PubMed

PubMed (pubmed.ncbi.nlm.nih.gov). Use this skill for ANY PubMed request — searching and reading data. Whenever a task involves PubMed, use this skill instead of calling the API directly.

Operate PubMed through your OOMOL-connected account. This skill calls the pubmed connector with the oo CLI; OOMOL injects credentials server-side, so you never handle raw tokens.

Running an action

Assume the user has already installed the oo CLI, signed in, and connected PubMed. Do not run oo auth login or open the connection URL proactively — just run the action. Fall back to First-time setup only when a command actually fails with an auth or connection error.

1. Inspect the contract to get the authoritative input/output schema before building a payload:

bash

oo connector schema "pubmed" --action "<action_name>"

2. Run the action with a JSON payload that matches the input schema:

bash

oo connector run "pubmed" --action "<action_name>" --data '<json>' --json

• --data takes a JSON object string or @path/to/file.json; omit it to send {}.
• The response is { "data": ..., "meta": { "executionId": "..." } }; the execution id lives under meta.executionId.

Each action is listed below with a one-line description; actions that change state carry a [write] or [destructive] tag. Before constructing --data, fetch the action's live schema with oo connector schema to get its authoritative input fields.

Available actions

• convert_article_ids — Convert PMID, PMCID, DOI, or author manuscript identifiers with the PMC ID Converter. Complete mappings are available only for articles represented in PubMed Central.
• find_related_articles — Find normalized PubMed articles related to one source PMID.
• get_article — Get one normalized PubMed article by PMID.
• get_article_references — Get normalized PubMed references for one source PMID. References are available only when supplied by publishers or recoverable from PMC data.
• get_articles — Get multiple normalized PubMed articles by PMID in one request.
• get_citing_articles — Get normalized PubMed articles known to cite one source PMID. PubMed citation coverage depends on data supplied by publishers and NCBI sources and may be incomplete.
• match_citation — Match one raw biomedical citation to PubMed and return normalized candidate articles.
• search_articles — Search PubMed with the official query syntax and return normalized article records.

Safety

• Untagged actions are reads (get / list / search) — safe to run directly.
• Actions tagged [write] change PubMed state — confirm the exact payload and effect with the user before running.
• Actions tagged [destructive] remove or overwrite data — always confirm the target and get explicit approval first.

First-time setup

These are one-time steps — do not repeat them on every call. Run a step only when a command fails for the matching reason.

• oo: command not found — install the oo CLI (other platforms: https://cli.oomol.com/install-guide.md):

  bash

  curl -fsSL https://cli.oomol.com/install.sh | bash    # macOS / Linux
  

  powershell

  irm https://cli.oomol.com/install.ps1 | iex           # Windows PowerShell
  

• Not signed in / authentication error — sign in to your OOMOL account once:

  bash

  oo auth login
  

• scope_missing / credential_expired / app_not_ready / app_not_found — PubMed is not connected, or the connection expired or lacks a scope. Connect once (auth type: API key) at:

  text

  https://console.oomol.com/app-connections?provider=pubmed
  

• HTTP 402 / OOMOL_INSUFFICIENT_CREDIT — billing stop. Recharge at https://console.oomol.com/billing/token-recharge before retrying.

Resources

• PubMed homepage: https://pubmed.ncbi.nlm.nih.gov/