reactome-database

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Quality

78%

Does it follow best practices?

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Securityby

High

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tessl review fix ./backend/cli/skills/databases/reactome-database/SKILL.md

Quality

Content

82%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 body is highly actionable with executable examples and good progressive disclosure into real reference and script files. The main improvements are tightening redundant overview prose and adding explicit error-handling/validation checkpoints in the analysis workflow.

Suggestions

Trim the Overview paragraph and 'When to Use' list that restate the description and core capabilities already covered elsewhere.

Add explicit validation checkpoints in the analysis workflow, e.g. checking HTTP status and handling empty/unmapped identifier results before reading the token.

Surface the helper script earlier and link its subcommands to the relevant sections so users discover it alongside the inline code.

Dimension	Reasoning	Score
Conciseness	Largely efficient with executable code, but the Overview restates the frontmatter description and some prose (e.g. 'free, open-source, curated pathway database') could be trimmed; minor over-explanation rather than padding.	4 / 5
Actionability	Provides copy-paste ready, executable code for the common cases — query, overrepresentation, expression, projection, visualization — plus a documented CLI helper script covering the main operations.	5 / 5
Workflow Clarity	The analysis flow (submit identifiers → capture token → retrieve results) is clearly sequenced with the token-validity note, but error-handling/validation checkpoints are mostly implicit; operations are read-only so the destructive cap does not apply.	4 / 5
Progressive Disclosure	Body is an overview that points to real one-level-deep bundle files (references/api_reference.md and scripts/reactome_query.py), clearly signaled; bulk API detail is appropriately offloaded, with only minor organization gaps.	4 / 5
	Total	17 / 20 Passed

Description

75%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 specific and distinct, clearly conveying what the skill does across multiple concrete capabilities. Its main weakness is the absence of an explicit 'Use when...' trigger clause, which limits completeness.

Suggestions

Add an explicit 'Use when...' clause naming concrete triggers, e.g. 'Use when performing pathway enrichment, mapping genes to pathways, or analyzing expression data against Reactome.'

Include more natural user-facing synonyms and artifact terms (gene lists, Reactome IDs, .tsv expression files) to broaden trigger coverage.

Consider mentioning species comparison and visualization, which are covered in the body but not in the description.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis' — giving comprehensive coverage of the skill's capabilities.	5 / 5
Completeness	Clearly answers 'what' with a list of capabilities but lacks any explicit 'Use when...' trigger clause; per the judging guidelines this caps completeness at 3.	3 / 5
Trigger Term Quality	Includes good natural keywords like 'pathway analysis', 'enrichment', and 'systems biology', but misses common synonyms and concrete artifact terms (e.g. gene lists, Reactome IDs) a user would naturally say.	4 / 5
Distinctiveness Conflict Risk	Targets a clear niche (Reactome pathway analysis) with distinct triggers and minimal overlap risk with other skills.	5 / 5
	Total	17 / 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
metadata_version	'metadata.version' is missing	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	14 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/databases/reactome-database/SKILL.md
Commit: 3a6c3a9

Reviewed: 1 day ago

Table of Contents

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