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.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-gene-dbgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gene-db)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gene-db"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gene-db/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gene-db"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-gene-db.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00085 | $0.01950 |
| Opus 5.5 | $0.00034 | $0.00780 |
| Sonnet 5.5 | $0.00017 | $0.00390 |
| Haiku 4.5 | $0.00009 | $0.00195 |
Grade A, and why
alterlab-gene-db 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 1mo 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.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 201 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Gene Database
Overview
NCBI Gene is a comprehensive database integrating gene information from diverse species. It provides nomenclature, reference sequences (RefSeqs), chromosomal maps, biological pathways, genetic variations, phenotypes, and cross-references to global genomic resources.
When to Use This Skill
This skill should be used when working with gene data including searching by gene symbol or ID, retrieving gene sequences and metadata, analyzing gene functions and pathways, or performing batch gene lookups.
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Ensembl IDs, VEP consequences, orthologs, or GRCh37↔GRCh38 mapping | alterlab-ensembl |
| Protein-level function, domains, PTMs, or UniProt ID mapping | alterlab-uniprot |
| Variant clinical significance | alterlab-clinvar |
| Pathway membership / enrichment for a gene list | alterlab-reactome |
| Quick one-off gene lookups from a CLI across databases | alterlab-gget |
Quick Start
NCBI provides two main APIs for gene data access:
- E-utilities (Traditional): Full-featured API for all Entrez databases with flexible querying
- NCBI Datasets API (Newer): Optimized for gene data retrieval with simplified workflows
Choose E-utilities for complex queries and cross-database searches. Choose the Datasets API for straightforward gene metadata retrieval (one gene report per request; transcript/protein RefSeq accessions come from the separate product_report endpoint).
Common Workflows
Search Genes by Symbol or Name
To search for genes by symbol or name across organisms:
- Use the
scripts/query_gene.pyscript with E-utilities ESearch - Specify the gene symbol and organism (e.g., "BRCA1 in human")
- The script returns matching Gene IDs
Example query patterns (tags checked against einfo.fcgi?db=gene; an unknown tag such
as [disease], [phenotype], or [pathway] is silently rewritten to [All Fields] —
always read querytranslation in the ESearch response):
- Gene symbol:
INS[sym] AND human[organism]([gene]/[sym]match symbols, soinsulin[gene name]finds nothing — useinsulin[Gene Full Name]for names) - Gene with disease:
dystrophin[Gene Full Name] AND "muscular dystrophy"[Disease/Phenotype] - Cytogenetic location:
human[organism] AND 17q21[Default Map Location]([chromosome]holds chromosome numbers only, e.g.17[chromosome])
What ships with it
6 files 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.
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.
- 1mo ago Changed · +17 lines 086327d81fbb
- 1mo ago First seen · 184 lines · 85 tokens per session scan A 0463bfb7b742
alterlab-gene-db is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 4d ago), licensed MIT. It adds 85 tokens to every session and 1,950 once invoked, about $0.0003 per session on Opus 5.5. 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 2026-09-03.
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