NOTE: The README has been updated on 05/28/2024 to reflect that we are no longer appending all files together. Each dataset is processed into PrimeKG format and uploaded to Dropbox after the preprocessing step.
Guidelines for Adding New Data to AlzKG
If you're contributing new data from a research paper to AlzKG, please follow these steps:
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Prepare your data for PrimeKG format using the convert_csv_kgraw_format.ipynb notebook. Follow the example usage provided in the code. This will generate an AlzKG file from your CSV file, with
node_idinitially set to "tbd." Note: Make sure that any new celltypes/states used in the code is entered into cell_data_dict.csv. -
Document edge types by copying and pasting the unique edge types printed by the convert_csv_kgraw_format.ipynb into the edge_type_data_dict.csv file
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Do a postprocessing step using the postprocess_kg_conversion.ipynb script. The output of convert_csv_kgraw_format.ipynb is the input to this postprocessing step.
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Upload your individual AlzKG files by creating a folder named after your research paper within the provided Dropbox link. Place your AlzKG files in this folder.
PrimeKG Files List. Location: https://www.dropbox.com/home/CATS-OMICS/AlzKG/PrimeKG
Original PrimeKG Files:
- kg_raw_orig_filtered
- nodes_orig_filtered
