Use this skill for "search for papers", "find citations", "look up a DOI", "get BibTeX", "download PDF", "convert PDF to markdown", "find canonical papers", "convert identifiers", "batch download papers", "configure opencite", "literature review", "find related papers", "what papers cite this", "export references", "read this paper", or mentions of opencite, Semantic Scholar, OpenAlex, PubMed, academic literature search, citation management, or paper retrieval.
OpenCite is a CLI tool for academic literature search and citation management. It aggregates results from Semantic Scholar, OpenAlex, PubMed, arXiv, and bioRxiv/medRxiv, deduplicates them, and outputs formatted results. It also supports PDF retrieval, PDF-to-markdown conversion, and batch operations.
# Recommended
uv pip install opencite
# Alternative: run without installing
uvx opencite --version
PDF conversion support (markitdown and markit-mistral) is included by default. When MISTRAL_API_KEY is set, markit-mistral handles math, tables, and complex layouts. Otherwise, markitdown (free, local) is the fallback.
For development:
uv sync --extra dev
Follow this end-to-end workflow for literature research, paper retrieval, or reading material on a topic.
Choose the search strategy based on the request:
uvx opencite canonical "topic" --max 10uvx opencite search "query" --max 20 --sort citationsuvx opencite cite "DOI" --direction bothReview results considering citation count, relevance, recency, and open access availability. Present a summary and confirm which papers to retrieve.
For multiple papers (preferred): Save search results as JSON and use batch-fetch:
uvx opencite search "topic" --max 10 -f json -o results.json
uvx opencite batch-fetch --from-json results.json --convert -o ./papers --summary report.json
batch-fetch --convert automatically creates this directory structure:
papers/
├── pdf/ # downloaded PDFs
└── markdown/ # converted markdown files
└── img/ # per-paper image directories (mistral only)
For individual papers:
uvx opencite pdf "10.1234/example" -o papers/pdf/ --convert
Note: pdf --convert places the markdown file next to the PDF and does not extract images. For the organized subdirectory layout with image extraction, use batch-fetch.
Read the converted markdown files for deeper analysis:
batch-fetch, markdown is in papers/markdown/ and extracted images (markit-mistral only) are in per-paper subdirectories under papers/markdown/img/uvx opencite lookup "DOI" -f bibtex --append-bib refs.bib| Command | Purpose |
|---|---|
search | Find papers matching a query across multiple APIs |
lookup | Look up a specific paper by DOI, PMID, PMCID, or other identifier |
cite | Get citing/cited-by papers for a given identifier |
canonical | Find the most-cited, foundational papers for a topic |
pdf | Download a PDF for a paper by identifier |
convert | Convert a local PDF file to markdown |
ids | Convert between identifier types (DOI, PMID, PMCID) |
batch-fetch | Download PDFs for multiple papers with optional conversion |
config | Manage opencite configuration (init, show, path) |
For full option listings, see references/cli-reference.md.
Initialize configuration and check resolved values:
uvx opencite config init # create ~/.opencite/config.toml template
uvx opencite config show # display resolved config (keys masked)
Key environment variables:
SEMANTIC_SCHOLAR_API_KEY - Semantic Scholar APIPUBMED_API_KEY - NCBI/PubMed APIOPENALEX_API_KEY - OpenAlex API (required since Feb 2026)MISTRAL_API_KEY - Enhanced PDF-to-markdown conversion (optional)For full configuration details including publisher tokens and loading priority, see references/api-keys-and-config.md.
--source.