literature-experiment-extract

name	literature-experiment-extract
description	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).
license	MIT
author	AIPOCH

Source: 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.)
  • Experimental methods (assays, protocols, instruments, conditions)