What is alterlab-databases?

A collection of connectors to scientific databases such as PubMed, ChEMBL, UniProt, GEO, and clinical-trial repositories. These databases contain published research, chemical compounds, proteins, genes, and biomedical study data.

Use it to search scientific literature, genes, proteins, compounds, clinical trials, genomic datasets, medical records, and other research databases.

It reduces the effort needed to find and retrieve specialised research data from many separate sources.

alterlab-databases — Plugin for Claude Code by AlterLab-IEU

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.

Clone the repo

git clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills

Made for: Claude Code.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases/github.svg)](https://agentmods.dev/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases)

Your own site

<a href="https://agentmods.dev/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases"><img src="https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases/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.

Your own site · 80×15

<a href="https://agentmods.dev/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases"><img src="https://agentmods.dev/badge/plugins/alterlab-ieu/alterlab-academic-skills/alterlab-databases.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session not measured What this adds to a session before it is invoked.

When invoked not measured The manifest loads nothing itself; its 39 skills cost 4,090 tokens a session between them.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Security

Grade A, and why

alterlab-databases scanned grade A with 0 findings 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.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude-plugin/marketplace.json#alterlab-databases · 92 lines

How it starts

The opening of the file, as written. The whole thing — 92 lines — stays where its author put it; the contents beside it link to each section on GitHub.

{
  "name": "alterlab-databases",
  "source": "./skills/databases",
  "description": "Connectors to scientific databases (PubMed, ChEMBL, UniProt, GEO, and more) (39 skills)",
  "version": "3.0.1",
  "author": {
    "name": "AlterLab @ Izmir University of Economics",
    "url": "https://github.com/AlterLab-IEU"
  },
  "homepage": "https://github.com/AlterLab-IEU/AlterLab-Academic-Skills",
  "license": "MIT AND CC-BY-3.0 AND CC-BY-4.0 AND CC0-1.0 AND LGPL-3.0",
  "category": "data",
  "keywords": [
    "database",
    "api",
    "pubmed",
    "uniprot",
    "chembl",
    "bioinformatics"
  ],
  "strict": false,
  "skills": [
    "./alterlab-alphafold-db",
    "./alterlab-arxiv",
    "./alterlab-bindingdb",
    "./alterlab-biorxiv",
    "./alterlab-brenda",
    "./alterlab-cbioportal",
    "./alterlab-chembl",
    "./alterlab-clinicaltrials",
    "./alterlab-clinpgx",
    "./alterlab-clinvar",
    "./alterlab-cosmic",
    "./alterlab-datacommons",
    "./alterlab-depmap",
    "./alterlab-drugbank",
    "./alterlab-ena",
    "./alterlab-ensembl",
    "./alterlab-fda",
    "./alterlab-gene-db",
    "./alterlab-geo",
    "./alterlab-gnomad",
    "./alterlab-gtex",
    "./alterlab-gwas",
    "./alterlab-hmdb",
    "./alterlab-imaging-data-commons",
    "./alterlab-interpro",
    "./alterlab-jaspar",
    "./alterlab-kegg",
    "./alterlab-metabolomics-wb",
    "./alterlab-monarch",
    "./alterlab-openalex",
    "./alterlab-opentargets",
    "./alterlab-pdb",
    "./alterlab-pubchem",
    "./alterlab-pubmed",
    "./alterlab-reactome",
    "./alterlab-string-db",
    "./alterlab-uniprot",
    "./alterlab-uspto",
    "./alterlab-zinc-db"
  ],
  "mcpServers": "./.mcp.json",
  "userConfig": {
    "openalex_api_key": {
      "type": "string",
      "title": "OpenAlex API key (recommended)",
      "description": "Free key from https://openalex.org/settings/api. OpenAlex meters usage per day (since February 2026); keyless requests share a small per-IP budget and fail with HTTP 4

Read the full file on GitHub · 92 lines

Contents

What it installs

The manifest is a name and a version. 39 skills travel with it, and installing the plugin installs all of them — 4,090 tokens a session between them. Each is measured on its own page, and each can be installed alone.

Files

What ships with it

1 file beside marketplace.json#alterlab-databases 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.

marketplace.json 27 KB

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.

1mo ago Changed · +28 lines c7ffcb6d7820
1mo ago First seen · 64 lines scan A 8c440488ea8a

Subscribe to this mod's changes

alterlab-databases is a plugin published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 2d ago), licensed MIT. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

Databases Research academic-research anthropic bioinformatics data-science prompt-engineering research-tools

alterlab-databases

Getting it into your agent

Wrote this? Show the measurements

Grade A, and why

Nothing flagged

How it starts

What it installs

What ships with it

What this file has done since we first saw it

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