is a Data Source.
Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species, providing information about gene expression in different anatomical structures, developmental stages, and species.
biological systems, organisms
infores:bgee
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| bgee.site | Bgee Web Interface | www.bgee.org | GraphicalInterface | ❔ | Web interface for exploring Bgee data |
| bgee.sparql | Bgee SPARQL Endpoint | sparql | ProgrammingInterface | ❔ | SPARQL endpoint for querying Bgee RDF... |
| bgee.expr_calls | Bgee Expression Calls | gene-expression-calls | Product | tsv | Complete data dump of Bgee expression... |
| bgee.rdf | Bgee RDF Data | rdf_easybgee.zip (29.4 GB) | Product | ttl | RDF version of the Bgee data for sema... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| spoke.graph | SPOKE Graph | ❔ | GraphProduct | ❔ | The SPOKE knowledge graph containing ... |
| alzkb.browser | AlzKB Graph Database Browser | login | GraphicalInterface | http | A browser interface for a knowledge g... |
| alzkb.data | AlzKB Data Release (Version 2.0.0) | v2.0.0 | GraphProduct | ❔ | Memgraph data release for AlzKB. |
| indra.cogex.code | INDRA CoGEx Build Code | indra_cogex | ProcessProduct | ❔ | INDRA CoGEx is a graph database integ... |
| kg-monarch.graph | KGX Distribution of KG-Monarch | monarch-kg.tar.gz (220.2 MB) | GraphProduct | kgx | KGX Distribution of KG-Monarch |
| kg-monarch.graph.jsonl | KGX JSON-L Distribution of KG-Monarch | monarch-kg.jsonl.tar.gz (301.0 MB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.rdf | RDF Distribution of KG-Monarch | monarch-kg.nt.gz (838.5 MB) | GraphProduct | rdfxml | RDF Distribution of KG-Monarch |
| kg-monarch.graph.neo4j | Neo4j Dump of KG-Monarch | monarch-kg.neo4j.dump (1.3 GB) | GraphProduct | ❔ | Neo4j Dump of KG-Monarch |
| kg-monarch.graph.duckdb | DuckDB database of KG-Monarch | monarch-kg.duckdb (6.4 GB) | GraphProduct | ❔ | DuckDB database of KG-Monarch |
| kg-monarch.graph.jsonl.edges | KGX JSON-L Distribution of KG-Monarch Edges | monarch-kg_edges.jsonl (14.2 GB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.jsonl.nodes | KGX JSON-L Distribution of KG-Monarch Nodes | monarch-kg_nodes.jsonl (1.1 GB) | GraphProduct | kgx-jsonl | KGX JSON-Lines Distribution of KG-Mon... |
| kg-monarch.graph.neo4j.edges | Neo4j Dump of KG-Monarch Edges | monarch-kg_edges.neo4j.csv (4.1 GB) | GraphProduct | neo4j | Neo4j Dump of KG-Monarch Edges |
| kg-monarch.graph.neo4j.nodes | Neo4j Dump of KG-Monarch Nodes | monarch-kg_nodes.neo4j.csv (333.4 MB) | GraphProduct | neo4j | Neo4j Dump of KG-Monarch Nodes |
| genecards.expression.data ⚠ | GeneCards Expression Data | www.genecards.org | Product | http | Gene expression data aggregated from ... |
| ibkh.graph | iBKH Knowledge Graph | ❔ | GraphProduct | ❔ | The integrative Biomedical Knowledge ... |
| translator.bgee.graph | Translator Bgee KGX Graph | latest | GraphProduct | kgx-jsonl | KGX JSONL graph package for Bgee - Ge... |
| translator.translator_kg.graph | Translator Aggregate KGX Graph | latest | GraphProduct | kgx-jsonl | Aggregated KGX JSONL graph package co... |
Bgee (Background Expression) is a database for retrieval and comparison of gene expression patterns across multiple animal species. It integrates multiple data types (RNA-Seq, Affymetrix microarrays, in situ hybridization, EST data, and single-cell RNA-Seq) to provide a unified view of gene expression patterns across diverse anatomical structures, developmental stages, and species.
The key features of Bgee include:
Bgee is widely used in comparative genomics, evolutionary developmental biology, and functional genomics to understand gene expression patterns and their evolution across species. The database currently covers more than 29 animal species including key model organisms such as human, mouse, zebrafish, and Drosophila.
The data is available through a user-friendly web interface, a SPARQL endpoint for semantic web queries, programmatic access via R and Python packages, and bulk downloads of data dumps for large-scale analyses.
Created: May 07, 2025 | Last modified: February 20, 2026