In Sage-Bionetworks/dccvalidator: Metadata Validation for Data Coordinating Centers

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dccvalidator

dccvalidator is a package and Shiny app to perform data validation and QA/QC. It's used in the AMP-AD and PsychENCODE consortia to validate data prior to data releases.

Installation

You can install dccvalidator from CRAN:

install.packages("dccvalidator")

To install the development version from GitHub, run:

devtools::install_github("Sage-Bionetworks/dccvalidator")

Many functions in dccvalidator use reticulate and the Synapse Python client. See the reticulate documentation for information on how to set R to use a specific version of Python if you don't want to use the default Python installation on your machine. Whichever Python installation you choose should have synapseclient installed.

Because dccvalidator uses reticulate, it is not compatible with the synapser package.

Check data

dccvalidator provides functions for checking the following common data quality issues:

Annotation keys and values conform to a controlled vocabulary
Column names match those of an associated metadata template
Certain columns are not empty
Certain columns are complete
Identifiers match between two metadata files (e.g. all individuals in one file are also present in another)
Check that identifiers are unique within a file

Data submission validation

This package contains a Shiny app to validate manifests and metadata for AMP-AD studies. It uses the dccvalidator package to check for common data quality issues and gives realtime feedback to the data contributor on errors that need to be fixed. The reporting UI is heavily inspired by the MetaDIG project's metadata quality reports.

The application also allows users to submit documentation of their study, a description of the methods used, etc.

See the customizing dccvalidator vignette for information on how to spin up a customized version of the application

Requesting New Features or Bug Fixes

For new feature requests or bug fixes, please create an issue to let the maintainers know. If you’ve found a bug, create an associated issue and illustrate the bug with a minimal reprex. If there is agreement that the problem exists or that a new feature is desired, then the issue will be triaged for future development based on priority.

Please note that the dccvalidator project is released with a Contributor Code of Conduct. By contributing to this project via issue creation, comment, or pull request, you agree to abide by its terms.