neuromechanist-opencite

OpenCite

Academic literature search, citation management, and PDF retrieval CLI.

Searches Semantic Scholar, OpenAlex, and PubMed in parallel, deduplicates results, and supports BibTeX output, citation graph traversal, PDF retrieval, batch downloads, and PDF-to-markdown conversion.

Quick Start

Install and set up your API keys:

uv pip install opencite                # or: pip install opencite
opencite config init                   # creates ~/.opencite/config.toml

Add your API keys to ~/.opencite/config.toml or export them as environment variables:

export SEMANTIC_SCHOLAR_API_KEY=your_key
export PUBMED_API_KEY=your_key
export OPENALEX_API_KEY=your_key

Start searching:

opencite search "transformer attention mechanism"
opencite lookup 10.1038/nature12345
opencite canonical "deep learning" --min-citations 500
opencite cite 10.1038/nature12345
opencite pdf 10.1038/nature12345 -o paper.pdf --convert

[!NOTE] Claude Code plugin: Type /plugin, select "Add marketplace", enter neuromechanist/opencite, and restart. Then use /opencite or ask Claude directly.

[!TIP] PDF conversion is included by default. If MISTRAL_API_KEY is set, markit-mistral is used (better for math/complex layouts); otherwise markitdown (free, local).

Commands

search - Find papers

opencite search "query" [--max N] [--source all|openalex|s2|pubmed]
    [--year-from YYYY] [--year-to YYYY] [--oa-only]
    [--sort relevance|citations|year] [-f text|json|bibtex|csv] [-o FILE] [-v]

lookup - Look up papers by identifier

opencite lookup IDENTIFIER [IDENTIFIER ...] [--enrich] [--append-bib FILE]
    [-f text|json|bibtex] [-o FILE] [-v]

Accepts DOI, pmid:X, pmc:X, arxiv:X, S2 ID, or OpenAlex ID. Supports multiple IDs.

cite - Citation graph

opencite cite IDENTIFIER [--direction citing|references|both] [--max N]
    [--sort citations|year] [--min-citations N] [-f text|json|bibtex] [-o FILE]

canonical - Most-cited papers in a field

opencite canonical "topic" [--max N] [--year-from YYYY] [--min-citations N]
    [-f text|json|bibtex] [-o FILE]

pdf - Download PDF

opencite pdf IDENTIFIER [-o PATH] [--filename NAME] [--convert]
    [--converter auto|markitdown|mistral]

-o accepts a file path (e.g., paper.pdf) or directory. With --convert, also generates a markdown file alongside the PDF.

convert - PDF to markdown

opencite convert FILE.pdf [-o FILE] [--converter auto|markitdown|mistral]
    [--extract-images] [--images-dir DIR]

Auto mode uses markit-mistral when MISTRAL_API_KEY is set (better for math and complex layouts), otherwise falls back to markitdown (free, local).

batch-fetch - Batch download PDFs

opencite batch-fetch FILE [-o DIR] [--convert] [--concurrency N] [--summary FILE]
opencite batch-fetch --from-json FILE [options]
opencite batch-fetch --from-stdin [options]

Downloads PDFs for multiple papers with controlled concurrency. Supports text files (one ID per line), JSON files (array of DOIs or opencite search results), and stdin. With --convert, output is organized into pdf/, markdown/, and markdown/img/ subdirectories.

Example workflow:

# Search and save as JSON, then batch download with conversion
opencite search "tDCS motor cortex" --max 30 -f json -o results.json
opencite batch-fetch --from-json results.json --convert --summary report.json -o ./papers

ids - Convert between identifiers

opencite ids IDENTIFIER [IDENTIFIER ...] [-f text|json]

Converts between DOI, PMID, and PMCID using the NCBI ID Converter API.

config - Manage configuration

opencite config init    # create ~/.opencite/config.toml template
opencite config show    # display resolved config (keys masked)
opencite config path    # show config file location

Output Formats

All search/lookup/cite/canonical commands support -f/--format:

• text (default) - human-readable output
• json - structured JSON
• bibtex - BibTeX entries for citation managers
• csv - comma-separated values (search only)

Use -o/--output FILE to write to a file instead of stdout.

Installation

# uv (recommended)
uv pip install opencite

# pip
pip install opencite

# uvx (no install needed, runs from cache)
uvx opencite --version

PDF conversion support (markitdown and markit-mistral) is included by default.

For development:

git clone https://github.com/neuromechanist/opencite.git
cd opencite
uv sync --extra dev

Configuration

OpenCite supports TOML config, .env files, and environment variables.

opencite config init    # creates ~/.opencite/config.toml with template
opencite config show    # display resolved config (keys masked)
opencite config path    # show config file location

Config loading priority

Later sources override earlier ones: