DOI Generation

README.md

@@ -437,34 +437,50 @@ We ask that you cite this dataset and associated papers if you make use of it in
 
 ## Citation
 
-<!-- TODO: generate DOI and finalize citation -->
-<!-- TODO: Check Citation Format -->
-**Data:**
+If you use these embeddings, please cite this dataset **and** the embedding model whose config you used. Because the embeddings are derived from TreeOfLife-200M, please also cite the source dataset and its constituent data providers as appropriate.
+
 ```bibtex
 @misc{treeoflife_200m_embeddings,
   author = {Zhang, Net and Campolongo, Elizabeth and Thompson, Matthew and Gu, Jianyang},
   title = {{TreeOfLife-200M Embeddings}},
   year = {2026},
   url = {https://huggingface.co/datasets/imageomics/TreeOfLife-200M-Embeddings},
+  doi = {<TODO: doi once generated>},
   publisher = {Hugging Face}
 }
 ```
 
-Please also cite the source dataset and embedding model (include data sources as appropriate):
+### Embedding Models
 
-**TreeOfLife-200M:**
+**BioCLIP 2** (config `bioclip-2_float16`):
 ```bibtex
-@dataset{treeoflife_200m,
-  title = {{T}ree{O}f{L}ife-200{M} (Revision 94bbc0b)}, 
+@software{Gu_BioCLIP_2_model,
   author = {Jianyang Gu and Samuel Stevens and Elizabeth G Campolongo and Matthew J Thompson and Net Zhang and Jiaman Wu and Andrei Kopanev and Zheda Mai and Alexander E. White and James Balhoff and Wasila M Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
-  year = {2025},
-  url = {https://huggingface.co/datasets/imageomics/TreeOfLife-200M},
-  doi = {10.57967/hf/8980},
-  publisher = {Hugging Face}
+  license = {MIT},
+  title = {{BioCLIP 2}},
+  url = {https://huggingface.co/imageomics/bioclip-2},
+  version = {1.0.0},
+  doi = {10.57967/hf/5765},
+  publisher = {Hugging Face},
+  year = {2025}
+}
+```
+
+**BioCLIP 2.5 Huge** (config `bioclip-2.5-vith14_float16`):
+```bibtex
+@software{Gu_BioCLIP_2.5_Huge_model,
+  author = {Jianyang Gu and Samuel Stevens and Elizabeth G Campolongo and Matthew J Thompson and Net Zhang and Jiaman Wu and Andrei Kopanev and Zheda Mai and Alexander E. White and James Balhoff and Wasila M Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
+  license = {MIT},
+  title = {{BioCLIP 2.5 Huge}},
+  url = {https://huggingface.co/imageomics/bioclip-2.5-vith14},
+  version = {1.0.0},
+  doi = {10.57967/hf/10131},
+  publisher = {Hugging Face},
+  year = {2026}
 }
 ```
 
-**BioCLIP 2 Paper:**
+**BioCLIP 2 paper**:
 ```bibtex
 @inproceedings{NEURIPS2025_94da80cb,
  author = {Gu, Jianyang and Stevens, Sam and Campolongo, Elizabeth and Thompson, Matthew and Zhang, Net and Wu, Jiaman and Kopanev, Andrei and Mai, Zheda and White, Alexander and Balhoff, James and Dahdul, Wasila and Rubenstein, Daniel and Lapp, Hilmar and Berger-Wolf, Tanya and Chao, Wei-Lun (Harry) and Su, Yu},
@@ -472,30 +488,97 @@ Please also cite the source dataset and embedding model (include data sources as
  editor = {D. Belgrave and C. Zhang and H. Lin and R. Pascanu and P. Koniusz and M. Ghassemi and N. Chen},
  pages = {102778--102811},
  publisher = {Curran Associates, Inc.},
- title = {{BioCLIP 2:} Emergent Properties from Scaling Hierarchical Contrastive Learning},
+ title = {BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning},
  url = {https://proceedings.neurips.cc/paper_files/paper/2025/file/94da80cbfe870c1db958c88a8a27018c-Paper-Conference.pdf},
  volume = {38},
- year = {2025}
+ year = {2025},
+ doi = {10.52202/085713-3436}
 }
+
 ```
 
-<!--https://arxiv.org/abs/2505.23883-->
+### Source Dataset
+
+**TreeOfLife-200M**:
 
