Paper Lookup

Source: https://github.com/aipoch/medical-research-skills

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.

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 (Reference Template)

Use the template below as the default output format, but adjust flexibly based on user queries. Core principle: Structured presentation > raw data dump.

Default Reference Template

## Search Results Report

### Query Overview
| Item | Content |
|------|------|
| Query terms | [user's query] |
| Databases searched | [databases actually queried] |
| Total results | [deduplicated count] |

### Search Results
| # | Title | Authors | Year | Source Journal | DOI/PMID | Source Database | Full-text Status |
|---|------|------|:----:|---------|:--------:|:--------:|:--------:|
| 1 | [Title] | [Authors] | 2025 | [Journal] | [DOI] | PubMed | Published |
| 2 | [Title] | [Authors] | 2024 | bioRxiv | [DOI] | bioRxiv | Preprint |

### Legend
- Published / Preprint / Open Access / Needs verification

When to Adjust Format

Available Databases

Read the relevant reference file before making any API call.

Biomedical Literature

Preprint Servers

Multidisciplinary Indexes

Open Access & Full Text