scientific-skills/Evidence Insights/scholar-evaluation/SKILL.md
Implements the ScholarEval framework to evaluate scholarly documents; trigger when the user provides a PDF/DOCX/TXT file or pasted text and requests critique, scoring, or quality assessment.
npx skillsauth add aipoch/medical-research-skills scholar-evaluationInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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scripts/extract_text.py (intended as the first step for file inputs).references/evaluation_framework.md).scripts/calculate_scores.py from a JSON score file.requirements.txt for pinned Python package versions (install via pip install -r requirements.txt).python scripts/extract_text.py "paper.pdf"
scores.json):{
"problem_formulation": 4,
"literature_review": 3,
"methodology": 4,
"data_quality": 3,
"analysis": 4,
"results": 3,
"writing_quality": 4,
"citations": 3
}
python scripts/calculate_scores.py --scores scores.json
references/evaluation_framework.mdIf the user pastes text directly (e.g., abstract, full paper text), skip extraction and evaluate immediately using the 8 dimensions and the 1–5 scale.
python scripts/extract_text.py "<filename-or-path>"
The framework evaluates:
Detailed criteria and guidance are defined in:
references/evaluation_framework.mdpython scripts/calculate_scores.py --scores <path_to_scores_json>
tools
Generates complete conventional oncology bulk-transcriptome biomarker and hub-gene research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, prognostic filtering or risk modeling, PPI-based hub-gene prioritization, diagnostic/prognostic evaluation, clinical association, immune infiltration context, methylation context, and optional tissue or cell validation. Covers five study patterns (signature-first prognostic workflow, hub-gene-first biomarker workflow, hybrid signature-to-hub workflow, immune-context biomarker workflow, translational validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...
development
Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction. Use when a study centers on multi-dataset bulk transcriptome integration, DEG analysis, process-gene intersection, enrichment analysis, GSEA, PPI hub-gene prioritization, TF/miRNA regulatory networks, ROC-based biomarker evaluation, and immune infiltration analysis. Covers five study patterns (process-DEG discovery, enrichment/GSEA interpretation, hub-gene prioritization, regulatory-network and immune interpretation, multi-layer public validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
tools
Plans confounder control, variable adjustment logic, and bias mitigation strategies at the protocol stage for clinical, epidemiologic, translational, observational, and biomarker studies. Always use this skill when a user needs to identify major confounders, decide which variables should or should not be adjusted for, compare matching/stratification/weighting approaches, anticipate selection or measurement bias, or pressure-test a study design before execution. Focus on bias sensing, causal structure awareness, variable-role classification, and critical design review rather than generic statistical advice.
testing
Generates complete comparative network-toxicology research designs from a user-provided exposure pair, shared toxic phenotype, and validation direction. Use when a study centers on two related exposures under one outcome and needs target collection, shared-vs-specific target decomposition, enrichment, PPI hub prioritization, docking, optional transcriptomic cross-checks, and conservative mechanistic synthesis. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.