Update description of dataset components

Add configs, rationale, considerations, extra notes, log file description

README.md

@@ -11,67 +11,96 @@ tags:
 - separated wings
 - mimicry
 - CV
+- erato
+- melpomene
+- hybrids
+- cross types
+- wild
+- lab-bred
 pretty_name: Jiggins Heliconius Collection
 size_categories:
 - 10K<n<100K
 language:
 - en
+configs:
+- config_name: full_master
+  data_files:
+  - split: train
+    path: "Jiggins_Zenodo_Img_Master.csv"
+- config_name: heliconius
+  data_files:
+  - split: train
+    path: "Jiggins_Heliconius_Master.csv"
+- config_name: dorsal
+  data_files:
+  - split: train
+    path: "Jiggins_Zenodo_dorsal_Img_Master.csv"
 ---
 # Dataset Card for Jiggins Heliconius Collection
 
 ## Dataset Description
 
+<!--
 - **Homepage:** 
 - **Repository:** 
 - **Paper:** 
 - **Leaderboard:** 
 - **Point of Contact:** 
+-->
 
 ### Dataset Summary
 
-Subset of the collection records from the research group of Chris Jiggins at the University of Cambridge derived from almost 20 years of field studies. 
-This subset contains approximately 49,359 RGB images of 12,586 specimens (34,929 images of 9,546 specimens across all Heliconius). Many records include images as well as locality data. 
-All detached wings were photographed with a DSLR camera with a 100 mm macro-lens in standardized conditions; images and full records with data are stored in the [EarthCape database](https://heliconius.ecdb.io/default.aspx) and on [Zenodo](https://zenodo.org/communities/butterfly?q=&l=list&p=1&s=10&sort=newest) (across 32 records from the Butterfly Genetics Group).
+Subset of the collection records from Chris Jiggins' research group at the University of Cambridge, collection covers nearly 20 years of field studies. 
+This subset contains approximately 44,809 RGB images of 11,991 specimens (34,265 images of 10,109 specimens across all Heliconius). Many records have both images and locality data. 
+
+Most images were photographed with a DSLR camera with a 100 mm macro-lens in standardized conditions. 
+More information can be found at the individual Zenodo record pages.
+Images and full records with data are stored in the [EarthCape database](https://heliconius.ecdb.io/default.aspx) and on [Zenodo](https://zenodo.org/communities/butterfly?q=&l=list&p=1&s=10&sort=newest) (across 31 records from the Butterfly Genetics Group).
 
 Both dorsal and ventral images available. Contains both whole butterfly, and 4 wings separate. Large variation in image content.
 
 <!---
 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).
 --->
+<!--
 ### Supported Tasks and Leaderboards
 
-[More Information Needed]
+[More Information Needed] -->
 
 ### Languages
 
-[More Information Needed]
+English, Latin
 
 ## Dataset Structure
 
-* **Jiggins_Zenodo_Img_Master.csv:** Information for the approximately 49,0000 unprocessed image files included in the Jiggins Heliconius Collection. Image types are `jpg`, `raw` (.CR2) and `tif`. `genus`, `species`, and `subspecies` are included columns.
-     * To access the images combine columns `zenodo_link` and `Image_name`:
-       ```
-       zenodo_link + '/files/' + Image_name
-       ```
+* **Jiggins_Zenodo_Img_Master.csv:** Information for the approximately 45,0000 unprocessed image files included in the Jiggins Heliconius Collection. Image types are `jpg`, `raw` (.CR2) and `tif`. `genus`, `species`, and `subspecies` are included columns.
 
