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extract-clinical-entities-to-fhir

Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle. Use when an agent must turn local clinical NER output into Conditions, MedicationStatements, Observations, or other FHIR resources without inventing terminology codes.

73

Quality

92%

Does it follow best practices?

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SKILL.md
Quality
Evals
Security

Quality

Content

90%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 lean, actionable, and well-structured with an executable example and a clear procedure that includes validation. It falls just short of top marks on workflow clarity (no explicit error-recovery loop) and progressive disclosure (a broken external reference).

Suggestions

Add an explicit validate->fix->retry loop after the to_bundle/profile-validation step, e.g. 'If validation fails, read the OperationOutcome, fix the offending resource, and re-run to_bundle before retrying validation.'

Fix or remove the broken reference to ../../examples/first_five_minutes_redact_extract_fhir.py so the Repository example points to a file that actually exists in the bundle.

Consider showing the MedicationStatement/Observation mapping alongside the Condition example to make the multi-resource workflow more concretely actionable.

DimensionReasoningScore

Conciseness

Lean and efficient with no padding about concepts Claude already knows; the only prose reinforces a safety rule rather than explaining basics, and the substantial code block is earned executable content.

5 / 5

Actionability

Provides fully executable, copy-paste-ready Python with real imports, a concrete model name and confidence threshold, an install command, and the to_bundle call, covering the common Condition-mapping case.

5 / 5

Workflow Clarity

A clear 6-step sequence includes a validation step (step 6 and a Safety check to validate against the profile), but there is no explicit validate->fix->retry feedback loop for batch resource assembly and clinical-status assertions.

4 / 5

Progressive Disclosure

Well-organized sections with a clearly signaled single-level reference to a repository example; the referenced file (../../examples/first_five_minutes_redact_extract_fhir.py) does not exist in the bundle, a minor organization gap keeping it just below 5.

4 / 5

Total

18

/

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.

The description is specific, complete, and distinct: it states concrete extraction and FHIR-mapping actions plus an explicit 'Use when' trigger tied to clinical NER output. Trigger-term coverage is strong but slightly technical, leaving a few natural synonyms on the table.

DimensionReasoningScore

Specificity

Names multiple concrete actions ('Extract clinical entities', 'map them into deterministic FHIR R4 resources and a Bundle', 'turn local clinical NER output into Conditions, MedicationStatements, Observations') with comprehensive coverage of the target domain.

5 / 5

Completeness

Explicitly answers both 'what' (extract clinical entities and map to FHIR resources/Bundle) and 'when' ('Use when an agent must turn local clinical NER output into... FHIR resources without inventing terminology codes') with concrete trigger phrasing.

5 / 5

Trigger Term Quality

Good keyword coverage with clinical terms (FHIR R4, NER, MedicationStatements, terminology codes), but the natural user phrasings skew technical and a few common synonyms are missing.

4 / 5

Distinctiveness Conflict Risk

Occupies a narrow, specific niche (clinical NER to FHIR R4 mapping with a no-invented-codes constraint) with distinct triggers and minimal overlap risk with other skills.

5 / 5

Total

19

/

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

relative_links

Relative link issues: 1 suspicious

Warning

Total

15

/

16

Passed

Repository

maziyarpanahi/openmed

Path

skills/extract-clinical-entities-to-fhir/SKILL.md

Reviewed

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