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

69%

Does it follow best practices?

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Securityby

Low

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

Quality

Content

63%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, verified code and clear workflows, but it is over-long and redundant across its capability, workflow, and helper-script sections, and it under-uses progressive disclosure by inlining content that belongs in reference files.

Suggestions

Collapse the redundant presentation: keep one concrete example per function in the capability sections and remove the overlapping 'Common Workflows' re-demonstrations, or move the workflows into a separate reference file.

Surface references/api_reference.md earlier as a navigation hub and move the detailed parsing/format sections and full workflow code into reference files so SKILL.md reads as an overview.

Trim introductory duplication — the 'When to Use' list and Overview restate the frontmatter description — to reduce token cost.

Dimension	Reasoning	Score
Conciseness	At ~700 lines the body is noticeably verbose: the 9 capability demos, 6 full workflows, and 3 helper-script function lists substantially re-demonstrate the same functions, creating several padded, redundant sections that could be tightened.	2 / 5
Actionability	Examples are fully executable and copy-paste ready — real imports from scripts.brenda_client/brenda_queries (verified to exist), concrete EC numbers, expected output strings, and complete error-handling blocks covering the common cases.	5 / 5
Workflow Clarity	Six clearly sequenced multi-step workflows with code, plus a dedicated error-handling section and best-practice validation guidance (validate EC numbers, handle missing data); minor gap is that validation checkpoints are not embedded directly inside the workflows.	4 / 5
Progressive Disclosure	Structure and the one-level reference to references/api_reference.md (verified present) plus bundled scripts are good, but a large volume of capability demos and full workflows is inlined in SKILL.md that could be externalized, and the api_reference link is surfaced only near the end rather than as primary navigation.	3 / 5
	Total	14 / 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 distinctive, naming concrete capabilities and a clear niche, but it omits an explicit 'Use when' trigger clause, which caps its completeness. Trigger-term coverage is strong but not exhaustive.

Suggestions

Add an explicit 'Use when...' clause naming natural triggers, e.g. 'Use when retrieving enzyme kinetic parameters (Km, kcat, Vmax), reaction equations, or organism-specific enzyme data from BRENDA.'

Include a few additional natural user terms such as Vmax, EC number, and inhibition/activation data to round out trigger coverage.

Lead with the trigger phrase so the 'when' is as prominent as the 'what'.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'Access BRENDA enzyme database via SOAP API', 'Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information' — with comprehensive coverage of the API's capabilities.	5 / 5
Completeness	It clearly states what the skill does but lacks an explicit 'Use when...' clause or equivalent trigger guidance; 'for biochemical research and metabolic pathway analysis' only weakly implies when, so completeness is capped at 3 per the guidelines.	3 / 5
Trigger Term Quality	Good coverage of natural domain terms (kinetic parameters, Km, kcat, reaction equations, organism data, substrate, metabolic pathway analysis), but a few natural terms a user might say are absent (e.g. Vmax, EC number, enzyme data, inhibition).	4 / 5
Distinctiveness Conflict Risk	'BRENDA enzyme database via SOAP API' is a clear, narrow niche with distinct triggers and minimal risk of firing for an unrelated skill.	5 / 5
	Total	17 / 20 Passed

Validation

75%

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 — 12 / 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
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	12 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/databases/brenda-database/SKILL.md
Commit: 7dabbf0

Reviewed: 4 days ago

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