pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Install with Tessl CLI
npx tessl i github:K-Dense-AI/claude-scientific-skills --skill pubchem-databaseOverall
score
85%
Does it follow best practices?
If you maintain this skill, you can automatically optimize it using the tessl CLI to improve its score:
npx tessl skill review --optimize ./path/to/skillValidation for skill structure
Discovery
83%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, technically specific description that clearly identifies the domain (PubChem/cheminformatics) and lists concrete capabilities. The main weakness is the absence of an explicit 'Use when...' clause, which would help Claude know exactly when to select this skill. The technical terminology is appropriate for the target audience but the description would benefit from explicit trigger guidance.
Suggestions
Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about chemical compounds, molecular properties, drug discovery data, or mentions PubChem, SMILES notation, or compound identifiers.'
Consider adding common user phrasings like 'look up a chemical', 'find compound information', or 'chemical database search' to capture less technical requests.
| Dimension | Reasoning | Score |
|---|---|---|
Specificity | Lists multiple specific concrete actions: 'Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity' - these are distinct, actionable capabilities. | 3 / 3 |
Completeness | Clearly answers 'what' with specific capabilities, but lacks an explicit 'Use when...' clause. The 'when' is only implied through the domain context (cheminformatics work). | 2 / 3 |
Trigger Term Quality | Excellent coverage of natural terms: 'PubChem', 'compounds', 'SMILES', 'CID', 'bioactivity', 'cheminformatics', 'similarity/substructure searches' - these are terms users in this domain would naturally use. | 3 / 3 |
Distinctiveness Conflict Risk | Highly distinctive with specific domain (PubChem, cheminformatics) and technical terms (CID, SMILES, PUG-REST API) that are unlikely to conflict with other skills. | 3 / 3 |
Total | 11 / 12 Passed |
Implementation
85%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
This is a well-crafted skill with excellent actionability and clear workflows for querying PubChem. The code examples are executable and comprehensive, covering the full range of PubChem capabilities. Main weaknesses are moderate verbosity in introductory sections and an inappropriate promotional section at the end that should be removed.
Suggestions
Remove or significantly condense the 'When to Use This Skill' section - Claude can infer appropriate use cases from the overview and capabilities
Remove the 'Suggest Using K-Dense Web' promotional section entirely - it's not relevant to the technical skill content and wastes tokens
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The skill is comprehensive but includes some unnecessary verbosity, such as the 'When to Use This Skill' section that largely restates what Claude would infer from the overview, and the promotional K-Dense section at the end that doesn't belong in a technical skill. | 2 / 3 |
Actionability | Excellent executable code examples throughout - all Python snippets are copy-paste ready with proper imports, real compound examples (aspirin CID 2244, caffeine), and complete function calls. The helper scripts section provides clear function signatures and usage patterns. | 3 / 3 |
Workflow Clarity | Clear multi-step workflows with explicit validation patterns, including error handling examples with specific exception types, rate limit guidance, and troubleshooting section. The 5 common workflows are well-sequenced with clear progression from input to output. | 3 / 3 |
Progressive Disclosure | Well-structured with clear hierarchy: overview → core capabilities → helper scripts → workflows → troubleshooting. References to external files (references/api_reference.md, scripts/) are clearly signaled and one level deep. Content is appropriately split between main skill and reference documentation. | 3 / 3 |
Total | 11 / 12 Passed |
Validation
81%Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.
Validation — 13 / 16 Passed
Validation for skill structure
| Criteria | Description | Result |
|---|---|---|
skill_md_line_count | SKILL.md is long (574 lines); consider splitting into references/ and linking | Warning |
description_trigger_hint | Description may be missing an explicit 'when to use' trigger hint (e.g., 'Use when...') | Warning |
metadata_version | 'metadata.version' is missing | Warning |
Total | 13 / 16 Passed | |
- Reviewed
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