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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

89%

Does it follow best practices?

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SKILL.md
Quality
Evals
Security

Quality

Content

81%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 well-structured operational skill: clear phased workflow with verification checkpoints, fallback chains, concrete tool calls with real values, and evidence grading. The main deductions are narrative padding around 'verified live' anecdotes, the undefined 'tu' entry point, and duplication between the workflow sections and the Tool Reference catalog.

Suggestions

Trim the 'verified live' narration in the Identifier Resolution and Cheminformatics sections to bare operational facts — keep the genuinely non-obvious quirks (the 'InChIKey=' prefix to strip, the py3Dmol install error) but drop the run-by-run storytelling.

Define or initialize 'tu' (e.g., one import/setup line for the ToolUniverse session) so the Python snippets are fully copy-paste ready.

De-duplicate tool details: the 'Tool Reference' section repeats OPSIN's parsed=false behavior and re-lists tools already demonstrated in Phase 1/2 — consolidate to a single source per tool.

DimensionReasoningScore

Conciseness

Efficient and operational throughout — no explanations of concepts Claude already knows (it never explains what PubChem or SMILES are) and the fallback/evidence tables are dense and useful. Not a 5 because the Identifier Resolution and Cheminformatics sections carry narrative padding: the phrase 'verified live' appears ~6 times, and results are narrated ('also resolves a CAS number... Useful as a second name-resolution path') where a bare operational note would do.

4 / 5

Actionability

Mostly executable guidance with real parameter values and real outputs: 'tu.tools.OPSIN_name_to_structure(name="2-acetoxybenzoic acid")' with its return shape, the NCICACTUS→UniChem chained workflow on aspirin's actual InChIKey, and 'python3 src/tooluniverse/tools/smiles_verifier.py --smiles "SMILES_STRING"'. Not a 5 because 'tu' is never defined or initialized, so the code snippets are not copy-paste ready without guessing the ToolUniverse setup step.

4 / 5

Workflow Clarity

Phases 0–3 are clearly sequenced with conditional entry ('Phase 0: Clarify (only if highly ambiguous — skip for unambiguous names or specific IDs)'), an explicit Phase 1 verification checkpoint ('Verify: CID + ChEMBL ID + canonical SMILES + stereochemistry + salt forms'), fallback chains as error-recovery loops, a SMILES-validation step with rationale, and an Evidence Grading table that acts as a checklist for cross-database confidence. This matches the top anchor's validation steps, feedback loops, and checklists.

5 / 5

Progressive Disclosure

No bundle files exist, so everything is inline in a single well-sectioned SKILL.md with clear headers (Workflow, Fallback Chains, Evidence Grading, Tool Reference) that is easy to navigate. Not a 5 because the ~150-line body mixes overview workflow with detailed tool behavior, and the 'Tool Reference' section partially duplicates tool details already given in Phase 1 and the Identifier Resolution section (e.g., OPSIN's parsed=false behavior is stated twice); a consolidated reference or split would remove the duplication.

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 strong description: concrete actions, an explicit 'Use for...' trigger clause with specific identifier terms, third-person voice, and a well-delineated niche. The only gap is missing common synonyms (molecule, chemical structure, drug, CAS number) that some users would naturally use.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions — retrieving compound data from PubChem and ChEMBL, resolving names to SMILES/InChI/CID/ChEMBL IDs, OPSIN IUPAC-name-to-structure parsing, fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity — giving comprehensive capability coverage. It exceeds the score-4 anchor ('several specific actions; minor gaps') because no capability area of the skill is left unmentioned.

5 / 5

Completeness

Explicitly answers both questions: the 'what' ('Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling') and the 'when' ('Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs... fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity') with concrete trigger phrases. It also adds behavioral guidance (English-first names, flagging ambiguous queries like 'Vitamin D has multiple forms'), reinforcing rather than weakening the answer.

5 / 5

Trigger Term Quality

Good keyword coverage with natural domain terms users would say: 'compound names', 'SMILES', 'InChI', 'CID', 'ChEMBL IDs', 'IUPAC', 'molecular properties', 'isomers', 'stereo forms', 'PubChem', 'ChEMBL'. Not a 5 because common variations and synonyms are missing — e.g., 'molecule', 'chemical structure', 'drug identifier', or 'CAS number' — phrases a user might naturally use when they need this skill.

4 / 5

Distinctiveness Conflict Risk

A clear niche (chemical compound retrieval from PubChem/ChEMBL) with distinct, domain-specific triggers (SMILES, InChI, CID, ChEMBL, IUPAC, stereochemistry) that no general-purpose or adjacent-domain skill would claim. It matches the 'clear niche with distinct triggers; minimal conflict risk' anchor.

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

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

Reviewed

Table of Contents

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