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hmdb-database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

59

Quality

69%

Does it follow best practices?

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Adds up to 20 points to the overall score

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SecuritybySnyk

Low

Low-risk findings worth noting

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tessl review fix ./backend/cli/skills/databases/hmdb-database/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

67%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 well-organized, actionable for a database skill with no public API, and uses a clean one-level reference structure. It would benefit from trimming generic explanatory prose and adding explicit verification steps to the workflows.

Suggestions

Remove or condense generic explanatory prose (e.g. the HMDB overview paragraph and Best Practices repetition) that Claude already knows, to improve token efficiency.

Add explicit verification/validation checkpoints to the research workflows (e.g. 'Verify candidate by cross-checking molecular weight and MS-MS fragmentation before confirming identification').

Tighten the Reference Documentation section by linking the data-fields reference inline where the 130+ data fields are first mentioned.

DimensionReasoningScore

Conciseness

Mostly efficient and well-structured, but includes unnecessary explanation Claude likely already knows (e.g. the generic HMDB overview) and repetitive Best Practices sections that could be tightened.

3 / 5

Actionability

Provides concrete guidance — specific URLs, example HMDB IDs, an install command for hmdbQuery, contact emails, and download formats — with only minor gaps since no public API exists to demonstrate.

4 / 5

Workflow Clarity

Numbered multi-step workflows for metabolite ID, biomarker discovery, pathway analysis, and DB integration are clearly sequenced, though validation checkpoints are mostly implicit rather than explicit.

4 / 5

Progressive Disclosure

Good structure with a single clearly-signaled one-level-deep reference (references/hmdb_data_fields.md) and well-organized sections; minor organization gaps keep it just below a 5.

4 / 5

Total

15

/

20

Passed

Description

71%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 with strong action coverage, but lacks an explicit 'Use when...' trigger clause, leaving the 'when' only weakly implied. Adding a concrete trigger phrase would lift completeness.

Suggestions

Add an explicit 'Use when...' clause naming concrete triggers, e.g. 'Use when identifying metabolites, analyzing NMR/MS spectra, or researching biomarkers and metabolic pathways.'

Include common synonyms and file extensions users might say (e.g. '.sdf', 'mass spec', 'untargeted metabolomics') to broaden trigger term coverage.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways' — with comprehensive coverage of the database's capabilities.

5 / 5

Completeness

Has a clear 'what' but no explicit 'Use when...' clause; 'for metabolomics and identification' only weakly implies when, so per the guideline a missing explicit trigger caps this at 3.

3 / 5

Trigger Term Quality

Includes natural domain terms users would say ('metabolomics', 'biomarker', 'NMR/MS spectra', 'metabolites') but is missing some synonyms and file extensions, fitting the 'good coverage, a few natural terms missing' anchor.

4 / 5

Distinctiveness Conflict Risk

Targets a clear niche (HMDB metabolomics database) with distinct triggers, with only minor overlap risk against general chemistry databases.

4 / 5

Total

16

/

20

Passed

Validation

87%

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

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

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
Reviewed

Table of Contents

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