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neoantigen-predictor

Predict neoantigens that may be recognized by the immune system based.

40

Quality

39%

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SecuritybySnyk

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tessl review fix ./scientific-skills/Data Analysis/neoantigen-predictor/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

50%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 domain-rich, largely actionable skill document with real executable code, CLI examples, and a complete output schema, but it is noticeably verbose with generic boilerplate sections and inlines bulk reference material that would be better split into named files. Workflow validation checkpoints are present at the edges but underdeveloped in the core prediction path.

Suggestions

Trim or remove generic boilerplate sections ('Lifecycle Status', 'Risk Assessment', 'Evaluation Criteria', generic 'Workflow'/'Output Requirements') that restate process Claude already knows, to recover token budget.

Move the large HLA support list, scoring-algorithm details, and full output schema into reference files (e.g., references/hla_alleles.md, references/scoring.md) and link to them by name from the body.

Add an explicit validation feedback loop to the core prediction workflow (run py_compile, execute on sample mutations, verify output against expected schema, fix and re-run) rather than leaving checkpoints implicit.

DimensionReasoningScore

Conciseness

The body runs ~450 lines and includes several padded/generic boilerplate sections ('Lifecycle Status', 'Risk Assessment', 'Evaluation Criteria', generic 'Workflow', 'Output Requirements') that explain process Claude already knows, alongside dense useful domain content, matching the 'noticeably verbose; several unnecessary explanations or padded sections' anchor.

2 / 5

Actionability

It provides concrete, mostly executable guidance — an importable Python API example (NeoantigenPredictor class, real in scripts/main.py), CLI invocations with real flags, a full output JSON schema, and weighted scoring formulae — with only minor gaps such as the symbolic 'Σ(wi × fi)' immunogenicity expression, fitting the 'mostly executable guidance with minor gaps' anchor.

4 / 5

Workflow Clarity

A sequenced 'Workflow' with Quick Check (py_compile) and Audit-Ready Commands provides some checkpoints, but the core prediction workflow lacks explicit validation feedback loops (validate -> fix -> retry) for the multi-step analysis, sitting at the 'steps listed but validation gaps; checkpoints implicit' anchor.

3 / 5

Progressive Disclosure

Sections are well-headed and references are one level deep with real files (references/README.md, example_mutations.csv, scripts/main.py verified to exist), but large reference-style blocks (HLA support list, scoring algorithms, output schema) are inlined and references are signaled generically ('See references/ directory') rather than by named file, matching the 'some structure but could be better organized; references not clearly signaled' anchor.

3 / 5

Total

12

/

20

Passed

Description

28%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 a grammatically truncated, near-verbatim restatement of the skill name that names the domain but lists no concrete actions and provides no 'Use when' trigger guidance. It needs to be completed and expanded with specific capabilities and explicit trigger phrases.

Suggestions

Finish the truncated sentence and replace generic phrasing with concrete actions (e.g., 'Extract variant peptides from tumor mutations, predict HLA binding affinity with NetMHCpan, and rank immunogenic neoantigen candidates').

Add an explicit 'Use when...' clause with natural trigger terms users would say (e.g., 'Use when the user asks to predict neoantigens, identify tumor-specific peptide candidates, or screen HLA-binding variants for immunotherapy').

Include natural synonyms and file/format terms (tumor, cancer, HLA, VCF, immunotherapy, vaccine) to improve trigger-term coverage and distinctiveness.

DimensionReasoningScore

Specificity

The description names the domain ('Predict neoantigens that may be recognized by the immune system based') but the single action is generic and the sentence is truncated mid-thought; no concrete actions are enumerated, matching the anchor that names the domain with minimal/generic actions.

2 / 5

Completeness

It offers only a vague, truncated 'what' and no 'when'/'Use when' trigger guidance at all, matching the anchor for a vague 'what' with no 'when'; per the cap rule a missing trigger clause would not exceed 3, and the what is too weak to rise above 2.

2 / 5

Trigger Term Quality

It includes one or two relevant domain keywords ('neoantigens', 'immune system') but the phrase is truncated and missing common natural variations users would say ('tumor', 'cancer', 'HLA', 'immunotherapy', 'vaccine'), fitting the anchor with generic keywords missing natural phrases.

2 / 5

Distinctiveness Conflict Risk

Neoantigen prediction is a fairly distinct niche unlikely to overlap unrelated skills, but the truncated/generic phrasing keeps it from being crisp, so it sits at the 'somewhat specific but could still overlap' anchor.

3 / 5

Total

9

/

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.

Validation15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

Table of Contents

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