cross-reference

A research cross-referencing tool that connects ENCODE experiments with scientific publications, preprints, clinical trials, and genetic databases. ENCODE is a project that maps functional parts of the human genome.

In plain words
What is it for?
It helps find papers and preprints, identify related clinical trials, and link ENCODE results with resources such as PubMed, bioRxiv, ClinVar, GTEx, and the GWAS Catalog.
Why use it?
It helps connect experimental data to related evidence without searching each scientific database separately.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/ammawla/encode-toolkit/cross-reference
Any agent
npx skills add ammawla/encode-toolkit --skill cross-reference
Clone the repo
git clone --depth 1 https://github.com/ammawla/encode-toolkit

Made for: Claude Code, Codex.

Per session 88 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,795 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. Scan, not verified.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00088 $0.08795
Opus 5 $0.00044 $0.04398
Sonnet 5 $0.00018 $0.01759
Haiku 4.5 $0.00009 $0.00880

Measured 2d ago against content hash 47382b7a44c5, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

cross-reference scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gds&db=sra&id=GDS_UID&tool=encode_mcp&email=YOUR_EMAIL"
plugin/skills/cross-reference/SKILL.md · 688 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2d ago First seen · 688 lines · 88 tokens per session scan A 47382b7a44c5

Subscribe to this mod's changes

cross-reference is a skill published in the GitHub repository ammawla/encode-toolkit (24 stars, last pushed 1mo ago), licensed AGPL-3.0. It adds 88 tokens to every session and 8,795 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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