unichem

is an Aggregator.

UniChem is a large-scale non-redundant database maintained by EMBL-EBI that provides cross-references between chemical structures across multiple chemistry resources. It serves as a unified system for creating and maintaining structure-based hyperlinks between chemistry databases, particularly optimized for on-the-fly link creation via REST web services. UniChem aggregates compound identifiers from major chemistry resources including ChEMBL, ChEBI, SureChEMBL, PubChem, DrugBank, and many others, enabling efficient cross-database chemical structure queries using InChI, InChIKey, or source-specific identifiers.

Domains

chemistry and biochemistry, drug discovery, pharmacology

License

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Homepage

unichem

Repository

Unknown

Infores ID

infores:unichem

FAIRsharing ID

Unknown

Product Summary

Products

From this Resource
ID Name URL Category Format Description
unichem.search UniChem Search Interface search GraphicalInterface http Web-based search interface for findin...
unichem.api UniChem REST API docs ProgrammingInterface http RESTful web services API for programm...
unichem.sources UniChem Source Database List sources Product http Comprehensive list of all integrated ...
unichem.docs UniChem Documentation unichem DocumentationProduct http Complete documentation covering UniCh...
unichem.docs.uci UCI Documentation Entry Point compoundsources?type=uci&compound=1 DocumentationProduct http UniChem compound sources page illustr...
From other Resources
ID Name URL Category Format Description
unibiomap.links UniBioMap Graph Links unibiomap.links.csv (1.3 GB) GraphProduct csv Core UniBioMap graph edges file.
unibiomap.auxs UniBioMap Graph Auxiliaries unibiomap.auxs.tsv (563.9 MB) GraphProduct tsv Auxiliary UniBioMap graph annotations...
unibiomap.pred UniBioMap Predicted Graph unibiomap.pred.csv (2.3 GB) GraphProduct csv Predicted UniBioMap graph edges with ...
unibiomap.pred.full UniBioMap Predicted Graph (Full) unibiomap.pred.full.csv (5.9 GB) GraphProduct csv Full unfiltered UniBioMap predicted g...

Details

UniChem

Overview

UniChem is a unified chemical identifier cross-reference system developed and maintained by EMBL-EBI. It provides a large-scale, non-redundant database of pointers between chemical structures and chemistry resources, with particular focus on EMBL-EBI chemistry databases and services.

Primary Purpose

UniChem is designed to optimize the efficiency with which structure-based hyperlinks can be built and maintained between chemistry-based resources. The system is particularly suitable for creating such links “on the fly” through REST web services, making it ideal for dynamic web applications and data integration pipelines.

Integrated Resources

UniChem primarily serves to maintain cross-references between:

Primary Chemistry Resources:

  • ChEMBL (bioactive drug-like small molecules)
  • ChEBI (Chemical Entities of Biological Interest)
  • SureChEMBL (chemistry from patent documents)

Other EBI Resources with Chemical Data:

  • Gene Expression Atlas
  • PDBe (Protein Data Bank in Europe)

External Chemistry Databases:

  • PubChem
  • DrugBank
  • ZINC
  • Many other chemistry and drug databases

Key Features

UniChem’s connectivity search allows users to find all source identifiers for compounds that share the same molecular connectivity (based on standard InChI representation). This enables:

  • Discovery of the same compound across multiple databases
  • Identification of alternative identifiers for the same structure
  • Cross-database structure queries

Find all databases that contain information about a specific compound using:

  • Source-specific database IDs
  • InChI (International Chemical Identifier)
  • InChIKey (hashed version of InChI)
  • unichem (UniChem Compound Identifier)

REST API

The UniChem API provides programmatic access for:

  • Batch structure lookups
  • Real-time cross-reference retrieval
  • Integration into computational workflows
  • Building automated data pipelines

Use Cases

  1. Cross-Database Linking: Creating hyperlinks between chemical databases
  2. Data Integration: Merging chemical information from multiple sources
  3. Structure Searching: Finding the same compound across different repositories
  4. Identifier Translation: Converting between different chemical identifier systems
  5. Resource Discovery: Identifying which databases contain information about specific compounds

Information Resource ID

This resource has the Information Resource identifier: infores:unichem

Technical Details

  • Structure Representation: Uses standard InChI for chemical structure matching
  • Connectivity Matching: Based on first connectivity layer of InChI
  • Update Frequency: Regular updates from source databases
  • Access Methods: Web interface and REST API

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Created: November 04, 2025 | Last modified: November 04, 2025