-* **Jiggins_Zenodo_dorsal_Img_Master.csv:** Subset of 24,318 images from `Jiggins_Zenodo_Img_Master.csv` with a dorsal view of the butterflies (note that some have both dorsal and ventral). This subset includes 12,296 unique specimens. Accessing the images from Zenodo works the same as above, and image types are `jpg`, `raw` (.CR2) and `tif`.
+* **Jiggins_Zenodo_dorsal_Img_Master.csv:** Subset of 22,175 images from `Jiggins_Zenodo_Img_Master.csv` with a dorsal view of the butterflies (note that some have both dorsal and ventral). This subset includes 12,296 unique specimens. Image types and columns are the same as for the Master file.
 
-* **Jiggins_Heliconius_Master.csv:** The 34,929-image subset of all Heliconius images from `Jiggins_Zenodo_Img_Master.csv`. This subset includes 9,546 unique specimens. Accessing the images from Zenodo works the same as above, and image types are `jpg`, `raw` (.CR2) and `tif`. `species` and `subspecies` columns are also included.
+* **Jiggins_Heliconius_Master.csv:** The 34,265-image subset of all Heliconius images from `Jiggins_Zenodo_Img_Master.csv`. This subset includes 10,109 unique specimens. IImage types and columns are the same as for the Master file.
 
 
-
-* Note: The notebooks that generated these files and stats are included in the `notebooks` folder.
-
+**Notes:**
+- The notebooks that generated these files and stats are included in the `notebooks` folder.
+    - The original Jiggins Zenodo Master file was compiled from the CSVs provided with the included Zenodo records from the Butterfly Genetics Group. Christopher Lawrence selected which of these provided columns to include. Further processing and standardization (all documented in the Jupyter Notebooks) was performed by Elizabeth Campolongo.
+    - Taxonomic information for records [5526257](https://zenodo.org/record/5526257), [2554218](https://zenodo.org/record/2554218), and [2555086](https://zenodo.org/record/2555086) was recovered from information on their Zenodo pages, as the provided CSVs did not contain that information. 
+    - Be advised that there may be overlap between images in [record 2548678](https://zenodo.org/records/2548678) and [record 3082688](https://zenodo.org/records/3082688).
+- The `scripts` folder has a download and checksum script. 
+    - Images are downloaded to the provided images directory with subfolders labeled by the `Taxonomic_Name`, with filenames `<X>_<Image_name>`.
+    - The checksum script is called by `download_jiggins_subset.py` to generate an MD5 for all download images and creates a CSV with `filepath`, `filename`, and `md5` columns in the same folder as the source CSV (named `<source CSV>_checksums.csv`). This helps to ensure FAIR and Reproducible results, though this will _**not**_ distinguish between the raw and jpg versions of the same image.
+    - A log of the download is also generated in the same folder as the source CSV (named `<source CSV>_log.json`).
+- `metadata/Missing_taxa_Jiggins_Zenodo_Master.csv` contains a record of the images that did not have easily reconcilable taxonomic information (see `notebooks/standardize_datasets.ipynb` for more information on this data). There are 1,630 such images distributed across 18 records.
 
 ### Data Instances
 
 `Jiggins_Heliconius_Master.csv` contains multiple species of Heliconius (including erato and melpomene), most are labeled down to the subspecies level. The `Jiggins_Zenodo_Img_Master.csv` also contains species from other genera, with just over half labeled to the subspecies level (these are predominantly Heliconius subspecies).
+
 Detached wings in four quadrants (generally).
 Some subspecies may be photographed differently, needs segmentation preprocessing.
 
 * **Type:** JPG/jpg/tif(very few)
 * **Size (x pixels by y pixels):** Unknown yet
-* **Background (color or none):** multiple (needs to be normalized)
+* **Background (color or none):** multiple (needs to be normalized, often grey or lime green)
 * **Fit in frame:**
 * **Ruler or Scale:** Some with Ruler
 * **Color (ColorChecker, white-balance, None):** None
@@ -90,12 +119,12 @@ CSV Columns are as follows:
 
