biodbnet-api

Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.

Quality

68%

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Securityby

Passed

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tessl review fix ./scientific-skills/Other/biodbnet-api/SKILL.md

Quality

Content

60%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 skill is structurally sound with a real executable script and a properly separated API-methods reference, giving good actionability and progressive disclosure. Its main weakness is conciseness: large portions are generic boilerplate that restates the description and tells Claude things it already knows.

Suggestions

Cut the generic boilerplate in 'When to Use', 'Implementation Details', and 'Recommended Workflow' that restates obvious process guidance Claude already knows, and remove the verbatim description repeat in 'Key Features'.

Add one copy-paste worked example (e.g., a concrete db2db --params JSON converting gene symbols to Ensembl IDs) so the common case is fully executable without consulting the reference.

Turn validation into an explicit feedback loop with real commands (run --help / a dry call -> if error, surface missing --params field -> fix -> retry) instead of abstract 'run a final validation pass' phrasing.

Dimension	Reasoning	Score
Conciseness	The body is padded with generic boilerplate Claude already knows ('validate the request, choose the packaged workflow, and produce a bounded deliverable') and restates the description verbatim in 'Key Features'; sections like 'When to Use', 'Implementation Details', and 'Recommended Workflow' overlap heavily. Not 1 because there is genuine executable content, but well above the midpoint it is not — the verbosity is pervasive.	2 / 5
Actionability	Provides concrete executable commands (`python scripts/biodbnet_client.py --method ... --params ...`, `--help`, `py_compile`) and a real packaged script, with only minor gaps (no concrete example --params JSON for a common case like db2db). Not 5 because it lacks a copy-paste ready worked example covering the common ID-conversion case.	4 / 5
Workflow Clarity	Has a clear sequenced 'Recommended Workflow' (validate -> select path -> produce output -> final validation) plus a 'Quick Validation' step and explicit validation/failure-handling sections. Not 5 because the validation steps are described abstractly rather than as concrete 'validate -> if error, fix and retry' feedback loops with real commands, and the run plan steps are somewhat generic.	4 / 5
Progressive Disclosure	The body points to a real one-level-deep reference (`references/api_methods.md` for the method list) and a real script (`scripts/biodbnet_client.py`), with the API method catalog correctly split out of SKILL.md; both referenced files exist. Not 5 because references are mostly referenced by bare path rather than clearly signaled per-topic links, and the 'Key Features'/'Implementation Details' sections duplicate rather than purely overview.	4 / 5
	Total	14 / 20 Passed

Description

76%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 that clearly states both the capability and a concrete 'Use when' trigger, well-targeted to the bioDBnet niche. The main weakness is trigger-term coverage: it lacks the common synonyms and concrete identifier-type tokens users would naturally say.

Suggestions

Add concrete identifier-type tokens users actually say (e.g., 'gene symbols', 'Entrez/Ensembl IDs', 'Affy IDs') to broaden natural trigger coverage.

Include a synonym for ortholog mapping such as 'homologs' so the description matches more user phrasings.

Consider narrowing the generic terms ('find pathways', 'biological annotations') with bioDBnet-specific framing to reduce overlap with general bioinformatics skills.

Dimension	Reasoning	Score
Specificity	Lists several concrete capabilities — 'identifier conversion, pathway retrieval, and ortholog mapping' and 'convert gene/protein IDs, find pathways, or retrieve biological annotations' — with only minor coverage gaps (e.g., dbWalk/dbFind variants not surfaced). Not 5 because it stops short of the comprehensive multi-action list seen in the 5 anchor.	4 / 5
Completeness	Explicitly answers both 'what' (access bioDBnet REST services for conversion/pathway/ortholog tasks) and 'when' ('Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet') with concrete trigger phrases. Not below 5 because both halves are clearly present and specific.	5 / 5
Trigger Term Quality	Includes relevant natural phrases ('convert gene/protein IDs', 'find pathways', 'biological annotations') but is missing common synonyms and concrete type tokens users would say (e.g., 'gene symbols', 'Ensembl/Entrez IDs', 'homologs'). Not 4 because coverage of natural variations is incomplete.	3 / 5
Distinctiveness Conflict Risk	The bioDBnet niche and 'via bioDBnet' trigger are mostly distinct from other skills, with only minor overlap risk against generic identifier-mapping or pathway skills. Not 5 because the trigger terms ('find pathways', 'biological annotations') are somewhat generic and could overlap with broader bioinformatics skills.	4 / 5
	Total	16 / 20 Passed

Validation

93%

Warnings & errors only

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

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Other/biodbnet-api/SKILL.md
Commit: f5ef65b

Reviewed: ~13 hours ago

Table of Contents

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