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bioservices

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and integrated biological data workflows with BioServices.

69

Quality

87%

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SecuritybySnyk

Low

Low-risk findings worth noting

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 a strong reference-style skill: copy-paste-ready code with failure guards, explicit workflow checkpoints including batch-operation validation, and a clean one-level reference/script structure where every link resolves. The only notable trimmable content is review-process metadata and a few repeated hedges, which keeps conciseness at 4 rather than 5.

DimensionReasoningScore

Conciseness

Quotes: 'mapping() returns a results/failedIds envelope, not a source-to-list dictionary', 'KEGG get permits at most ten entries; KGML permits one pathway per request', 'k.TIMEOUT = 30 merely creates an unused attribute' — dense with non-obvious, version-specific gotchas Claude cannot know, with no basic-concept padding. Not 5 because review-process metadata ('the bundled tests were run in an isolated Python 3.13 environment. The previous 3.12 upper bound was not a package requirement') and repeated hedging ('Service availability is not guaranteed') could be trimmed.

4 / 5

Actionability

Quotes: executable snippets with real parameters and failure guards ('if not isinstance(mapping, dict) or "results" not in mapping: raise RuntimeError', 'u.search("gene_exact:ZAP70 AND organism_id:9606 AND reviewed:true", frmt="tsv", ...)'), plus runnable CLI commands ('python scripts/batch_id_converter.py input_ids.txt --from UniProtKB_AC-ID --to KEGG'). The one non-executable snippet (BLAST, undefined protein_sequence) is explicitly justified as illustrative with a comment, satisfying the rubric's flexibility exception.

5 / 5

Workflow Clarity

Quotes: a numbered five-step Workflow ('Review search hits before selecting one', 'Run a small lookup before batching; honor provider limits and retain failures separately from confirmed empty results') with explicit checkpoints, and per-service error handling ('Poll with a delay and deadline. Stop on FAILURE, ERROR, or NOT_FOUND; only retrieve completed jobs. Retain the job ID when a local wait times out'). Batch operations are covered with validation and failure separation, so the batch-cap at 3 does not apply.

5 / 5

Progressive Disclosure

Quotes: '[the service reference](references/services_reference.md)', '[identifier mapping](references/identifier_mapping.md)', '[workflow patterns](references/workflow_patterns.md)' — all three are real files in references/, one level deep with no nested chains, and the four scripts in scripts/ are each linked with a one-line summary in 'Bundled workflows'. The SKILL.md body stays an overview of gotchas while bulk detail lives in the reference files, matching the clear split the anchor describes.

5 / 5

Total

19

/

20

Passed

Description

78%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 strong: third-person voice, concrete domain and actions, six named service triggers, and an explicit 'Used for' clause covering both what and when. Its only weaknesses are the vague closing phrase 'integrated biological data workflows' and the absence of explicit user-mention triggers and common synonyms like 'gene' or 'sequence'.

Suggestions

Add an explicit user-mention trigger clause, e.g. 'Use when the user mentions UniProt, KEGG, ChEMBL, protein annotation, pathway retrieval, or mapping chemical identifiers', to raise completeness from 4 to 5.

Include natural synonyms users say for covered capabilities — 'gene', 'sequence', 'BLAST', 'protein-protein interactions' — to improve trigger term coverage.

Replace the generic 'integrated biological data workflows' with a concrete action (e.g. 'combine protein, pathway, and compound data across databases') to remove the one vague capability claim.

DimensionReasoningScore

Specificity

Quotes: 'cross-database protein annotation, pathway retrieval, chemical identifier mapping' lists several concrete actions alongside six named services, but the fourth action 'integrated biological data workflows with BioServices' is generic, leaving a minor coverage gap. Not 3 because more than 1-2 concrete actions are listed; not 5 because comprehensive coverage would require replacing the vague final clause with a concrete action.

4 / 5

Completeness

Quotes: 'Provides a Python interface to bioinformatics services including UniProt, KEGG...' answers 'what' concretely, and 'Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping' provides equivalent trigger guidance for 'when'. Not 5 because the 'when' clause describes use cases rather than explicit user-mention triggers ('use when the user mentions UniProt or KEGG'); not 3 because an explicit 'Used for...' clause is present, not merely implied.

4 / 5

Trigger Term Quality

Quotes: 'UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem', 'protein annotation', 'pathway retrieval', 'chemical identifier mapping', 'bioinformatics' — good natural keyword coverage, as users would say these service names directly. Not 5 because common variations like 'gene', 'sequence', 'BLAST', and 'protein-protein interactions' are absent even though the skill handles them.

4 / 5

Distinctiveness Conflict Risk

Quotes: 'UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem' — naming six specific databases carves out a clear niche with distinct trigger words that virtually no other skill would claim. Not 4 because the overlap risk is limited to hypothetical dedicated single-service skills, which is minimal conflict.

5 / 5

Total

17

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_field

'metadata' should map string keys to string values

Warning

Total

15

/

16

Passed

Repository

K-Dense-AI/scientific-agent-skills

Path

skills/bioservices/SKILL.md

Reviewed

Table of Contents

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