pubmed-database

The saved excerpt is a snapshot from review. The external source remains the complete and most current version.

---
name: pubmed-database
description: >-
  Search PubMed for scientific literature, including published clinical trials.
  Fetch abstracts and full text. Link published research to biological databases
  (gene, protein, nucleotide, PubChem) to discover associations between papers
  and specific compounds or genes. Verify medical spelling, match raw citations,
  and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC
  BioC APIs.
---

# PubMed API

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/pubmed_database_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://pubmed.ncbi.nlm.nih.gov/disclaimer/
    and https://www.ncbi.nlm.nih.gov/home/about/policies/ 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.  **`NCBI_API_KEY`** (optional): Raises the NCBI E-utilities rate limit from 3
    to 10 requests/second. The skill works without it, but a key is recommended
    if the user plans many queries or encounters a 429 error. You can register
    for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You
    **MUST** use the safe credentials protocol in the `credentials` skill to
    check for and request this key if this skill looks relevant to the user's
    request.
5.  **`USER_EMAIL`** (optional): Identifies the caller to NCBI (recommended by
    their Terms of Use). You **MUST** use the safe credentials protocol in the
    `credentials` skill to check for and request this credential if this skill
    looks relevant to the user's request.

This skill provides CLI access to the NCBI PubMed and PubMed Central APIs via
`scripts/pubmed_api.py` — a single CLI with 10 functions covering search, fetch,
linking, full text, spelling, discovery, citation matching, and caching.

## Core Rules

-   **API Use**: Always use the provided wrapper `scripts/pubmed_api.py` which
    manages rate limits automatically and prevents API abuse. Setting the
    `NCBI_API_KEY` environment variable raises the rate limit from 3 to 10
    requests/second. Querying the API any other way (e.g. via curl, wget, or
    hand-written code) is strictly forbidden.
-   **JSON Processing**: Use `jq` to filter and transform JSON output (or python
    equivalents if `jq` is not available) to prevent hallucinations and context
    overflow.
-   **Temporary Files**: To avoid polluting the working directory with JSON
    files, use a temporary directory inside the current directory. When running
    multiple agents or tasks in parallel, ensure each uses a unique subdirectory
    name (e.g., `tmp_$TASK_ID/`) to avoid file collisions.
-   **Notification**: 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.

## Structure of the skill folder

-   `SKILL.md` - This file
-   `scripts/pubmed_api.py` - The skill CLI
-   `references/` - Directory with detailed function specifications
    -   `advanced-linking.md`
    -   `advanced-search.md`
    -   `bulk-workflows.md`
    -   `citation-matching.md`
    -   `cross-database-linking.md`
    -   `fetch-and-resolve.md`
    -   `search-and-discovery.md`
    -   `utilities.md`

## CLI Usage

```bash
uv run scripts/pubmed_api.py <output_file> <function_name> <required_args> [--flag value ...]
```

-   **Positional Arguments**: Arguments are positional; list arguments are
    passed as comma-separated strings without spaces (e.g.
    `"35113657,31234568"`).
-   **Flag Options**: Optional arguments can be passed as `--flag value` instead
    of positional args.
-   **Outp