-**BioCLIP 2.5 Huge Model:**
 ```bibtex
-@software{Gu_BioCLIP_2.5_Huge_model,
+@dataset{treeoflife_200m,
+  title = {{T}ree{O}f{L}ife-200{M} (Revision 94bbc0b)}, 
   author = {Jianyang Gu and Samuel Stevens and Elizabeth G Campolongo and Matthew J Thompson and Net Zhang and Jiaman Wu and Andrei Kopanev and Zheda Mai and Alexander E. White and James Balhoff and Wasila M Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
-  license = {MIT},
-  title = {{BioCLIP 2.5 Huge}},
-  url = {https://huggingface.co/imageomics/bioclip-2.5-vith14},
-  version = {1.0.0},
-  doi = {10.57967/hf/10131},
-  publisher = {Hugging Face},
-  year = {2026}
+  year = {2026},
+  url = {https://huggingface.co/datasets/imageomics/TreeOfLife-200M},
+  doi = {10.57967/hf/8980},
+  publisher = {Hugging Face}
 }
 ```
 
+#### Source Data Providers
+
+The `source_dataset` column identifies the provider for every row. Please cite those whose records you use accordingly. 
+
+**GBIF:**
+```bibtex
+@misc{GBIF-DOI,
+  doi = {10.15468/DL.BFV433},
+  url = {https://doi.org/10.15468/dl.bfv433},
+  keywords = {GBIF, biodiversity, species occurrences},
+  author = {GBIF.org},
+  title = {{GBIF} Occurrence Download},
+  publisher = {The Global Biodiversity Information Facility},
+  month = {May},
+  year = {2024},
+  copyright = {Creative Commons Attribution Non Commercial 4.0 International}
+}
+```
+
+**EOL:** 
+```bibtex
+@misc{eol,
+    author = {{Encyclopedia of Life (EOL)}},
+    url = {https://eol.org},
+    note = {Accessed August 2024}
+}
+```
+
+**BIOSCAN-5M:**
+```bibtex
+@inproceedings{gharaee2024bioscan5m,
+    title={{BIOSCAN-5M}: A Multimodal Dataset for Insect Biodiversity},
+    booktitle={Advances in Neural Information Processing Systems},
+    author={Zahra Gharaee and Scott C. Lowe and ZeMing Gong and Pablo Millan Arias
+        and Nicholas Pellegrino and Austin T. Wang and Joakim Bruslund Haurum
+        and Iuliia Zarubiieva and Lila Kari and Dirk Steinke and Graham W. Taylor
+        and Paul Fieguth and Angel X. Chang
+    },
+    editor={A. Globerson and L. Mackey and D. Belgrave and A. Fan and U. Paquet and J. Tomczak and C. Zhang},
+    pages={36285--36313},
+    publisher={Curran Associates, Inc.},
+    year={2024},
+    volume={37},
+    url={https://proceedings.neurips.cc/paper_files/paper/2024/file/3fdbb472813041c9ecef04c20c2b1e5a-Paper-Datasets_and_Benchmarks_Track.pdf},
+}
+```
+
+**FathomNet:**
+```bibtex
+@article{katija_fathomnet_2022,
+    title = {{FathomNet}: {A} global image database for enabling artificial intelligence in the ocean},
+    volume = {12},
+    issn = {2045-2322},
+    shorttitle = {{FathomNet}},
+    url = {https://www.nature.com/articles/s41598-022-19939-2},
+    doi = {10.1038/s41598-022-19939-2},
+    number = {1},
+    urldate = {2025-05-13},
+    journal = {Scientific Reports},
+    author = {Katija, Kakani and Orenstein, Eric and Schlining, Brian and Lundsten, Lonny and Barnard, Kevin and Sainz, Giovanna and Boulais, Oceane and Cromwell, Megan and Butler, Erin and Woodward, Benjamin and Bell, Katherine L. C.},
+    month = sep,
+    year = {2022},
+    pages = {15914},
+}
+```
 
+For license and citation information by image, see the TreeOfLife-200M revision `94bbc0b` [provenance file](https://huggingface.co/datasets/imageomics/TreeOfLife-200M/blob/94bbc0b90cd26cbb15f94d3144941026f4b41213/dataset/metadata/provenance.parquet) (join on `uuid`).
 
 ## Acknowledgements