This repository keeps track of the process of manually curating Parkinson's metadata. The resulting metadata and accompanying assay data can be accessed with parkinsonsMetagenomicData.

At the moment, we are prioritizing the curation of the following metadata features: Case/Control Status (for Parkinson's Disease), Age, and Sex. Curation is carried out following the data dictionary, merging schema, and ontology maps outlined in OmicsMLRepoData (OmicsMLRepoData contains the latest version of curatedMetagenomicData curation) where possible.

Original metadata files are stored in original_metadata/, and each dataset is curated in its respectively named R script, stored in scripts/. Also within scripts/, harmonization.R loads all of the original metadata for visualization. Harmonized metadata will be output to curated_metadata/. Finally, uuid_mapping/ contains a script describing how UUIDs are assigned to each sample, and the tables that map these generated UUIDs to the rest of the metadata. We also include the tables used to input these samples to the curatedMetagenomicsNextflow pipeline.