literature-search-openalex

name	literature-search-openalex
category	science
version	1.0.0
kind	python
description	Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords. Use when searching academic papers, resolving DOIs, downloading open-access PDFs, finding an author's publications, aggregating bibliometric data (citation counts, h-index, impact factor), exploring the research taxonomies, or performing DOI lookups.

OpenAlex Skill

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.

2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://developers.openalex.org/ and to always check the license of the papers retrieved by the skill for any restrictions, then (2) create the file recording the notification text and timestamp.

3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist.

4. OPENALEX_API_KEY (optional but recommended): Enables the OpenAlex Premium API with higher rate limits. The skill works without it (using the free "polite pool"). If the variable is missing from .env, do NOT ask the user to paste it into the chat (this would leak the key into the agent's context). Instead, give the user this command — substituting ENV_FILE with the resolved literal path to the .env file:

   printf "Enter OpenAlex API key (typing hidden): " && read -s key && echo && echo "OPENALEX_API_KEY=$key" >> "ENV_FILE" && echo "Saved."
   

   The scripts load credentials automatically via dotenv. NEVER read, print, or inspect the .env file or its variables (e.g. no cat, grep, echo, printenv, or os.environ.get on keys). Credentials must stay out of the agent's context. See the Rate Limits section for more details.

Core Rules

1. List Sources. If this skill is used, ensure this is mentioned in the output AND list the URLs of all papers that were used in producing the output.
2. Resolve before filter. NEVER filter by name. Always resolve a name to an ID first, then use that ID in --filter.
3. Use the CLI only. Never call the API via curl/urllib. The CLI handles retries and rate limiting.
4. No fabrication. Never invent OpenAlex IDs or DOIs. Use resolve/get to look them up. Report empty results accurately.
5. API key. If a command returns 401/429 or you need high-volume queries, follow the prerequisite instructions above to help the user add OPENALEX_API_KEY to the .env file. Keys are at OpenAlex.org → account settings.
6. Keep output small. Always use --select and --per-page 5–10 for overview queries. Pipe filter output to a file (> results.json), then slim with jq before reading into context.

Rate Limits

• With key: ~10 req/s, $1/day free budget.
• Without key: Very limited, $0.01/day budget.

Operation	Cost
Singleton get	Free
filter	$0.0001
--search / resolve	$0.001
download-pdf	$0.01

CLI Reference

uv run scripts/openalex_cli.py [--api-key KEY] <command> [flags]

Entity types (shared across commands): works, authors, sources, institutions, topics, domains, fields, subfields, sdgs, countries, continents, languages, keywords, publishers, funders, work-types, source-types, institution-types, licenses

Commands

resolve <entity> <query> — Name → ID candidates. Returns id, display_name, hint. Use --per-page N for more candidates.

get <entity> <id> — Full metadata for one entity. Accepts short ID (W2741809807), full URL, or DOI URL. Use --select to limit fields.

filter <entity> — Search/filter entities. Key flags are:

• --search <query>: Full-text search (10× cost of --filter)
• --filter <expr>: Filter expressions. Use , for AND and | for OR.
• --sort <field:dir>: Sort results (e.g., cited_by_count:desc)
• --select <fields>: Limit the fields returned in the output.
• --group-by <field>: Aggregate results by a specific field.
• --per-page <N>: Number of results per page (default 25, max 100).
• --page <N>: Specify the page number to retrieve.
• --sample <N>: Get a random sample of up to 10,000 results.
• --seed <N>: Seed for reproducible sampling.

download-pdf <work-id> <output-path> — Download PDF (requires API key). Falls back to alternative pdf_url locations if primary fails. Whenever you download a PDF, verify it is not empty or corrupted.

rate-limit — Check current rate limit status (requires API key).

Search Tips

• If resolve returns no matches, try alternate spellings or abbreviations.
• If --search returns 0 results, try broader terms (max 3 retries).
• If resolve returns multiple candidates, present them to the user with display_name and hint for manual selection.

Entity References

Consult references/ for valid filter, sort, and group-by fields per entity:

• Works — Authors — Sources
• Institutions — Topics — Taxonomy
• Geo & Language — Publishers & Funders
• Type Values

Common Workflows

# Author's works (resolve → filter)
uv run scripts/openalex_cli.py resolve authors "Geoffrey Hinton"
uv run scripts/openalex_cli.py filter works \
  --filter "authorships.author.id:A5108093963" \
  --sort "cited_by_count:desc" --per-page 10 > papers.json
cat papers.json | jq '[.results[] | {id, title: .display_name, year: .publication_year, citations: .cited_by_count}]'

# DOI lookup
uv run scripts/openalex_cli.py get works "https://doi.org/10.1038/s41586-021-03819-2"

# Bulk DOI lookup (up to 100)
uv run scripts/openalex_cli.py filter works \
  --filter "doi:10.1234/a|10.1234/b|10.1234/c" --per-page 100 > results.json

# Institutional impact by year
uv run scripts/openalex_cli.py resolve institutions "MIT"
uv run scripts/openalex_cli.py filter works \
  --filter "authorships.institutions.id:I63966007" \
  --group-by "publication_year" > mit_by_year.json

# Random sample
uv run scripts/openalex_cli.py filter works \
  --filter "publication_year:2023,is_oa:true" \
  --sample 100 --seed 42 > results.json

Error Handling

Code	Meaning	Action
401	Unauthorized	Help user add API key to .env (see prereqs)
403	Plan upgrade needed	Inform user; see https://openalex.org/pricing
404	Not found	Verify ID; try resolve first
429	Rate limited	Wait and retry; suggest adding API key to .env

Known premium-only filters: from_updated_date, to_updated_date.

Never fabricate results on empty responses — report accurately and suggest alternate search terms.