Dataset Upload Guidelines

This is a protocol for sharing datasets on Zenodo. We have instructions on converting Excel spreadsheets (.xls/.xlsx) into comma-separated values (.csv) files.

In addition, inspired by the Open Data Institute’s open data certification badges (https://certificates.theodi.org/en/about/badgelevels), which identifies different “levels of achievement” in publishing data openly, we developed questions for researchers to categorize their own .csv datasets as Bronze or Silver. Bronze datasets are smaller, single-release, often self-assembled datasets that require minimal computer interaction. Examples of bronze datasets could include a list of materials (e.g. antibodies) used in an experiment, gene expression data from a hand-curated list, or summary patient data from a truncated cohort. Silver datasets are larger, often machine-generated datasets that will be processed and analyzed predominantly by programs or algorithms. Examples of silver datasets could include a comprehensive list of cancer cell lines and characteristics, -omics data, or an export of all patient information from a clinical trial. Both categories of dataset can be validated using Data Curator, an open-source software program with a graphic user interface, that allows researchers to validate (bronze) and/or annotate the dataset with suitable machine-readable metadata (silver) according to our instructions.

This protocol is part of a manuscript, "An institutional approach to open science: operationalizing the sharing of biomedical research objects through relevant publication platforms," that is in preparation. This project was supported by funding from the Cancer Early Detection Advanced Research (CEDAR) center at Oregon Health & Science University’s Knight Cancer Institute.