emdb-database
Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
npx skills add BioTender-max/awesome-bio-agent-skills --skill emdb-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# EMDB Database ## Overview The Electron Microscopy Data Bank (EMDB) at EBI archives 3D electron microscopy density maps — primarily cryo-EM and cryo-ET — for macromolecular assemblies (30,000+ entries: ribosomes, membrane proteins, viruses, large complexes). Access is split across two services: - **EMDB Entry API** (`https://www.ebi.ac.uk/emdb/api/entry/{EMD-XXXXX}`) — the canonical per-entry JSON containing metadata, map header, fitted PDB list, and citation. Sub-endpoints like `/map`, `/fitted`, `/publications` do **not** exist — all those data live inside the single entry response. - **EBI Search WS** (`https://www.ebi.ac.uk/ebisearch/ws/rest/emdb`) — the real keyword search backend (the bare `https://www.ebi.ac.uk/emdb/api/search/` endpoint ignores the query and just returns recent entries). No authentication or API key is required. ## When to Use - Finding cryo-EM density maps by keyword (e.g., "spike protein", "ribosome 70S") - Fetching the download URL of a `.map.gz` density file for use in ChimeraX / PyMOL - Identifying fitted PDB atomic models for an EMDB map (and the reverse) - Retrieving entry metadata — resolution, reconstruction method, organism, sample - Listing cryo
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Keyword Search (EBI Search WS)
- Query 2: Entry Metadata
- Query 3: Map Header / Download Info
- Query 4: Fitted PDB Atomic Models
- Query 5: Citation and Publications
- Query 6: Sample and Organism
- Key Concepts
- Field-Path Map (/api/entry/{id} document)
- Search vs. Entry
pip install requests pandas matplotlib
What does the emdb-database skill do?
Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill emdb-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.