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tooluniverse-sequence-retrieval

Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions. Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference.

71

Quality

86%

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SecuritybySnyk

Low

Low-risk findings worth noting

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

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, actionable skill body: the phased workflow has explicit checkpoints and error-recovery loops, and tool usage is concrete. The main weaknesses are redundant restatements of the RefSeq/GenBank hierarchy and placeholder-variable code samples, plus reference tables that belong in separate files.

Suggestions

Consolidate the RefSeq-vs-GenBank quality hierarchy into one authoritative location (e.g., the Curation Level Tiers table) and reference it from Domain Reasoning and the Reasoning Framework instead of restating it three times; do the same for the 'ENA lacks RefSeq' rule.

Make the Phase 2 code sample fully copy-paste ready by binding the placeholder variables (e.g., showing one concrete call such as organism="Escherichia coli", gene="lacZ") and demonstrating how to parse the returned accession/sequence fields.

Move the Search Parameters Reference and Curation Level Tiers tables into a reference file (e.g., references/accessions.md) and link to it from the body, keeping SKILL.md as a lean overview.

DimensionReasoningScore

Conciseness

The body is dense and tabular with no explanations of concepts Claude already knows, but the RefSeq-over-GenBank hierarchy is repeated in "Domain Reasoning", the "Curation Level Tiers" table, and "Reasoning Framework", and "ENA doesn't have RefSeq" appears three times (CRITICAL note, fallback table, error table). Not 5 because this redundancy could be consolidated; not 3 because there is no padded or over-explained content.

4 / 5

Actionability

Concrete tool calls with real parameter names and values ("tu.tools.NCBI_search_nucleotide(operation=\"search\", ... limit=10)", "format=\"fasta\""), plus fallback chains and an error-response table give mostly executable guidance. Not 5 because the code samples use unbound placeholder variables and only the UID step shows output handling; not 3 because the guidance is genuinely executable, not pseudocode.

4 / 5

Workflow Clarity

A clearly sequenced Phase 0→3 pipeline with an Identity Checklist as an explicit checkpoint, fallback chains, an Error Handling table providing feedback loops, and Synthesis Questions ("Is the sequence from the expected organism/strain?") that verify results. Not 4 because validation checkpoints and error-recovery loops are all explicitly present; the operations are read-only, so no destructive-op cap applies.

5 / 5

Progressive Disclosure

The single file is well-organized with clear section headers, a workflow overview, and no nested or buried references (no bundle files exist). Not 5 because at ~145 lines the "Search Parameters Reference" and "Curation Level Tiers" tables are reference material that could be split into separate files; not 3 because everything present is clearly signaled and navigable.

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: it states concrete third-person capabilities, includes an explicit "Use for..." clause with specific trigger scenarios, and occupies a well-delineated niche. The only gap is missing common synonym terms like "FASTA" or ".fasta" that users might naturally say.

DimensionReasoningScore

Specificity

"Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation" plus "fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval" lists multiple concrete actions covering the domain comprehensively in third-person voice. Not 4 because coverage has no notable gaps; nothing above 5 exists on the scale.

5 / 5

Completeness

Both questions are explicitly answered: the "what" ("Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation" plus the quality hierarchy) and a concrete "when" ("Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference"). This matches the score-5 anchor's structure of concrete what-and-when trigger phrases.

5 / 5

Trigger Term Quality

Natural trigger terms like "sequence", "accession", "gene-symbol", "transcript-isoform", "NCBI", "ENA", "RefSeq", and "GenBank" are present and match what users would say. Not 5 because common variations such as "FASTA", "nucleotide", "protein sequence", or file extensions like ".fasta" are missing; not 3 because the core phrasings users actually use are all covered.

4 / 5

Distinctiveness Conflict Risk

"Retrieve DNA/RNA/protein sequences from NCBI and ENA" carves out a clear niche with database-specific triggers (accession prefixes, RefSeq/GenBank) that no adjacent skill would claim. Not 4 because overlap risk is minimal, not lower because the triggers are uniquely identifying.

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
Reviewed

Table of Contents

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