rare-disease-hpo-mapper

Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis.

Quality

48%

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Securityby

Passed

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tessl review fix ./scientific-skills/Evidence Insight/rare-disease-hpo-mapper/SKILL.md

Quality

Content

42%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 content pairs a real, working script with executable validation commands and a one-level reference, but it is weighed down by generic process boilerplate and lacks a complete end-to-end usage example with a validation feedback loop. Tightening the inline boilerplate and adding a concrete mapping invocation would materially raise quality.

Suggestions

Trim or relocate generic boilerplate (Risk Assessment, Security Checklist, Lifecycle Status, Evaluation Criteria, Response Template) into a reference file so the body stays HPO-specific.

Add a complete, copy-paste example invocation such as `python scripts/main.py --symptoms "seizures,short stature"` showing real input and expected HPO output.

Insert an explicit output-validation checkpoint in the Workflow (e.g. verify each symptom mapped or list unmatched symptoms) to create a validate-fix-retry loop.

Dimension	Reasoning	Score
Conciseness	The body carries several generic padded sections (Risk Assessment, Security Checklist, Lifecycle Status, Evaluation Criteria, Output Requirements, Response Template) that are skill-process boilerplate unrelated to HPO, fitting 'noticeably verbose; several unnecessary padded sections' rather than the mostly-efficient 3.	2 / 5
Actionability	Concrete executable commands exist ("python -m py_compile scripts/main.py", "python scripts/main.py --help") and a real script is referenced, but the core mapping invocation is only described as "Run python scripts/main.py with the validated inputs" with no complete example, leaving key execution details missing.	3 / 5
Workflow Clarity	The Workflow lists five sequenced steps with a fallback path and a compile Quick Check, but validation checkpoints for the actual mapping output are implicit rather than explicit, matching 'steps listed but validation gaps'.	3 / 5
Progressive Disclosure	There is one clearly signaled one-level reference ([references/audit-reference.md]) and a packaged script, but substantial generic content (security, risk, lifecycle, evaluation) is inlined in SKILL.md that could be split out, fitting 'some structure but could be better organized'.	3 / 5
	Total	11 / 20 Passed

Description

53%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 states a clear, specialized purpose but stops at a single action and omits any "Use when..." trigger guidance, leaving completeness and trigger-term coverage at the midpoint. It is distinct within its niche yet could sharpen when-to-use phrasing and add common synonyms.

Suggestions

Add an explicit 'Use when...' clause naming concrete triggers, e.g. 'Use when mapping clinical symptoms to HPO terms for rare-disease or exome/genome diagnosis.'

Include natural synonyms and the abbreviation users actually say, such as 'HPO', 'phenotype', 'phenotyping', and 'rare disease'.

List 1-2 more concrete actions (e.g. 'suggest differential-diagnosis genes and score confidence') to lift specificity above a single mapping action.

Dimension	Reasoning	Score
Specificity	Quotes "Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis" name the domain and one concrete action (symptoms -> HPO terms), but coverage is not comprehensive, matching the anchor for 1-2 concrete actions rather than the multiple-action 5.	3 / 5
Completeness	The description gives a clear "what" (map symptoms to HPO terms) but has no "Use when..." clause or equivalent trigger guidance, which per the judging guidelines caps completeness at 3.	3 / 5
Trigger Term Quality	Terms like "patient symptoms", "Human Phenotype Ontology", and "gene diagnosis" are relevant niche keywords, but common variations such as the abbreviation "HPO", "phenotype", or "rare disease" are missing, fitting the 'some relevant keywords but missing synonyms' anchor.	3 / 5
Distinctiveness Conflict Risk	The HPO/gene-diagnosis niche is mostly distinct with specialized triggers, but without an explicit "Use when" clause there is minor overlap risk with related clinical-genetics skills, so it is one step below the minimal-conflict anchor of 5.	4 / 5
	Total	13 / 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/Evidence Insight/rare-disease-hpo-mapper/SKILL.md
Commit: 63c61d3

Reviewed: 8 hours ago

Table of Contents

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