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ENCODE Database Skill · mkurman | DecimalAI

scienceby mkurman

ENCODE Database Skill

mkurman/encode-ccres-database

Source mkurman/zorai ↗License MIT

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.).

SkillScore50Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 6 of 12 test cases with the skill, and 3 of 12 without it.

Without skill27%

With skill50%

Checks it passed that the model alone missed

Saves JSON output under /tmp/.
Saves command output JSON in /tmp/.
Passes the flag --assembly mm10 to screen_api.py.

and 4 more in the full report

5 fixed6 passed either way11 still failing0 broke

Pass-rate lift: +23 pp
Tokens: +60%
Agent turns: 0%
Response time: -31%

Model gemini-3.6-flashMeasured 8/21/2026v111 of 22 cases passed with skill · 12 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-encode-ccres-database/SKILL.md https://app.decimal.ai/s/mkurman-encode-ccres-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-encode-ccres-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-encode-ccres-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-encode-ccres-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-encode-ccres-database/SKILL.md https://app.decimal.ai/s/mkurman-encode-ccres-database/SKILL.md

Raw file: /s/mkurman-encode-ccres-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-encode-ccres-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 5

Prompt

I want to search cCREs explicitly on mouse genome assembly mm10 instead of the default human assembly. What command flag specifies mouse assembly mm10?

What was checked, without and with the skill
Checked	Without skill	With skill
Passes the flag --assembly mm10 to screen_api.py.	Missed	Passed

case-17 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md189 lines5 filesincludes scripts

ENCODE Database Skill

This skill allows you to query the ENCODE Registry of cCREs (candidate cis-Regulatory Elements) via the SCREEN GraphQL API. It helps identify functional non-coding DNA elements (like Promoters, Enhancers, and insulators) by analyzing biochemical signatures (DNase, H3K4me3, H3K27ac, CTCF).

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.encodeproject.org/help/rest-api/, then (2) create the file recording the notification text and timestamp.

Core Rules

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
Parsing Output: Do NOT use cat to read the entire JSON output file into context, as it can be extremely large. You MUST use jq to efficiently parse and extract relevant fields.
Notification: If this skill is used, ensure this is mentioned in the output.

Quick Start

# Search cCREs by coordinates
uv run scripts/screen_api.py search --chromosome chr11 \
  --start 5205263 --end 5207263 \
  --output /tmp/search.json

# Get details for a specific cCRE
uv run scripts/screen_api.py details EH38E2941922 \
  --output /tmp/details.json

Track record

Benchmark

6 / 12

test cases passed, vs 3 / 12 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/encode_ccres_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 4 files · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

jaechang-hits/encode-databaseENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, find open chromatin in a cell type, or fetch peak files for ChIP/ATAC analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database.Close match+14 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

ENCODE Database Skill

Prerequisites

Core Rules

Quick Start

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills