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literature-experiment-extract

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Extract experimental models, experimental methods, and biomarker information from paper Markdown (typically produced by PDF-to-Markdown tools) when a user provides paper Markdown and needs a structured, evidence-backed summary (1 Markdown + 3 CSVs).

scientific-skills/Evidence Insight/literature-experiment-extract/SKILL.md

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Nov 9, 2026

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2,042
Repository last updated
Sep 17, 2026
License
MIT

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)


## When to Use

- You have a paper converted to Markdown (e.g., via PDF-to-Markdown) and need to extract **cell/animal models** used in experiments.
- You need a structured list of **experimental methods/protocols** described in the paper, with traceable evidence.
- You want to compile **biomarkers / detection indicators** (e.g., genes, proteins, assays, readouts) reported in the study.
- You need standardized outputs for downstream analysis: **one Markdown summary plus three CSV tables**.
- The paper Markdown includes page markers (e.g., `## Page XX`) and you want evidence organized **by page**.

## Key Features

- Extracts three entity groups from paper Markdown:
  - **Experimental models** (cell lines, animal models, strains, genotypes, etc.)
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