ppi-network-analysis

Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary graph databases, multi-omics integration, or non-STRING interaction sources.

Quality

93%

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Securityby

Passed

No findings from the security scan

Quality

Content

93%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The content is a lean, table-driven reference with runnable commands, complete arguments, input/output specs, error recovery, and an exemplary progressive-disclosure navigation table. The only soft spot is the absence of an explicit validation checkpoint in the main workflow, though the non-destructive single-action nature limits that impact.

Dimension	Reasoning	Score
Conciseness	The body is almost entirely high-value reference — runnable commands, compact tables for arguments/outputs/errors — with no padding or explanation of concepts Claude already knows; every token earns its place.	5 / 5
Actionability	Copy-paste-ready Rscript commands, a complete argument table with types/defaults, concrete TXT/CSV input examples, expected output file lists, and runnable smoke tests fully cover the common cases.	5 / 5
Workflow Clarity	The single-purpose CLI flow is clear with an error-code-to-fix table providing recovery guidance and a testing section listing expected outputs as verification, but there is no explicit validate-then-retry checkpoint in the main run flow.	4 / 5
Progressive Disclosure	A 'When to Read External Files' table maps situations to real one-level-deep references (algorithm.md, main.R, troubleshooting.md, cli-guide.md — all confirmed present), giving a clear overview with well-signaled navigation.	5 / 5
	Total	19 / 20 Passed

Description

92%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is concrete, well-triggered, and sharply bounded, with multiple specific actions and explicit 'when' guidance plus negative-scope boundaries. Its only gap is missing common synonyms like PPI or STRING-db that a user might naturally say.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'build a protein-protein interaction network', 'export node and edge tables', 'render a reproducible PDF network plot' from a local gene list and offline STRING cache — giving comprehensive concrete coverage.	5 / 5
Completeness	Explicit 'Use when you need...' trigger plus a clear 'what' (build network, export tables, render plot) and explicit negative boundaries ('NOT for online API fetching...') jointly answer what and when.	5 / 5
Trigger Term Quality	Strong natural terms ('protein-protein interaction network', 'gene list', 'STRING cache', 'node and edge tables') are present, but common synonyms/abbreviations a user might say (PPI, STRING-db) are missing.	4 / 5
Distinctiveness Conflict Risk	The offline-STRING-from-local-gene-list niche is highly specific, and explicit exclusion of online APIs, graph databases, and multi-omics integration minimizes conflict risk.	5 / 5
	Total	19 / 20 Passed

Validation

87%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning
referenced_paths_exist	Referenced path issues: 1 missing	Warning

	Total	14 / 16 Passed

Repository: aipoch/medical-research-skills
Path: awesome-med-research-skills/Data Analysis/ppi-network-analysis/SKILL.md
Commit: 63c61d3

Reviewed: 8 hours ago

Table of Contents

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