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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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SecuritybySnyk

Low

Low-risk findings worth noting

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 dense, actionable skill body with concrete tool calls, a clear phased workflow, fallback chains, and an evidence-grading checklist. The main improvement is consolidating the duplicated OPSIN explanation and making the verification step an explicit retry loop.

Suggestions

Consolidate the OPSIN 'trade/trivial names return parsed=false' note so it appears in only one place (Phase 1 or Tool Reference), removing the duplicated explanation.

Turn the Phase 1 'Verify' checkpoint into an explicit validate→fix→retry loop (e.g., 'If CID and ChEMBL ID disagree, re-resolve via SMILES fallback before proceeding').

Consider moving the full Tool Reference list to a separate REFERENCE.md and signaling it here, keeping SKILL.md as a tighter overview.

DimensionReasoningScore

Conciseness

Mostly lean and free of basic-concept padding, but the OPSIN behavior ('trade/trivial names return parsed=false') is explained twice — once in Phase 1 and again in the Tool Reference — which could be consolidated; minor over-explanation only.

4 / 5

Actionability

Provides copy-paste-ready, executable calls such as 'tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)', 'OPSIN_name_to_structure(name="2-acetoxybenzoic acid")', and a concrete verifier command, with named tools covering the common cases.

5 / 5

Workflow Clarity

Clear Phase 0–3 sequence with a 'Verify' checkpoint and Evidence Grading checklist plus explicit Fallback Chains for error recovery; falls just short of a 5 because there is no explicit validate→fix→retry loop in the main flow.

4 / 5

Progressive Disclosure

Well-organized into clear sections (Workflow, Fallback Chains, Evidence Grading, Tool Reference) with no nested references and easy navigation; the inlined Tool Reference is appropriate for a tool-invocation skill, though it is reference material kept in the main file.

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 high-quality description that concretely states capabilities and provides an explicit 'Use for' trigger clause with domain-specific keywords. Minor room to add synonyms like 'molecule'/'drug'/'chemical structure' for even broader trigger coverage.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Retrieve chemical compound data', 'resolving compound names to SMILES/InChI/CID/ChEMBL IDs', 'OPSIN deterministic IUPAC-name-to-structure parsing', 'fetching molecular properties', 'distinguishing isomers/stereo forms', 'cross-validating identity' — giving comprehensive coverage of the skill's capabilities.

5 / 5

Completeness

Explicitly states the what ('Retrieve chemical compound data... with disambiguation, cross-referencing, and stereochemistry handling') and the when via a concrete 'Use for resolving compound names to...' trigger clause, satisfying both halves with concrete triggers.

5 / 5

Trigger Term Quality

Strong domain-natural terms (PubChem, ChEMBL, SMILES, InChI, CID, IUPAC, isomers, stereo) but missing common synonyms such as 'molecule', 'drug', 'chemical structure' and there are no file-extension triggers; just shy of comprehensive.

4 / 5

Distinctiveness Conflict Risk

A tightly scoped niche (PubChem/ChEMBL compound retrieval with OPSIN parsing) with distinct, specialized triggers that would not plausibly fire for unrelated skills.

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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