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Update description of datasets to include the mimicry group information

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  1. README.md +10 -2
README.md CHANGED
@@ -17,6 +17,7 @@ tags:
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  - cross types
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  - wild
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  - lab-bred
 
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  pretty_name: Heliconius Collection (Cambridge Butterfly)
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  size_categories:
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  - 10K<n<100K
@@ -60,6 +61,8 @@ Please note that the [EarthCape Database](https://heliconius.ecdb.io/Occurrence_
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  Both dorsal and ventral images available. Contains primarily separated wings, with some whole butterfly images. There is variation in image content (whitestandard, background color, etc. based on the needs of the project).
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  <!---
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  This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
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  --->
@@ -150,6 +153,7 @@ CSV Columns are as follows:
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  - `filename`: Unique filename assigned to image at download (`<X>_<Image_name>.<jpg/tif/CR2>`) using `scripts/download_jiggins_subset.py`.
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  - `filepath`: Filepath of the downloaded image (`<image_folder>/<Taxonomic_Name>/<filename>`) using `scripts/download_jiggins_subset.py`.
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  - `md5`: MD5 of the downloaded image. This was used as the measure of uniqueness (at the pixel level) to address duplication of images across Zenodo records.
 
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  **Note:**
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  - `Jiggins_Zenodo_dorsal_Img_Master.csv` also has a column `CAM_dupe` indicating whether the `CAMID` has multiple images of the same file type within this subset. Most (11,446) specimens have only one dorsal image per file type.
@@ -169,6 +173,8 @@ CSV Columns are as follows:
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  The Butterfly Genetics Group has a large collection of butterfly images distributed across 31 Zenodo records. They do not all have the same information, and it is sometimes only provided in the record, but not the metadata. With this collection, we combine the provided information (metadata) into a shared format that is easily ingested into ML pipelines. We also add some other labels of interest (based on identification determined by the Butterfly Genetics Group), and endeavor to remove duplication, noting potential points of duplication and providing some assessment tools to help prevent data leakage. This de-duplication effort reduced the overall dataset to covering only 29 of these records, and it is documented in the `deduplication_process` directory.
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  Additionally, these datasets are prepared in a format that allows for easy integration with the Imageomics Institute's [Data Dashboard](https://huggingface.co/spaces/imageomics/dashboard-prototype) for distribution statistics and easy sampling of images by taxonomic information and view.
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  ### Source Data
@@ -184,6 +190,7 @@ The [original Master file](https://huggingface.co/datasets/imageomics/Heliconius
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  These images are of a mix of wild-caught and lab-bred butterflies, classified by the Butterfly Genetics Group.
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  ### Personal and Sensitive Information
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@@ -216,6 +223,7 @@ Please see [`README-supplemental.md`](https://huggingface.co/datasets/imageomics
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  **This Collection:**
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  * Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
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  * Elizabeth G. Campolongo (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0846-2413
 
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  ### Licensing Information
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@@ -225,9 +233,9 @@ Images can be matched to their source record through the `zenodo_link` or `recor
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  ### Citation Information
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- Christopher Lawrence and Elizabeth G. Campolongo. (2024). Heliconius Collection (Cambridge Butterfly). Hugging Face. https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly.
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- If you use this compilation, please cite the original datasets compiled by the Butterfly Genetics Group at University of Cambridge (bibtex citations for all 29 included Zenodo records are in [`jiggins.bib`](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/blob/main/metadata/jiggins.bib)) as well as this curated subset.
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  ### Contributions
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  - cross types
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  - wild
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  - lab-bred
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+ - mimic groups
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  pretty_name: Heliconius Collection (Cambridge Butterfly)
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  size_categories:
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  - 10K<n<100K
 
