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tooluniverse-chemical-compound-retrieval

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).

72

Quality

87%

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

The canonical home for this skill is tooluniverse-chemical-compound-retrieval in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

82%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.

A concise, actionable, well-sequenced skill body with concrete tool calls and validation grading. It falls just short of top marks on actionability and workflow clarity due to the absence of an explicit error-recovery feedback loop and a complete copy-paste script.

Suggestions

Add an explicit validate->fix->retry feedback loop for SMILES verification and failed lookups (e.g., 'If SMILES verification fails, re-resolve via OPSIN or PubChem name lookup before proceeding').

Provide one complete copy-paste example that chains Phase 1->2->3 for a representative compound to make the common path fully executable.

Consider moving the bulk Tool Reference function listing into a separate references file and linking it from the body to tighten progressive disclosure.

DimensionReasoningScore

Conciseness

The body is dense and lean throughout: compact Phase list, fallback/evidence tables, and direct tool-call snippets with no padding or explanation of concepts Claude already knows.

5 / 5

Actionability

Provides concrete executable Python tool calls with specific function names and parameters (e.g. tu.tools.PubChem_get_CID_by_compound_name) plus a verify command, but lacks a complete copy-paste script wrapper covering common cases end-to-end.

4 / 5

Workflow Clarity

Clear Phase 0-3 sequence with verification checkpoints (CID + ChEMBL ID + canonical SMILES + stereochemistry) and evidence-grading tiers, but there is no explicit validate->fix->retry feedback loop for the SMILES verification or retrieval failures.

4 / 5

Progressive Disclosure

Well-organized into clear sections with only a single one-level external path (smiles_verifier.py) and no nested references, but the inlined Tool Reference listing could arguably live in a separate reference file for a marginally cleaner split.

4 / 5

Total

17

/

20

Passed

Description

92%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.

A highly specific, well-triggered description that concretely states capabilities and explicit use-conditions with minimal conflict risk. The only minor gap is a few missing colloquial synonyms in the trigger terms.

DimensionReasoningScore

Specificity

Lists multiple concrete actions including 'disambiguation, cross-referencing, and stereochemistry handling', 'resolving compound names to SMILES/InChI/CID/ChEMBL IDs', OPSIN IUPAC parsing, and 'fetching molecular properties', giving comprehensive coverage.

5 / 5

Completeness

Clearly states what the skill does ('Retrieve chemical compound data... with disambiguation, cross-referencing, and stereochemistry handling') and explicitly when to use it via the 'Use for resolving compound names...' trigger clause with concrete phrases.

5 / 5

Trigger Term Quality

Strong natural domain terms like 'compound names', 'SMILES', 'InChI', 'CID', 'ChEMBL IDs', 'molecular properties', and 'Vitamin D' are present, but a few common synonyms a lay user might say are missing, so it sits just below the comprehensive anchor.

4 / 5

Distinctiveness Conflict Risk

The PubChem/ChEMBL chemical-compound-retrieval niche with ID-resolution and cross-validation triggers is clearly distinct from other skills and unlikely to fire for the wrong skill.

5 / 5

Total

19

/

20

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

Table of Contents

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