unichem-database
Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity. POST with a JSON body for all cross-reference queries; only /sources is GET. No auth required.
npx skills add BioTender-max/awesome-bio-agent-skills --skill unichem-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.
# UniChem Database ## Overview UniChem is a chemical structure cross-referencing service from EMBL-EBI that links compound records across 20+ public chemistry databases using InChI-based identifiers. It maps a single chemical entity to its corresponding IDs in ChEMBL, DrugBank, PubChem, ChEBI, PDB (RCSB and PDBe), SureChEMBL, HMDB, DrugCentral, BindingDB, and others. Access is via a free REST API at https://www.ebi.ac.uk/unichem/api/v1/ - no API key required. Important: every cross-reference query is sent as POST with a JSON body; only the catalogue endpoint GET /sources is implemented as a GET. ## When to Use - Translating a ChEMBL compound ID to a PubChem CID, DrugBank accession, or ChEBI ID for cross-database analysis - Resolving an InChIKey to all database sources where a compound appears - Finding all structurally related compounds (same connectivity, different stereochemistry/salts) across databases using connectivity search - Validating compound identity across sources before merging datasets from multiple databases - Building a compound cross-reference table for a drug discovery project (linking bioactivity data in ChEMBL to structural data in PDB) - Checking if a synthesiz
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: InChIKey Lookup - All Sources
- Query 2: Compound Lookup by Source-Specific ID
- Query 3: Connectivity Search - Structural Relatives
- Query 4: List All Data Sources
- Query 5: Per-Compound Loop (No Batch Endpoint)
- Query 6: Per-Compound Loop with Source-ID Inputs
- Key Concepts
- InChI vs InChIKey
- Source ID Reference Table (verified live against /sources)
pip install requests pandas matplotlib
What does the unichem-database skill do?
Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity. POST with a JSON body for all cross-reference queries; only /sources is GET. No auth required.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill unichem-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.