Paper Lookup

Database Selection Guide

Match the user's intent to the right database(s).

By Use Case

Cross-Database Queries

When a query spans multiple needs (e.g., "find papers about CRISPR and get me the PDFs"), query the relevant databases in parallel.

Common Identifier Formats

Different databases use different identifier systems. If a query fails, the identifier format may be wrong.

Cross-referencing IDs: Semantic Scholar accepts DOI, PMID, PMCID, and arXiv ID via prefixes (e.g., DOI:10.1038/nature12373, PMID:34567890, ARXIV:2103.15348). OpenAlex accepts DOI and PMID via prefixes (doi:10.1038/..., pmid:34567890). Use the PMC ID Converter to translate between PMID, PMCID, and DOI.

API Keys and Access

Most of these databases are fully open. A few benefit from API keys for higher rate limits.

Databases requiring or benefiting from API keys

Fully open databases (no key needed)

Loading API keys

1. Check the environment first -- the key may already be exported (e.g., $NCBI_API_KEY).
2. Fall back to .env -- check .env in the current working directory.
3. Proceed without -- most APIs still work at lower rate limits. Tell the user which key is missing and how to get one.

Making API Calls

Use your environment's HTTP fetch tool to call REST endpoints:

If the fetch tool fails, fall back to curl via whatever shell tool is available.

Special cases

• arXiv returns Atom XML, not JSON. Parse it or use curl and extract the relevant fields. Consider piping through a simple parser if available.
• PMC eFetch returns JATS XML for full text. This is expected -- full text articles are in XML format.
• Crossref and Unpaywall benefit from including a mailto parameter or email for the polite/fast pool.

Request guidelines

• For NCBI APIs (PubMed, PMC): max 3 req/sec without key, 10 with key. Make requests sequentially.
• For arXiv: max 1 request every 3 seconds. Be patient.
• For Crossref: 5 req/sec (public), 10 req/sec (polite pool with mailto).
• For other APIs with no strict limits, you can query multiple databases in parallel.
• If you get HTTP 429 (rate limit), wait briefly and retry once.

Error recovery

1. Check the identifier format -- use the Common Identifier Formats table. A PMID won't work in arXiv, an arXiv ID won't work in PubMed directly.
2. Try alternative identifiers -- if a DOI fails in one database, try the title or PMID instead.
3. Try a different database -- if PubMed returns nothing for a CS paper, try Semantic Scholar or OpenAlex.
4. Report the failure -- tell the user which database failed, the error, and what you tried instead.

Output Format

Structure your response like this:

## Databases Queried
- **PubMed** -- esearch + esummary for "CRISPR gene therapy"
- **Unpaywall** -- DOI lookup for 10.1038/...

## Results

### PubMed
[raw JSON response or formatted results]

### Unpaywall
[raw JSON response]

If results are very large, present the most relevant portion and note that more data is available. But default to showing the full raw JSON -- the user asked for it.

Available Databases

Read the relevant reference file before making any API call.

Biomedical Literature

Preprint Servers

Multidisciplinary Indexes

Open Access & Full Text