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  Both dorsal and ventral images available. Contains primarily separated wings, with some whole butterfly images. There is variation in image content (whitestandard, background color, etc. based on the needs of the project).
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+ Additionally, we added image-level Heliconius subspecies mimic group information to the entries. The two subspecies in this dataset that exhibit polymorphic mimicry (_Heliconius doris ssp. doris_ and _Heliconius melpomene ssp. martinae_) were labeled based on the specimen images (all mimicry groups are accurate for the images).
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+
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  <!---
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  This dataset card aims to be a base template for new datasets. It has been generated using [this raw template](https://github.com/huggingface/huggingface_hub/blob/main/src/huggingface_hub/templates/datasetcard_template.md?plain=1).
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  --->
 
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  - `filename`: Unique filename assigned to image at download (`<X>_<Image_name>.<jpg/tif/CR2>`) using `scripts/download_jiggins_subset.py`.
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  - `filepath`: Filepath of the downloaded image (`<image_folder>/<Taxonomic_Name>/<filename>`) using `scripts/download_jiggins_subset.py`.
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  - `md5`: MD5 of the downloaded image. This was used as the measure of uniqueness (at the pixel level) to address duplication of images across Zenodo records.
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+ - `mimic_group`: Mimicry group of the subspecies; only included for Heliconius subspecies. Polymorphic subspecies (_Heliconius doris ssp. doris_ and _Heliconius melpomene ssp. martinae_) are labeled based on the specimen images.
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  **Note:**
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  - `Jiggins_Zenodo_dorsal_Img_Master.csv` also has a column `CAM_dupe` indicating whether the `CAMID` has multiple images of the same file type within this subset. Most (11,446) specimens have only one dorsal image per file type.
 
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  The Butterfly Genetics Group has a large collection of butterfly images distributed across 31 Zenodo records. They do not all have the same information, and it is sometimes only provided in the record, but not the metadata. With this collection, we combine the provided information (metadata) into a shared format that is easily ingested into ML pipelines. We also add some other labels of interest (based on identification determined by the Butterfly Genetics Group), and endeavor to remove duplication, noting potential points of duplication and providing some assessment tools to help prevent data leakage. This de-duplication effort reduced the overall dataset to covering only 29 of these records, and it is documented in the `deduplication_process` directory.
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+ We added image-level Heliconius subspecies mimic group information to further our ability to study mimicry with ML; they also can help provide context or another layer of analysis for mistaken mimic predictions.
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+
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  Additionally, these datasets are prepared in a format that allows for easy integration with the Imageomics Institute's [Data Dashboard](https://huggingface.co/spaces/imageomics/dashboard-prototype) for distribution statistics and easy sampling of images by taxonomic information and view.
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  ### Source Data
 
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  These images are of a mix of wild-caught and lab-bred butterflies, classified by the Butterfly Genetics Group.
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+ Mimicry group labels were provided by [Neil Rosser](https://scholar.google.com/citations?user=bKyzoi0AAAAJ&hl=en) and added programmatically in [`notebooks/Data-gen-1-3.ipynb`](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/blob/main/notebooks/Data-gen-1-3.ipynb). The two Heliconius subspecies in this dataset that exhibit polymorphic mimicry (_Heliconius doris ssp. doris_ and _Heliconius melpomene ssp. martinae_) were given the `mimic_group` label for those particular specimens.
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  ### Personal and Sensitive Information
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  **This Collection:**
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  * Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
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  * Elizabeth G. Campolongo (Imageomics Institute, The Ohio State University) - ORCID: 0000-0003-0846-2413
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+ * Neil Rosser (Harvard University) - ORCID: 0000-0001-7796-2548
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  ### Licensing Information
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  ### Citation Information
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+ Christopher Lawrence, Elizabeth G. Campolongo, and Neil Rosser. (2024). Heliconius Collection (Cambridge Butterfly). Hugging Face. https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly. [Add updated DOI for mimic group update].
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+ If you use this compilation, please also cite the original datasets compiled by the Butterfly Genetics Group at University of Cambridge (bibtex citations for all 29 included Zenodo records are in [`jiggins.bib`](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly/blob/main/metadata/jiggins.bib)) as well as this curated subset.
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  ### Contributions
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