Paper Lookup

You have access to 10 academic paper databases through their REST APIs. Your job is to figure out which database(s) best serve the user's query, call them, and return the results.

Core Workflow

1. Understand the query -- What is the user looking for? A specific paper by DOI? Papers on a topic? An author's publications? Open access PDFs? Full text? This determines which database(s) to hit.

2. Select database(s) -- Use the database selection guide below. Many queries benefit from hitting multiple databases -- for example, searching PubMed for papers and then checking Unpaywall for open access copies.

3. Read the reference file -- Each database has a reference file in

   references/

   with endpoint details, query formats, and example calls. Read the relevant file(s) before making API calls.

4. Make the API call(s) -- See the Making API Calls section below for which HTTP fetch tool to use on your platform.

5. Return results -- Always return:

   • The raw JSON (or parsed XML for arXiv) response from each database
   • A list of databases queried with the specific endpoints used
   • If a query returned no results, say so explicitly rather than omitting it

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.

10.xxxx/xxxxx

10.1038/nature12373

34567890

PMC

PMC7029759

YYMM.NNNNN

2103.15348

W

W2741809807

649def34f8be...

0000-XXXX-XXXX-XXXX

0000-0001-6187-6610

XXXX-XXXX

0028-0836

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

doi:10.1038/...

pmid:34567890

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

NCBI_API_KEY

CORE_API_KEY

S2_API_KEY

OPENALEX_API_KEY

Fully open databases (no key needed)

mailto

email

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:

WebFetch

curl

web_fetch

curl

read_url_content

curl

curl

run_terminal_cmd

curl

shell

curl

execute_command

If the fetch tool fails, fall back to

curl

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

references/pubmed.md

references/pmc.md

Preprint Servers

references/biorxiv.md

references/medrxiv.md

references/arxiv.md

Multidisciplinary Indexes

references/openalex.md

references/crossref.md

references/semantic-scholar.md

Open Access & Full Text

references/core.md

references/unpaywall.md