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tooluniverse-natural-product-dereplication

Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).

80

Quality

100%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

100%

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

A high-quality workflow skill body: executable tool calls with real identifiers, a sequenced multi-phase process with validation checkpoints and error-recovery fallbacks, honest limitations, and a completeness checklist. Dense but every section is tool-specific operational knowledge rather than generic explanation.

DimensionReasoningScore

Conciseness

Lean and token-dense: a compact backing-tools table, executable snippets, and tool-specific gotchas Claude does not already know, with no padding explaining basics like what an InChIKey or IUPAC name is. Not a 2 because every section is operational rather than conceptual filler.

3 / 3

Actionability

Fully executable code with exact field paths ('rec["origin_organism"]["ancestors"]') and concrete worked values (NPA014588, InChIKey HKSZLNNOFSGOKW-FYTWVXJKSA-N); copy-paste ready rather than pseudocode.

3 / 3

Workflow Clarity

A clearly sequenced Phase 0–5 pipeline with explicit validation/feedback: PubChem cross-ref as a formula-mismatch red flag, 'classified:false' and 'parsed:false' fallbacks, and a final completeness checklist.

3 / 3

Progressive Disclosure

Single self-contained file (no bundle files present) organized into clear one-level sections (Backing Tools, Workflow, Interpretation Guidance, Worked Examples, Limitations, Out of Scope, Checklist) with no nested references; appropriate for a self-contained workflow skill.

3 / 3

Total

12

/

12

Passed

Description

100%

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

An exemplary description: concrete third-person actions, natural trigger phrasings, explicit when-to-use guidance, and sharp out-of-scope routing that prevents conflicts. It is dense but every clause earns its place.

DimensionReasoningScore

Specificity

Lists multiple concrete actions in third person ('Searches NPAtlas', 'assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire', 'resolves systematic IUPAC names to structure via OPSIN', 'cross-references identity in PubChem') rather than vague language.

3 / 3

Completeness

Explicitly answers both what (search/assign/resolve/cross-reference) and when via 'Use to answer...' trigger clauses; not below 3 because the 'when' is explicit, not implied.

3 / 3

Trigger Term Quality

Embeds natural phrasings a user would actually say ('is [compound] a known natural product', 'what microbe/organism produces [compound]', 'dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)') with strong coverage of variants.

3 / 3

Distinctiveness Conflict Risk

Clear niche (microbial NP dereplication + ChemOnt) with explicit exclusions ('NOT for general drug/compound identity or ADMET... use tooluniverse-chemical-compound-retrieval'), making wrong-skill triggering unlikely.

3 / 3

Total

12

/

12

Passed

Validation

100%

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

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

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