/Imageomics/bioclip/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
+### Visuals
 
-Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. 
+Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. These were created using the [`taxa_viz` script](https://github.com/Imageomics/bioclip/blob/main/scripts/evobio10m/taxa_viz.py).
 - `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.
+- `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.
+
+
+## Licensing Information
+
+The images shared in this repository (`data/taxa_files/sample_images/`) are shared under their original licenses as indicated in [`data/taxa_files/metadata.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/data/taxa_files/metadata.csv).
+
+The code in this repository is shared under an [MIT license](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/LICENSE.md).
+
+For more information on the dataset licensing and that of images mentioned or referenced throughout this repository, please see the [TreeOfLife-10M](https://huggingface.co/datasets/imageomics/TreeOfLife-10M) license files. The data (images and text) contain a variety of licensing restrictions mostly within the CC family. Each image and text in this dataset is provided under the least restrictive terms allowed by its licensing requirements as provided to us (i.e, we impose no additional restrictions past those specified by licenses in the license file).
+
+Please see the [iNat21 terms of use](https://github.com/visipedia/inat_comp/tree/master/2021#terms-of-use) for full information on use of their images.
+
+All BIOSCAN-1M images are licensed under [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/).
+
+EOL images contain a variety of licenses ranging from [CC0](https://creativecommons.org/publicdomain/zero/1.0/) to [CC BY-NC-SA](https://creativecommons.org/licenses/by-nc-sa/4.0/). For license and citation information by image, see the associated license files.
+
+## Acknowledgements
+
+This work was supported by the [Imageomics Institute](https://imageomics.org), which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
+
+## Citation
+
+As noted in the description of this dataset, it is not a finished product intended for re-use, but is provided in as an act of open-science. If the exploration or scripts are re-used, please cite our paper: 
+```
+@inproceedings{stevens2024bioclip,
+  title = {{B}io{CLIP}: A Vision Foundation Model for the Tree of Life}, 
+  author = {Samuel Stevens and Jiaman Wu and Matthew J Thompson and Elizabeth G Campolongo and Chan Hee Song and David Edward Carlyn and Li Dong and Wasila M Dahdul and Charles Stewart and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
+  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
+  year = {2024},
+  pages = {19412-19424}
+}
+```
+
+See also the citation instructions for [TreeOfLife-10M](https://huggingface.co/datasets/imageomics/TreeOfLife-10M#citation-information) and the [Rare Species Benchmark](https://huggingface.co/datasets/imageomics/rare-species), and please be sure to also cite the original data sources and all constituent parts as appropriate.
+
+- iNat21:
+```
+@misc{inat2021,
+  author={Van Horn, Grant and Mac Aodha, Oisin},
+  title={iNat Challenge 2021 - FGVC8},
+  publisher={Kaggle},
+  year={2021},
+  url={https://kaggle.com/competitions/inaturalist-2021}
+}
+```
+- BIOSCAN-1M:
+```
+@inproceedings{gharaee2023step,
+    title={A Step Towards Worldwide Biodiversity Assessment: The {BIOSCAN-1M} Insect Dataset},
+    booktitle = {Advances in Neural Information Processing Systems ({NeurIPS}) Datasets \& Benchmarks Track},
+    author={Gharaee, Z. and Gong, Z. and Pellegrino, N. and Zarubiieva, I. and Haurum, J. B. and Lowe, S. C. and McKeown, J. T. A. and Ho, C. Y. and McLeod, J. and Wei, Y. C. and Agda, J. and Ratnasingham, S. and Steinke, D. and Chang, A. X. and Taylor, G. W. and Fieguth, P.},
+    year={2023},
+}
+```
+- EOL: Encyclopedia of Life. Available from http://eol.org. Accessed 29 July 2023.
+For license and citation information by image, see our [license file](https://huggingface.co/datasets/imageomics/treeoflife-10m/blob/main/metadata/licenses.csv).
+
+
+- ITIS: Retrieved July, 20 2023, from the Integrated Taxonomic Information System (ITIS) on-line database, www.itis.gov, CC0
+https://doi.org/10.5066/F7KH0KBK
+
+
+## Dataset Card Author
+
+Elizabeth G. Campolongo
+
+## Dataset Card Contact
+
+Please use the [Community Tab](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions) for questions. More information on the _published_ project is available on our [project website](https://imageomics.github.io/bioclip/) and at the references therein.