 - `CAMID`: Unique identifier for each specimen that was photographed. Each `CAMID` corresponds to multiple images (based on factors such as `View` and `file_type`).
 - `X`: Unique identifier for each line in the master CSV.
-- `Image_name`: Filename of image.
+- `Image_name`: Filename of image (not unique, often `CAM<CAMID>_<v or d>`).
 - `View`: View of the butterfly in the image: `dorsal`, `ventral`, `forewing dorsal`, `hindwing dorsal`, `forewing ventral`, `hindwing ventral`, `dorsal and ventral`.
 - `zenodo_name`: Name of the CSV file with metadata used to populate this file from the associated Zenodo record.
 - `zenodo_link`: URL for the Zenodo record of the image.
 - `Sequence`: Mostly numeric IDs, not unique, please see the associated Zenodo record for more information on the meaning of these designations.
-- `Taxonomic_Name`: Indication of the Genus, Species, and possibly, subspecies, of the specimen. For Cross Types, this is just the Genus species pair (all _Heliconius erato_ or _Heliconius melpomene_).
+- `Taxonomic_Name`: Indication of the Genus, species, and possibly, subspecies, of the specimen. For Cross Types, the hybrid names are reduced to just the two subspecies (from the `Cross_Type` column) and non-specified crosses are labeled `<Genus> <species> cross hybrid`.
 - `Locality`: Likely location of specimen collection, varying levels of specificity. Please see the associated Zenodo record for more information on the meaning of these designations.
 - `Sample_accession`: Some type of ID, not unique, please see the associated Zenodo record for more information on the meaning of these designations.
 - `Collected_by`: Abbreviations (likely for those collecting the specimen), please see the associated Zenodo record for more information on the meaning of these designations.
@@ -114,44 +143,40 @@ CSV Columns are as follows:
 - `species`: Species of the specimen. There are 246 species represented in the full collection, 37 of these are species of Heliconius.
 - `subspecies`: Subspecies of the specimen (where available, mostly labeled for Heliconius). There are 155 subspecies represented in the full collection, 110 of which are Heliconius subspecies.
 - `genus`: Genus of the specimen. There are 94 unique genera represented in the full collection.
+- `file_url`: URL to download image from Zenodo: `zenodo_link + "/files/" + Image_name`. Allows for sample image display in [data dashboard](https://huggingface.co/spaces/imageomics/dashboard-prototype).
+- `hybrid_stat`: Hybrid status of the sample: `hybrid`, `non-hybrid`, or `None`. Hybrids are determined by an ` x ` or `hybrid` in the `Taxonomic_Name` column, all other images classified to the _subspecies_ level are labeled as `non-hybrid`, and the parent species of the one species-level hybrid is labeled as `non-hybrid` (only one of them is present in the dataset).
 
 **Note:**
- - `Jiggins_Heliconius_Master.csv` has all but the `genus` column, since all images are Heliconius.
- - `Jiggins_Zenodo_dorsal_Img_Master.csv` does not have the last four columns, but they can be added easily with the appropriate functions in `notebooks/standardize_taxa.ipynb`. This file also has a column `CAM_dupe` indicating whether the `CAMID` has multiple images within this subset.
+ - `Jiggins_Zenodo_dorsal_Img_Master.csv` also has a column `CAM_dupe` indicating whether the `CAMID` has multiple images within this subset.
+    - We do not leave the first instance as a non-duplicate, so to have a clear assessment of all duplication (eg., is it just across a couple records, file types, etc).
+    - `CAMID`s are necessarily duplicated for the images that are of just a dorsal forewing or hindwing, so we label those as `single_wing`.
+    - There are multiple jpg images & multiple raw images of the same specimen. Note that this does not necessarily mean these are duplicates of the same images. There are also jpg copies provided alongside raw images.
 
+<!--
 ### Data Splits
 
 [More Information Needed]
+-->
       
 ## Dataset Creation
 
 ### Curation Rationale
 
-[More Information Needed]
-
-### Source Data
+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. 
 
