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lamindb

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

65

Quality

82%

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SKILL.md
Quality
Evals
Security

Quality

Content

71%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.

This is a well-structured overview skill: it cleanly splits detailed material across six existing one-level-deep reference files, provides concrete install commands and four illustrative code workflows, and sequences onboarding through a clear checklist. Its main weaknesses are token efficiency (duplicated 'When to Use' and 'Reference Files' sections, and capability bullets that restate reference-file content) and use-case code that leans on undefined placeholder variables rather than fully executable examples.

Suggestions

Trim redundant sections: drop the trailing 'Reference Files' list (each pointer already appears inline in its capability section) and shorten 'When to Use This Skill' so it does not restate the frontmatter description verbatim.

Make the use-case examples executable by defining or commenting the placeholder inputs (e.g., show how 'schema' is constructed in Use Case 1 and replace bare 'data_files'/'tissues'/'conditions'/'train_model' with defined or clearly-marked examples).

Add an inline validation feedback loop for curation: a brief note after 'curator.validate()' on inspecting the error report and re-validating before 'save_artifact()', rather than deferring it entirely to references/annotation-validation.md.

DimensionReasoningScore

Conciseness

The body is list-dense rather than padded prose and avoids explaining concepts Claude already knows, but it is noticeably long for an overview: the 'When to Use' section restates the frontmatter description, the 'Reference Files' section at the end duplicates the per-capability 'Reference:' pointers already given inline, and the six capability sections enumerate bullet lists that largely mirror the reference files.

3 / 5

Actionability

Guidance is mostly executable: four complete Python use cases, concrete install commands ('uv pip install lamindb', 'lamin init --storage ...'), and specific API calls ('ln.track()', 'curator.validate()', 'bt.CellType.import_source()'). However, several examples rely on undefined placeholders ('schema', 'data_files', 'tissues', 'conditions', 'train_model'), which keeps it just short of fully copy-paste ready.

4 / 5

Workflow Clarity

The 'Getting Started Checklist' gives a clear six-step sequence, use cases follow a consistent track/validate/finish pattern, and the curation process is explicitly ordered (validation → standardization → annotation) with a validate-before-save checkpoint. The checkpoint exists but error-recovery guidance (what to do when curator.validate() fails) is deferred to a reference file rather than stated inline, a minor gap.

4 / 5

Progressive Disclosure

The body is a true overview that points to six well-signaled, one-level-deep reference files ('Read this for detailed information on...'), all of which exist in the bundle, with each capability section summarizing its file's scope and a consolidated 'Reference Files' section plus external links. Structure and navigation are easy to follow with no nested-reference chains.

5 / 5

Total

16

/

20

Passed

Description

87%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 explicitly covers both what the skill does and when to use it, with domain-specific trigger terms (scRNA-seq, flow cytometry, ontologies, Nextflow/Snakemake, W&B/MLflow) that make it highly distinguishable from other skills. It could edge closer to the top specificity anchor by replacing the abstract FAIR/value framing with more concrete operations and adding a few common synonyms such as 'single-cell' or 'spatial transcriptomics'.

DimensionReasoningScore

Specificity

The description lists many specific concrete actions — 'managing biological datasets (scRNA-seq, spatial, flow cytometry)', 'curating and validating data with biological ontologies', 'schema validation', 'integrations with workflow managers (Nextflow, Snakemake)' — but opens with the somewhat abstract value framing 'makes data queryable, traceable, reproducible, and FAIR' rather than concrete operations, leaving minor gaps versus the comprehensive anchor.

4 / 5

Completeness

Both 'what' ('an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR', with the enumerated coverage areas) and 'when' ('Use when managing biological datasets..., tracking computational workflows, curating and validating data...') are explicitly answered with concrete trigger phrases, matching the top anchor.

5 / 5

Trigger Term Quality

Natural keywords users would actually say are well covered: 'LaminDB', 'scRNA-seq', 'flow cytometry', 'biological datasets', 'data lakehouses', 'lineage', 'reproducibility', 'Nextflow', 'Snakemake', 'W&B', 'MLflow'. A few common variations are missing (e.g., 'single-cell', 'spatial transcriptomics' spelled out, 'AnnData'/'h5ad'), so it does not reach the comprehensive-synonym anchor.

4 / 5

Distinctiveness Conflict Risk

The description names a clear niche — biological data management with LaminDB, biological ontologies, scRNA-seq/flow cytometry, and workflow-manager/MLOps integrations — giving it distinct triggers and minimal conflict risk with other skills; it is written in third person with no first/second-person voice.

5 / 5

Total

18

/

20

Passed

Validation

87%

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

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

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

Warning

Total

14

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/lamindb/SKILL.md

Reviewed

Table of Contents

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