brenda-database

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

Quality

66%

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Securityby

Passed

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tessl review fix ./scientific-skills/brenda-database/SKILL.md

Quality

Content

58%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 comprehensive executable examples and well-signaled references to real bundle files, but it is over-long and padded with redundant sections and a promotional paragraph, and its workflows lack explicit validation checkpoints for batch operations.

Suggestions

Consolidate the Helper Scripts function listings into the capability sections or move them into references/api_reference.md to remove the duplicated function inventory.

Add explicit validate/verify checkpoints to the batch and pathway-building workflows (e.g. check returned data is non-empty, verify pathway feasibility before reporting), creating a feedback loop.

Remove or relocate the K-Dense Web promotional section so the skill body stays focused on task guidance.

Dimension	Reasoning	Score
Conciseness	The 700+ line body is mostly executable code with little concept-explanation fluff, but it is noticeably padded by a redundant Helper Scripts section that re-lists functions already demonstrated in the capabilities and workflows, plus an off-topic promotional K-Dense Web paragraph.	3 / 5
Actionability	Abundant copy-paste-ready Python with real imports and example outputs (e.g. get_km_values("1.1.1.1", organism="Saccharomyces cerevisiae")) covers the common cases and references real bundle scripts.	5 / 5
Workflow Clarity	Six named workflows give a clear sequence of API calls, but they lack explicit validation/verification checkpoints for batch operations (multi-organism comparison, pathway construction), which caps workflow_clarity at 3 per the batch-operation guidance.	3 / 5
Progressive Disclosure	Good structure with clearly signaled one-level-deep references ("For detailed BRENDA documentation, see references/api_reference.md") and real script files; minor gaps because a large amount of capability/workflow detail remains inlined rather than offloaded to the reference file.	4 / 5
	Total	15 / 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 well-targeted to a distinct niche, with strong domain keywords and concrete actions. Its main weakness is the absence of an explicit "Use when..." trigger clause, leaving the "when to use" guidance only weakly implied.

Suggestions

Add an explicit trigger clause, e.g. "Use when retrieving enzyme kinetic parameters, reaction equations, or organism-specific enzyme data for biochemical research or metabolic pathway analysis."

Include a few more natural synonyms users might say (e.g. "enzyme kinetics", "turnover number", "substrate specificity") to broaden trigger coverage.

Keep the current concrete action list but ensure the "what" and "when" are both stated as clearly as the good-overall examples.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information" — giving comprehensive coverage of the database's core data types.	5 / 5
Completeness	It clearly answers "what" ("Access BRENDA enzyme database via SOAP API") but lacks an explicit "Use when..." trigger clause; the trailing "for biochemical research and metabolic pathway analysis" only weakly implies "when", which caps completeness at 3 per the guidelines.	3 / 5
Trigger Term Quality	Strong domain keywords a user would naturally say ("kinetic parameters", "Km", "kcat", "reaction equations", "metabolic pathway analysis"), though a few natural variants/synonyms are missing.	4 / 5
Distinctiveness Conflict Risk	Targets a clearly distinct niche (BRENDA enzyme database via SOAP) with specific triggers, so conflict with other skills is minimal.	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
skill_md_line_count	SKILL.md is long (719 lines); consider splitting into references/ and linking	Warning
metadata_version	'metadata.version' is missing	Warning

	Total	14 / 16 Passed

Repository: googolme/run0204
Path: scientific-skills/brenda-database/SKILL.md
Commit: 4902409

Reviewed: 6 days ago

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