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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.

Quality

89%

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SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

77%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.

This is a highly actionable, well-sequenced skill body with excellent tool-level specificity, executable code, and built-in validation/feedback loops. Its weaknesses are length and self-containment: the trap summaries are duplicated in later sections and ~340 lines of per-database and computational detail are inlined in SKILL.md rather than split into one-level-deep reference files.

Suggestions

Split the self-contained computational procedures (ORF counting, restriction digest, segregation ratios) and the per-database deep dives (Human Protein Atlas, Allen Brain, FDA-label sections, gnomAD release table) into reference files under references/, leaving SKILL.md as a routing-table overview with one-level-deep pointers — this would materially cut token cost while preserving actionability.

De-duplicate the six-trap summary against the detail sections: keep one-line reminders in the trap list and move the worked examples (rs2475055 p-values, #F2483B, APOC2 pLI) to the single detailed section only, rather than restating each trap twice.

Trim rhetorical asides ('a guess wearing a citation', 'resist it', 'do not let this happen') to plain imperatives — the instruction lands the same with fewer tokens.

DimensionReasoningScore

Conciseness

The body is information-dense and avoids explaining concepts Claude already knows, but it could be tightened: the six traps are summarized up top and then each is re-explained at length below ('HPA subcellular locations pool every cell line' vs. the full 'Human Protein Atlas — report both location fields' section; the Allen Brain and gnomAD release items likewise), and some rhetorical padding ('a guess wearing a citation') adds tokens without adding instruction. Anchor 3 ('mostly efficient but... could be tightened') fits better than 4, where only minor trimming would be needed.

3 / 5

Actionability

Fully executable throughout: exact tool names with parameters (`MSigDB_get_gene_set_members`, `DisGeNET_get_disease_genes(disease=CUI)`, `SCREEN_search_cCREs_by_region`), exact set-name conventions (`MIR186_3P`, `MP_INCREASED_MELANOMA_INCIDENCE`), and three complete, runnable Python snippets (ORF counting, restriction digest, gamete ratios) with worked examples covering the common cases.

5 / 5

Workflow Clarity

Multi-step processes are explicitly sequenced with validation checkpoints and feedback loops: the MCQ procedure (Parse → Resolve → Query → Check → Answer), the 6-step differential gene–disease recipe, and the drug-vignette steps each embed error recovery ('If a tool errors on a name, re-derive the name... before concluding insufficient'; 'If RestrictionBatch raises on an enzyme name... re-run — do not fall back to guessing') and validation ('Always check the returned length against what the question asked for'; 're-read each option against the computed result before emitting [ANSWER]').

5 / 5

Progressive Disclosure

The body is well-sectioned with clear headers and internal cross-links, but it is a ~340-line monolith with no bundle files at all: content that clearly belongs in separate reference files — the three full computational procedures with code, the per-database deep dives (HPA, Allen Brain, FDA-label table, gnomAD release table) — is inlined. This sits between anchor 2 (content that belongs in separate files is inlined) and anchor 3 (some structure, could be better organized), but the section structure is genuinely good, so 3 rather than 2.

3 / 5

Total

16

/

20

Passed

Description

95%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 strong example: it states a concrete capability, enumerates natural trigger phrasings and databases, gives an explicit 'Use whenever' clause, and cleanly delimits its boundary against adjacent skills. Its only soft spot is that the action list is essentially a single lookup operation dressed in comprehensive triggers.

DimensionReasoningScore

Specificity

Concrete actions are named — 'querying ToolUniverse database tools instead of answering from memory' and 'one option must be verified against an authoritative source' — with a richly enumerated domain (gene/drug/variant/disease/pathway/miRNA/TF lookups, twelve named databases). Not a 5 because the core action set is essentially one lookup operation rather than multiple distinct capabilities; not a 3 because coverage of question types and exclusions leaves only minor gaps.

4 / 5

Completeness

Explicitly answers both what ('Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools') and when ('Triggers on any...lookup', 'Use whenever a single correct answer exists in a public biomedical database'), with concrete trigger phrases and explicit NOT-for exclusions.

5 / 5

Trigger Term Quality

Comprehensive natural phrasings users would actually say: 'which gene/drug/variant/disease/pathway/miRNA/TF...', 'according to <database>', 'multiple-choice biology/medicine knowledge questions', plus synonyms across twelve named databases. Would not be 4 because even the file-extension-style exclusion ('CSV/VCF/h5ad') and the negative triggers are covered.

5 / 5

Distinctiveness Conflict Risk

A clear niche — database-grounded biomedical fact lookup — with explicit carve-outs ('NOT for analyzing user-supplied data files (CSV/VCF/h5ad → use the data-analysis router) and NOT for open-ended literature synthesis') minimizing overlap with data-analysis or literature 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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-biomedical-fact-lookup/SKILL.md

Reviewed

Table of Contents

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