Data sources

This page provides information about the data sources used in this release of Bgee.

Genomics databases

Source for gene annotations, mappings to the Gene Ontology, mappings to Affymetrix probeset IDs, and cross-references to other databases
Source for miRNA families
OMA
Source of gene orthology information

RNA-Seq data sources

GEO
RNA-Seq data source for various species
GTEx RNA-Seq data
SRA
RNA-Seq data source for various species

Affymetrix data sources

Affymetrix data source for various species
GEO
Affymetrix data source for various species

In situ data sources

Drosophila in situ data source
Drosophila in situ data source
MGI
Mouse in situ data source
WormBase - Nematode Information Resource
Xenopus in situ data source
Zebrafish in situ data source

EST data sources

EST data for miRNAs
EST data source for various species

Ontologies

CIO
Confidence Information Ontology
Collection of developmental and life stage ontologies in animals. Integrated into Uberon.
GO
Filtered Gene Ontology
Integrated cross-species ontology covering anatomical structures in animals. Use of the subset "composite-metazoan".

Other sources

Define evolutionary relations between anatomical entities described in the Uberon ontology
Source for gene annotations, mappings to the Gene Ontology, mappings to Affymetrix probeset IDs, and cross-references to other databases
Source taxonomy used in Bgee