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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).

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**.

When not to use

• Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
• Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
• Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.

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