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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

The canonical home for this skill is tooluniverse-biomedical-fact-lookup in mims-harvard/ToolUniverse

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.

The body is an unusually actionable, well-sequenced operational playbook: exact tool routing, executable code, and validation checkpoints with recovery loops throughout. Its weaknesses are token efficiency (repeated cautions, duplicated release tables, inlined version-pinned values) and the total absence of progressive disclosure — a 29KB monolith with no reference or script files despite several self-contained sections.

Suggestions

Split the self-contained playbooks into bundle files: move the drug-vignette section, HPA/Allen details, and gene-disease recipe into references/ (linked one level deep from the routing table), and the count_orfs/digest/gamete_ratio code into scripts/ — keeping SKILL.md to the routing table, RULE ZERO, and the MCQ procedure.

De-duplicate repeated cautions: state the ORF single-strand rule and the final-answer-option-matching discipline once each, and keep the gnomAD release-pinning example (r4 vs r2.1 pLI) in a single location instead of both trap 6 and Limitations.

Isolate time-sensitive values (gnomAD r4/r2.1 numbers, miRDB v6.0, MSigDB collection versions) in a clearly-signaled version note so the durable guidance isn't entangled with release-pinned data that will age.

DimensionReasoningScore

Conciseness

The body is dense with non-obvious, hard-won specifics (set-name conventions, tool parameters, failure modes) and contains almost no conceptual padding Claude already knows, so it is above anchor 2. But it could be tightened: the single-strand ORF caution is stated at length three times, 'final-answer discipline' is repeated across two sections, the six-traps summary re-states the detail sections below it, the gnomAD release table effectively appears twice (trap 6 and Limitations), and release-pinned values (gnomAD r4/r2.1 pLI, miRDB v6.0) are inlined rather than isolated — matching anchor 3's 'mostly efficient but could be tightened' rather than anchor 4.

3 / 5

Actionability

Fully executable throughout: exact tool names with parameters (`DisGeNET_get_disease_genes(disease=C0152200)`, `PubTator3_GetEntityRelations(e1="@GENE_<sym>")`), exact set-name patterns (`MIR186_3P`, `PGM3_TARGET_GENES`, `MP_INCREASED_MELANOMA_INCIDENCE`), and three complete, copy-paste-ready Python functions (count_orfs, digest, gamete_ratio) with worked examples and expected outputs. This is a direct match for anchor 5's 'copy-paste ready code or commands; specific examples cover the common cases'.

5 / 5

Workflow Clarity

Every multi-step process is a numbered sequence with explicit validation checkpoints and recovery loops: the 5-step MCQ procedure ('Check each option ... Exactly one option should be supported'), the 6-step in-X-but-not-Y recipe with a text-mined fallback, the 3-step drug-vignette procedure, and computational checks like 'Always check the returned length against what the question asked for', 'match the computed value back to the option letters carefully and explicitly', and 'If a tool errors on a name ... re-derive the name before concluding insufficient'. Feedback loops and checklists are present, matching anchor 5; no destructive/batch cap applies.

5 / 5

Progressive Disclosure

No bundle files exist (no references/, scripts/, or assets/), so the whole ~29KB — routing table, four domain playbooks (Allen, HPA, drug vignettes, gene-disease), and three code-heavy computational procedures — is inlined in one file. Internal structure is good (clear ## / ### headers, a routing table acting as an index, 'the detail for each is further down' signaling), which lifts it above anchor 2's 'minimal structure'; but content that clearly belongs in separate files (the executable Python in scripts/, the per-database playbooks in references/) is all inline, which is exactly anchor 3's 'content that should be separate is inline'. It cannot score higher absent any one-level-deep reference split.

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.

An exemplary description: concrete 'what', explicit and repeated trigger guidance, named databases, and explicit exclusions that delimit it from adjacent skills. The only mild weakness is that the capability set is one workflow expressed across several question modalities rather than several distinct actions.

DimensionReasoningScore

Specificity

The description names concrete actions — "Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory" and verifying "one option ... against an authoritative source" — plus named databases (DisGeNet, OMIM, MSigDB, ClinVar, etc.). It sits between anchor 3 and 5: the core capability is really one workflow (query tool → verify option → answer) rather than multiple distinct actions, so it does not reach anchor 5's 'multiple specific concrete actions', but it is noticeably above the 1-2-action midpoint.

4 / 5

Completeness

Both halves are explicit: the 'what' is the opening sentence (query ToolUniverse tools instead of answering from memory), and the 'when' is stated twice with concrete triggers — "Triggers on any 'which gene...' lookup" and "Use whenever a single correct answer exists in a public biomedical database and could be looked up rather than guessed". It also adds explicit NOT-for boundaries, matching the anchor-5 example's structure exactly. Anti-drift check: anchor 4's 'when could be more explicit' does not apply — triggers are concrete and repeated.

5 / 5

Trigger Term Quality

Trigger phrases are comprehensive and match what users would naturally say: "any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup", "any question phrased 'according to <database>'", and 13 concrete database names plus "multiple-choice biology/medicine knowledge questions". Synonym coverage (factual / recall / multiple-choice / lookup) is complete; no natural phrasing of this task type is missing.

5 / 5

Distinctiveness Conflict Risk

The niche is unambiguous (biomedical database lookups via ToolUniverse) and it pre-empts the two adjacent skills by name: "NOT for analyzing user-supplied data files (CSV/VCF/h5ad → use the data-analysis router) and NOT for open-ended literature synthesis". Minimal overlap risk with any other skill.

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-biomedical-fact-lookup/SKILL.md

Reviewed

Table of Contents

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