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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).

Quality

91%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

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

SKILL.md
Quality
Evals
Security

Quality

Content

85%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 highly actionable, well-sequenced body with real tool outputs, explicit validation checkpoints, and error-recovery fallbacks. Its main weaknesses are redundancy in the Tool Reference section and monolithic inlining of all detailed tool documentation with no progressive disclosure to separate reference files.

Suggestions

Move the categorized Tool Reference listing into a separate reference file (e.g., references/tool_reference.md) and keep only the most-used tools inline with a clearly signaled link, eliminating the duplication with tools already documented in the workflow sections.

Split the verified-live usage notes for UniChem/NCICACTUS/RDKit tools into a references file, keeping one-line pointers in SKILL.md so the overview stays lean.

Bundle the smiles_verifier.py script under scripts/ (or reference a bundled path) so the 'python3 src/tooluniverse/tools/smiles_verifier.py' command is verifiable and copy-paste ready.

DimensionReasoningScore

Conciseness

Largely efficient: tables for fallback chains and evidence grading, terse tool-call snippets with real return values, and 'verified live' annotations that document actual tool behavior rather than padding. Not 5 because the Tool Reference section re-lists tools already documented in earlier sections, and the UniChem/NCICACTUS prose could be tightened; not 3 because nearly all content is operationally useful rather than explanatory.

4 / 5

Actionability

Fully executable guidance: concrete tool calls with parameters ('tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)', 'NCICACTUS_resolve(identifier="aspirin", representation="smiles")'), real returned values ('BSYNRYMUTXBXSQ-UHFFFAOYSA-N' with the InChIKey= prefix warning), a runnable CLI command for SMILES verification, and a worked chained-identifier example covering the common resolution cases.

5 / 5

Workflow Clarity

Clear four-phase sequence (Clarify → Disambiguate → Retrieve → Report) with an explicit validation checkpoint in Phase 1 ('Verify: CID + ChEMBL ID + canonical SMILES + stereochemistry + salt forms'), fallback chains serving as error-recovery feedback loops, and an evidence-grading table acting as a checklist for cross-database confirmation. Not 4 because both validation steps and recovery paths are explicit, not merely implied.

5 / 5

Progressive Disclosure

Everything is inlined in a single ~150-line file: the extensive categorized Tool Reference, verified-live usage notes, and chained workflow examples would naturally live in separate reference files for a skill this size. The one external path ('src/tooluniverse/tools/smiles_verifier.py') is not part of the bundle and cannot be verified. Not 4 because content that should be separate (the bulk tool catalog) is inline and the script reference is dangling; not 2 because section headers, tables, and grouped tool categories keep the file navigable.

3 / 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 strong description: third-person voice, comprehensive concrete capabilities, and an explicit 'Use for' trigger clause covering the main use cases. The only weakness is a few missing natural synonyms (e.g., 'molecule', 'drug', 'chemical structure') in the trigger terms.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions with comprehensive coverage: 'Retrieve chemical compound data from PubChem and ChEMBL', 'resolving compound names to SMILES/InChI/CID/ChEMBL IDs', 'OPSIN deterministic IUPAC-name-to-structure parsing', 'fetching molecular properties', 'distinguishing isomers/stereo forms', and 'cross-validating identity across databases'. Not 4 because coverage spans retrieval, disambiguation, stereochemistry, and cross-referencing with no meaningful gaps.

5 / 5

Completeness

Explicitly answers both: what ('Retrieve chemical compound data... with disambiguation, cross-referencing, and stereochemistry handling') and when ('Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs... fetching molecular properties... cross-validating identity'). The 'Use for' clause lists concrete trigger scenarios, matching the top anchor exactly.

5 / 5

Trigger Term Quality

Good keyword coverage including natural domain terms: 'compound names', 'SMILES', 'InChI', 'molecular properties', 'isomers', 'PubChem', 'ChEMBL', 'Vitamin D'. Not 5 because common user-facing synonyms like 'molecule', 'drug', 'chemical structure', or 'look up a compound' are absent; not 3 because the terms present are exactly what a user working with chemical data would say.

4 / 5

Distinctiveness Conflict Risk

Clear niche (chemical compound retrieval from PubChem/ChEMBL) with distinct triggers (SMILES, InChI, CID, ChEMBL IDs, IUPAC names) that are unlikely to fire for unrelated skills. The 'flags ambiguous queries (e.g., Vitamin D has multiple forms)' note further sharpens its scope.

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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugins/tooluniverse/skills/tooluniverse-chemical-compound-retrieval/SKILL.md

Reviewed

Table of Contents

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