paper-overlay

Generates .paper-overlay.md files with verbatim quotes and comments for RM paper reader annotations.

Updated Mar 20, 2026
One-click install
npx skills add https://github.com/McGheeLab/McGheeLabWebsite --skill paper-overlay-mcgheelab
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: paper-overlay
Source: https://github.com/McGheeLab/McGheeLabWebsite/tree/main/.claude/skills/paper-overlay
Command: npx skills add https://github.com/McGheeLab/McGheeLabWebsite --skill paper-overlay-mcgheelab

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Literature reviews require annotating the same paper differently for each grant or paper draft, but manually creating structured highlight files that match a web importer's parser is error-prone. This Skill authors a correctly formatted .paper-overlay.md file that the McGhee Lab RM paper reader can import to materialize scoped highlights and comments. ## Core Features & Use Cases - Scoped Overlay Authoring: Produces overlay files bound to a grant draft, paper draft, or legacy bucket id so the same paper carries different highlight sets per review task. - Parser-Compatible Formatting: Enforces the exact frontmatter and highlight-block schema (page, verbatim quote, type, color, comment, evidence_stance) expected by rm/js/paper-overlay-import.js. - Typed Highlights: Supports the closed type enum (evidence, method, result, limitation, claim, note, question) with evidence stance tagging for for/against framing. - Use Case: While reviewing a microfluidics paper for a GELS R01 proposal, ask for an overlay scoped to the grant; the Skill writes smith2024-gels-microfluidic.paper-overlay.md with verbatim quotes and lens-specific comments ready to drag-drop onto the RM paper reader. ## Quick Start Ask the assistant to create a paper overlay for a specific paper id or DOI scoped to your grant or draft id, providing the paper text and your review lens.

Frequently Asked Questions about paper-overlay

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I create a paper overlay file for the RM paper reader?

Provide the paper id or DOI, a scope id (grant or draft), the paper text, and your review lens. The Skill writes a `<slug>.paper-overlay.md` file in your working directory that you drag-drop onto the paper reader at the RM library page.

What format does a .paper-overlay.md file require?

It needs YAML frontmatter with paper_id or paper_doi plus a scope field (grant, draft_id, or bucket_id), followed by `## Highlight` blocks each containing a 1-based page number and a verbatim quote, with optional type, color, comment, and evidence_stance fields.

Why are my overlay highlights flagged as unmatched on import?

The importer searches the paper text layer for each quote, so quotes must be verbatim rather than paraphrased. Whitespace is normalized, but any content mismatch causes the highlight to be flagged and dropped.

Can one paper have different highlights for different grants?

Yes, that is the core design. Create one overlay file per (paper, scope) pair; each scope id (grant or draft) gets its own highlight set with comments explaining relevance to that specific review task.

What highlight types does the paper overlay support?

The type field accepts a closed enum: evidence, method, result, limitation, claim, note, or question, defaulting to note. The paper reader colors highlights by type and offers per-type filter pills.