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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.

77

1.17x
Quality

70%

Does it follow best practices?

Impact

89%

1.17x

Average score across 3 eval scenarios

SecuritybySnyk

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/hmdb-database/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Discovery

82%

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

This is a strong, domain-specific description with excellent specificity and distinctive terminology that clearly identifies its niche in metabolomics research. The main weakness is the lack of an explicit 'Use when...' clause, which would help Claude know exactly when to select this skill over others.

Suggestions

Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about metabolites, metabolomics analysis, compound identification, or needs to look up chemical/spectral data from HMDB.'

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions: 'Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways' - these are detailed, actionable capabilities.

3 / 3

Completeness

Clearly answers 'what' (access HMDB, search, retrieve various data types) but lacks an explicit 'Use when...' clause. The use cases are implied by listing 'for metabolomics and identification' but this is not explicit trigger guidance.

2 / 3

Trigger Term Quality

Includes strong natural keywords users would say: 'metabolites', 'metabolomics', 'NMR', 'MS spectra', 'biomarker', 'pathways', 'chemical properties', 'HMDB' (implied by Human Metabolome Database). Good coverage of domain-specific terms.

3 / 3

Distinctiveness Conflict Risk

Highly distinctive with clear niche - Human Metabolome Database is a specific resource, and terms like 'metabolites', 'NMR/MS spectra', 'metabolomics' are unlikely to conflict with other skills.

3 / 3

Total

11

/

12

Passed

Implementation

57%

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

This skill provides a comprehensive overview of HMDB with good organization and structure, but lacks the concrete, executable examples that would make it immediately actionable. The content is somewhat verbose, explaining database contents that Claude could infer, and workflows describe processes conceptually rather than with specific commands or code. The progressive disclosure is well-handled with clear navigation.

Suggestions

Add executable code examples for common tasks, such as Python code for parsing downloaded XML/CSV files or complete R examples using the hmdbQuery package

Trim the 'Database Contents' section significantly - Claude doesn't need to know there are '130+ data fields' or detailed counts; focus on what's actionable

Add concrete validation steps to workflows, e.g., 'Verify match by checking: molecular weight within 5 ppm, at least 3 matching MS-MS fragments'

Replace conceptual workflow descriptions with specific examples showing actual HMDB IDs, search queries, or expected output formats

DimensionReasoningScore

Conciseness

The content is reasonably organized but includes some unnecessary explanation (e.g., 'HMDB is a comprehensive, freely available resource') and could be tightened. The database contents section lists information Claude could infer or look up, and some sections are verbose without adding actionable value.

2 / 3

Actionability

Provides general guidance and workflow descriptions but lacks concrete, executable code examples. The R package mention includes an install command but no usage example. Workflows describe steps conceptually rather than with specific commands or code snippets.

2 / 3

Workflow Clarity

Multi-step workflows are listed (e.g., Metabolite Identification, Biomarker Discovery) with numbered steps, but they lack validation checkpoints and specific commands. Steps are descriptive rather than prescriptive with concrete verification points.

2 / 3

Progressive Disclosure

Content is well-organized with clear sections and headers. References external documentation appropriately ('See references/hmdb_data_fields.md') and organizes content logically from overview to specific use cases without deep nesting.

3 / 3

Total

9

/

12

Passed

Validation

90%

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

Validation10 / 11 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

Total

10

/

11

Passed

Repository
K-Dense-AI/claude-scientific-skills
Reviewed

Table of Contents

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