| name | alterlab-pdf-explore |
| description | Explore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and tables. Use when interrogating one paper or report end-to-end, pulling every occurrence of something inside a document, or reading data from a figure/table in a PDF, serving the literature-review and paper-review pipeline. To build a comparison table across MANY papers prefer alterlab-pdf-extract; to simply convert a PDF to Markdown prefer alterlab-markitdown; for reference/citation management prefer alterlab-pyzotero. Part of the AlterLab Academic Skills suite. |
| license | MIT |
| allowed-tools | Read Write Edit Bash(python:*) Bash(uv:*) |
| compatibility | Runs under `uv run python` with a PDF parser (e.g. `pymupdf`/`pdfplumber` — TODO(verify) preferred pin) plus, for scanned pages, an OCR pass. No GPU or account required. Parses the PDF once into a section/figure/table index that later questions reuse; large scanned PDFs are slower due to OCR. |
| metadata | {"skill-author":"AlterLab","version":"1.0.0"} |
PDF Explore (deep single-document Q&A)
Overview
Reading one paper or report thoroughly means jumping between the methods, a results figure,
a supplementary table, and an appendix — repeatedly. This skill parses a PDF once into a
reusable index of sections, figures, and tables, then answers many questions across the
whole document without re-parsing: compare what two sections say, extract every instance
of a pattern, and read values off charts/tables.
It is the single-document deep-dive counterpart to the corpus-level tools: to build a
comparison table across many papers use alterlab-pdf-extract; to just convert a PDF
to Markdown use alterlab-markitdown.
When to Use This Skill
Use this skill when the user wants to:
- Interrogate one paper/report end-to-end (methods vs. results vs. appendix).
- Extract every occurrence of a pattern within a document (all p-values, all sample sizes,
every mention of a gene).
- Read data off a figure or table inside the PDF.
- Feed precise, located answers into the literature-review or paper-review pipeline.
Does NOT Trigger
| Scenario | Use instead |
|---|
| Build a comparison table across many papers (one row per paper) | alterlab-pdf-extract |
| Convert a PDF/DOCX to clean Markdown | alterlab-markitdown |
| Manage references / DOIs / BibTeX | alterlab-pyzotero |
| Work with a Jupyter notebook | alterlab-open-notebook |
Core Capabilities
1. Parse-once, ask-many
Parse the PDF a single time into a structured index — page text with layout, detected section
headings, figure/table regions, and (for scans) OCR'd text — then answer subsequent questions
against that index instead of re-reading the file each time.
2. Cross-section questions
Answer questions that span the document: "does the discussion's claim match the methods'
design?", "which limitations does the appendix add beyond the main text?". Cite the page and
section for every answer so it is verifiable.
