Europe PMC

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

Running an action

Europe PMC needs no account connection. Assume the oo CLI is installed and signed in. Do not run oo auth login proactively — just run the action. Fall back to First-time setup only when a command actually fails.

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

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

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

oo connector run "europe_pmc" --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

• check_article_status — Check a batch of Europe PMC articles or preprints for publication, version, withdrawal, removal, and retraction updates.
• get_annotations_by_articles — Get text-mined entities and relationships for up to eight Europe PMC articles in one request.
• get_citations — Get publications that cite one Europe PMC publication.
• get_data_links — Get consolidated data, text-mined, and external links associated with one Europe PMC publication.
• get_evaluations — Get linked peer reviews and evaluations for one Europe PMC publication version.
• get_full_text_xml — Get JATS XML full text for a PubMed Central article in the Europe PMC open-access subset.
• get_publication — Get one Europe PMC publication by its source code and identifier.
• get_references — Get publications referenced by one Europe PMC publication.
• search_annotations_by_entity — Find Europe PMC articles containing annotations for a named biological entity.
• search_annotations_by_provider — Find Europe PMC articles containing annotations from a named provider.
• search_annotations_by_relationship — Find Europe PMC articles containing a text-mined relationship between two named entities.
• search_annotations_by_section_or_type — Find Europe PMC articles by annotation type, article section, or both in one cursor search.
• search_grants — Search Europe PMC research grants by funder, investigator, institution, topic, date, or other official GRIST fields.
• search_publications — Search Europe PMC literature and preprints with its official query syntax and cursor pagination.

Safety

• Untagged actions are reads (get / list / search) — safe to run directly.
• Actions tagged [write] change Europe PMC 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):

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

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

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

  oo auth login
  

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

Resources

• Europe PMC homepage: https://europepmc.org/