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tooluniverse-biomedical-fact-lookup

Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to <database>' (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar, ChEMBL, OpenTargets, Reactome, GtoPdb, UniProt...), and multiple-choice biology/medicine knowledge questions where one option must be verified against an authoritative source. NOT for analyzing user-supplied data files (CSV/VCF/h5ad → use the data-analysis router) and NOT for open-ended literature synthesis. Use whenever a single correct answer exists in a public biomedical database and could be looked up rather than guessed.

77

Quality

96%

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SKILL.md
Quality
Evals
Security

Quality

Content

92%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.

The body is exceptionally actionable — exact tools, parameters, conventions, and executable code with built-in validation discipline — and the MCQ workflow is clearly sequenced with error-recovery loops. Its weaknesses are token economy and structure: the six traps are stated twice, and ~350 lines of per-domain recipes that belong in reference files are all inlined in SKILL.md.

Suggestions

Split the per-domain deep dives (FDA clinical-vignette table, MGI phenotype route, computational procedures with their Python recipes, gnomAD release table) into references/ files, keeping SKILL.md to the routing table, RULE ZERO, the traps summary, and the MCQ procedure.

Remove the duplication between the 'Six traps' summary and the later full sections — either keep the traps as one-line pointers ('see §GWAS below') or drop the summary and let the detailed sections carry the detail once.

Tighten the dense routing-table rows by moving the multi-sentence 'How' cells into short sub-sections or reference files so the table reads as a quick routing index.

DimensionReasoningScore

Conciseness

Mostly efficient — no filler explaining concepts Claude already knows — but the six-traps summary is then re-explained in full in later sections (GWAS p-value, window counting, HPA, Allen Brain each appear twice), and dense routing-table rows plus long inline per-domain recipes (FDA vignette table, gnomAD release table) could be tightened or split out. This fits 'mostly efficient but includes some unnecessary explanation or could be tightened' rather than the lean score-5 anchor, and is well above the noticeably-verbose score-2 anchor.

3 / 5

Actionability

Fully executable guidance throughout: exact tool names and parameters ('MSigDB_check_gene_in_set, param gene', 'DisGeNET_get_disease_genes(disease=CUI)'), precise set-name conventions (MIR186_3P, PGM3_TARGET_GENES, MP_INCREASED_MELANOMA_INCIDENCE), and copy-paste-ready Python (count_orfs, digest, gamete_ratio with worked examples). Matches the score-5 anchor covering common cases.

5 / 5

Workflow Clarity

The MCQ procedure is a clear sequenced workflow (Parse → Resolve → Query → Check → Answer) with explicit validation checkpoints and recovery loops: 'Check the length you got against the length you asked for', re-derive set names before concluding 'insufficient', 're-read each option against the computed result before emitting [ANSWER]', and fallback escalation paths (MGI per-gene route, PubTator3 text-mined fallback). Matches the score-5 anchor with feedback loops for error recovery.

5 / 5

Progressive Disclosure

Headers, a routing table, and summary-then-detail sections give good in-file organization, but the skill is a single ~350-line monolith with no references/ or scripts/ bundle, and clearly separable content (computational code recipes, FDA vignette table, per-database deep dives) is inlined in SKILL.md. This fits 'some structure but... content that should be separate is inline'; the simple-skill exception does not apply given the length and topical breadth.

3 / 5

Total

16

/

20

Passed

Description

100%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.

The description is a model example: it states exactly what the skill does, gives dense natural trigger phrases including database names and file extensions, and explicitly fences off adjacent skills with NOT-for clauses. Every clause earns its place despite the length.

DimensionReasoningScore

Specificity

Concrete actions are explicit: 'Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory' and 'one option must be verified against an authoritative source', plus concrete exclusions ('analyzing user-supplied data files (CSV/VCF/h5ad)'). Coverage is comprehensive across the question types the skill handles, matching the score-5 anchor rather than the 'minor gaps' anchor at 4.

5 / 5

Completeness

Both 'what' ('Answer... by querying ToolUniverse database tools instead of answering from memory') and 'when' ('Triggers on any... lookup', 'Use whenever a single correct answer exists in a public biomedical database') are explicitly and concretely stated, matching the score-5 anchor exactly.

5 / 5

Trigger Term Quality

Natural trigger phrasing is exhaustive: 'which gene/drug/variant/disease/pathway/miRNA/TF... lookup', 'according to <database>', a long list of database names users would actually cite (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar...), and file extensions (CSV/VCF/h5ad). This matches the comprehensive synonym-plus-extension anchor at 5, not the 'a few natural terms missing' anchor at 4.

5 / 5

Distinctiveness Conflict Risk

A clear niche (database-verified biomedical facts) with explicit negative boundaries — 'NOT for analyzing user-supplied data files... NOT for open-ended literature synthesis' — routing away the nearest competing skills. Minimal conflict risk, matching the score-5 anchor.

5 / 5

Total

20

/

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
Reviewed

Table of Contents

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