Publication dates for PMC publications

Lookup tables in plain JSON, mapping PMC publication identifiers to their earliest respective publication dates.

The JSON files are archived in pmc-publication-dates-by-identifier.tar.gz. The archive contains files named after the first digit of the PMC publication identifiers they contain. E.g., the file PMC1.json will contain the data for identifiers PMC1234567, etc. Publication dates are given in the format YYYY[-MM[-DD]], i.e., the earliest date is given with the maximum of information that has been available from the PMC OAI-PMH metadata, at least the publication year, if available also the publication month and day.

Reproducibility

The Snakemake workflow that has produced this dataset has been archived and is available in pmc-publication-dates-workflow.tar.gz.

Running the workflow

To reproduce the dataset on a Linux machine, you need a version of the conda package manager installed on your system.

Run the following:

# Extract the archived workflow
tar -xf pmc-publication-dates-workflow.tar.gz
# Create conda environment from lock file
conda env create -n pmc-metadata --file conda-environment.lock.yaml
# Activate the environment
conda activate pmc-metadata
# Optionally, dry-run the workflow
snakemake -n
# Produce the output files
snakemake --keep-storage-local-copies --software-deployment-method conda -c <NUMBER OF CORES TO USE>

Workflow

To adapt/change the workflow, clone it from https://github.com/sdruskat/pmc-publication-metadata. The workflow version used to produce this dataset is available at https://doi.org/10.5281/zenodo.11350802.