-These images are a subset of the [Butterfly Genetics Group's Cambridge butterfly collection](https://zenodo.org/communities/butterfly?q=&f=subject%3ACambridge&l=list&p=1&s=10&sort=newest). This collection of butterfly images comes from the research group of Chris Jiggins at the University of Cambridge derived from almost 20 years of field studies.
+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.
 
-Data is pulled from the Zenodo Records in [`licenses.json`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/licenses.json). This file also contains full citation information for all records.
-
-#### Initial Data Collection and Normalization
-
-[More Information Needed]
-
-#### Who are the source language producers?
+### Source Data
 
-[More Information Needed]
+These images are a subset of the [Butterfly Genetics Group's Cambridge butterfly collection](https://zenodo.org/communities/butterfly?q=&f=subject%3ACambridge&l=list&p=1&s=10&sort=newest). This collection of butterfly images comes from the research group of Chris Jiggins at the University of Cambridge derived from almost 20 years of field studies. 
 
-### Annotations
+Data is pulled from the Zenodo Records in [`licenses.json`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/metadata/licenses.json). This file also contains full citation information for all records.
 
-#### Annotation process
 
-[More Information Needed]
+#### Initial Data Collection and Annotation
 
-#### Who are the annotators?
+These images are of a mix of wild-caught and lab-bred butterflies, classified by the Butterfly Genetics Group.
 
-[More Information Needed]
 
 ### Personal and Sensitive Information
 
@@ -159,17 +184,13 @@ None
 
 ## Considerations for Using the Data
 
-### Social Impact of Dataset
+### Discussion of Biases and Other Known Limitations
 
-[More Information Needed]
+- This dataset is imbalanced. Even among the Heliconius subset, some subspecies are more heavily represented than others. 
+- There are a mix of valid subspecies and hybrids that are labeled as such, but there are also images of butterflies classified only to the genus or species level, for which such a designation may not be clearly made (there are also instances of "_Heliconius <species> hybrid_", where the parent subspecies are not indicated. 
+- There may be overlap between images in [record 2548678](https://zenodo.org/records/2548678) and [record 3082688](https://zenodo.org/records/3082688).
+- There are multiple images of the same specimen for many specimens; sometimes this is due to different views (eg., dorsal or ventral side), sometimes it is due to JPG copies of the RAW photos, though it is also sometimes that new photos were taken of the same specimen at a different times.
 
-### Discussion of Biases
-
-[More Information Needed]
-
-### Other Known Limitations
-
-[More Information Needed]
 
 ## Additional Information
 
@@ -178,6 +199,7 @@ None
 * Christopher Lawrence (Princeton University) - ORCID: 0000-0002-3846-5968
 * Chris Jiggins (University of Cambridge) - ORCID: 0000-0002-7809-062X
 * Butterfly Genetics Group (University of Cambridge)
+* Elizabeth G. Campolongo - ORCID: 0000-0003-0846-2413
 
 ### Licensing Information
 
@@ -187,10 +209,10 @@ Images can be matched to their source record through the `zenodo_link` column in
 
 ### Citation Information
 
-Christopher Lawrence, Chris Jiggins, Butterfly Genetics Group (University of Cambridge). (2023). Jiggins Heliconius Collection. Hugging Face. https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection.
+Christopher Lawrence, Chris Jiggins, Butterfly Genetics Group (University of Cambridge), Elizabeth Campolongo. (2024). Jiggins Heliconius Collection. Hugging Face. https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection.
 
-If you use this dataset, please cite the original datasets (citations for all 32 Zenodo records are in licenses.json) as well as this curated subset. 
+If you use this dataset, please cite the original datasets (citations for all 31 Zenodo records are in licenses.json) as well as this curated subset. 
 
 ### Contributions
 
-The [Imageomics Institute](https://imageomics.org) is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) Institute 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).
+The [Imageomics Institute](https://imageomics.org) 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.