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README.md

DANDI Citations Collection

This folder contains citation collection configuration and outputs for DANDI dandisets using citations-collector.

Files

Usage

Quick Start

Run the full citation collection pipeline:

make all

This will:

  1. Discover citations from all configured sources (CrossRef, OpenCitations, DataCite, OpenAlex)
  2. Detect and merge preprints with their published versions
  3. Fetch open-access PDFs into pdfs/ directory

Individual Steps

make discover      # Step 1: Discover citations only
make merge         # Step 2: Detect/merge preprints only
make pdfs          # Step 3: Fetch PDFs only
make status        # Show current statistics
make clean         # Remove generated files

Using with DataLad

For reproducible execution tracking:

datalad run -m "Update DANDI citations" --output dandi-full-citations.tsv --output pdfs/ make all

BibTeX Source Integration

The collection now uses a BibTeX source pointing to ../dandi.bib, which is maintained by the dandi-citations tool. This allows:

  • External maintenance of dandiset metadata in BibTeX format
  • Automatic extraction of item IDs and version numbers from DOIs
  • Integration with existing bibliography management workflows

The BibTeX file contains all DANDI dandisets with versioned DOIs. The citation collector:

  1. Parses dandi.bib using regex pattern to extract item_id and flavor_id from DOIs
  2. Discovers citations for each dandiset version from multiple sources
  3. Deduplicates and merges preprints with published versions
  4. Fetches open-access PDFs where available

Viewing Results

For interactive exploration of the TSV file, we recommend visidata:

visidata dandi-full-citations.tsv

# Or directly from GitHub:
visidata https://raw.githubusercontent.com/dandi/dandi-bib/refs/heads/master/citations/dandi-full-citations.tsv

Configuration

Edit dandi-full.yaml to customize:

  • Citation sources to query
  • PDF output directory
  • Email for API polite pools
  • Regex pattern for BibTeX parsing

See citations-collector documentation for full configuration options.