encode-ccres-database

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.

Quality

92%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

85%Weight 40%Scale 1-3

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is highly actionable with complete executable examples, clear sequencing, and well-organized one-level-deep references; its main weakness is mild redundancy and conceptual explanation that could be trimmed for token efficiency.

Suggestions

Remove the duplicated Parsing Output guidance (it appears both in Core Rules and as its own section) and consolidate into one place.

Trim the introductory primer on what cCREs and biochemical signatures are, since Claude already knows this domain background; keep only the skill-specific behavior.

Move the long per-command example listing into a references file (or tighten to one canonical example plus a flag summary) to keep the overview lean.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with abundant executable examples, but includes redundant material (the Parsing Output guidance is stated twice) and explanatory background Claude largely knows (the cCRE/biochemical-signature primer, Type A biosample explanation), so it could be tightened further.	2 / 3
Actionability	Provides fully executable, copy-paste-ready commands for every subcommand plus concrete jq filtering examples, matching the 'fully executable code/commands' anchor.	3 / 3
Workflow Clarity	Clear sequence (prerequisites, core rules, quick start, command catalog) with explicit operational checkpoints — the license-file gate, mandatory wrapper/rate-limit enforcement, and the jq-parsing rule — giving a well-sequenced, checkpointed workflow for these read-only queries.	3 / 3
Progressive Disclosure	A concise overview that points one level deep to real bundle files — references/json_output_structure.md and references/graphql_schema.md (both present) — with detailed schema material appropriately split out and clearly signaled.	3 / 3
	Total	11 / 12 Passed

Description

100%Weight 40%Scale 1-3

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 distinctive, clearly stating concrete capabilities and an explicit use-when trigger tied to natural domain terminology.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — querying cCREs via the SCREEN GraphQL API and making custom queries to the ENCODE Portal REST API for experiments, files, and ChIP-seq peaks — matching the 'lists multiple specific concrete actions' anchor.	3 / 3
Completeness	Explicitly answers both what (query cCREs via SCREEN GraphQL / custom Portal REST queries) and when via the explicit 'Use when you want to query regulatory annotations or raw experimental data across human cell types' clause.	3 / 3
Trigger Term Quality	Uses natural domain terms a user would say — 'ENCODE', 'cCREs', 'ChIP-seq peaks', 'regulatory annotations', 'raw experimental data', 'human cell types' — giving good coverage rather than only some keywords.	3 / 3
Distinctiveness Conflict Risk	Targets a clearly distinct niche (ENCODE cCREs, SCREEN GraphQL, Portal REST, ChIP-seq) with triggers unlikely to fire for unrelated skills.	3 / 3
	Total	12 / 12 Passed

Validation

100%

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 — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: google-deepmind/science-skills
Path: skills/encode_ccres_database/SKILL.md
Commit: 0b42509

Reviewed: 8 days ago

Table of Contents

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