Add links for new files and description of final curation process.

README.md

@@ -81,15 +81,15 @@ English, Latin
 
 
 **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.
+- The notebooks that generated these files and stats are included in the `notebooks` folder, their only requirement is `pandas`.
+    - The [original Jiggins Zenodo Master file](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/metadata/Jiggins_Zenodo_Master.csv) 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. 
+- The `scripts` folder has a download and checksum script, their only requirement is `pandas`. 
     - 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 downloaded 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 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.
+- `metadata/Missing_taxa_Jiggins_Zenodo_Master.csv` contains a record of the images that did not have easily reconcilable taxonomic information (see `notebooks/Data-gen-0-3.ipynb` for more information on this data). There are 1,630 such images distributed across 18 records.
 
 ### Data Instances
 
@@ -175,6 +175,8 @@ These images are a subset of the [Butterfly Genetics Group's Cambridge butterfly
 
 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.
 
+The original Master file, created by Christopher, was fed into notebook Data-gen-0-1, and further processed in Data-gen-0-2 and Data-gen-0-3. The next data generation step (deduplication by MD5) involved downloading all images in `Jiggins_Zenodo_Img_Master_3477891Patch.csv` (created in Data-gen-1-1). MD5s of all downloaded images were taken and the results were explored in the EDA-DL series of notebooks; information and conclusions from this EDA are documented in the [`deduplication_process` README](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/deduplication_process/README.md). The outline described there was then implemented in the [Data-gen-1-2 notebook]((https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/notebooks/Data-gen-1-2.ipynb)), regenerating all current datasets. 
+
 
 #### Initial Data Collection and Annotation
 
@@ -195,7 +197,7 @@ None
 - 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 seems it is also sometimes that new photos were taken of the same specimen at a different times.
   - The master files contain only images that were determined to be unique (at the pixel level) through MD5 checksum. This does _**not**_ guarantee that there are not images that are cropped copies of other photos. For instance, [record 2553977](https://zenodo.org/records/2553977) has a number of images with `_cut_` in their name, some of which are close-up crops of the butterfly wings (though not all, some are just close-ups of the full butterfly).
 
-Please see the [`deduplication_process/README.md`]() for more details on the deduplication process and recommendations on how to split this data effectively without data leakage.
+Please see the [`deduplication_process/README.md`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/deduplication_process/README.md) for more details on the deduplication process and recommendations on how to split this data effectively without data leakage.
 
 
 ## Additional Information
@@ -211,13 +213,13 @@ Please see the [`deduplication_process/README.md`]() for more details on the ded
 
 The data (images and text) are all licensed under [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/). 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 this license on the original source files). Modified images are only restricted by this original license.
 
-Images can be matched to their source record through the `zenodo_link` or `record_number` column in the Master CSVs to the `url` or `record_number` in the licenses.json file, respectively.
+Images can be matched to their source record through the `zenodo_link` or `record_number` column in the Master CSVs to the `url` or `record_number` in the [`licenses.json`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/metadata/licenses.json) file, respectively.
 
 ### Citation Information
 
 Christopher Lawrence, Chris Jiggins, Butterfly Genetics Group (University of Cambridge), Elizabeth G. 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 29 included Zenodo records are in [jiggins.bib]()) as well as this curated subset. 
+If you use this dataset, please cite the original datasets (bibtex citations for all 29 included Zenodo records are in [`jiggins.bib`]([`licenses.json`](https://huggingface.co/datasets/imageomics/Jiggins_Heliconius_Collection/blob/main/metadata/jiggins.bib))) as well as this curated subset. 
 
 ### Contributions