is a Data Source.
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation, and transcriptional regulation
genomics
infores:ensembl-gene
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| ensembl.browser | Ensembl Genome Browser | www.ensembl.org | GraphicalInterface | ❔ | A web-based platform for browsing and... |
| ensembl.biomart | BioMart | martview | GraphicalInterface | ❔ | A data mining tool that allows extrac... |
| ensembl.vep | Variant Effect Predictor (VEP) | vep | ProcessProduct | ❔ | A tool to analyze variants and predic... |
| ensembl.blast | BLAST/BLAT | Blast | ProcessProduct | ❔ | Tool to search Ensembl genomes for DN... |
| ensembl.api.perl | Ensembl Perl API | Ensembl | ProgrammingInterface | ❔ | Programmatic access to all Ensembl da... |
| ensembl.api.rest | Ensembl REST API | rest.ensembl.org | ProgrammingInterface | ❔ | RESTful API that allows access to Ens... |
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| rtx-kg2.graph.nodes | RTX-KG2.10.1c KGX JSONL Nodes | kg2c-2.10.1-v1.0-nodes.jsonl.gz (359.1 MB) | GraphProduct | kgx-jsonl | Nodes for KGX distribution of the RTX... |
| rtx-kg2.graph.edges | RTX-KG2.10.1c KGX JSONL Edges | kg2c-2.10.1-v1.0-edges.jsonl.gz (1.7 GB) | GraphProduct | kgx-jsonl | Edges for KGX distribution of the RTX... |
| rtx-kg2.neo4j | RTX-KG2 Neo4j | arax.ncats.io | ProgrammingInterface | ❔ | Neo4j distribution of the RTX-KG2 as ... |
| ncbigene.gene2ensembl | Gene to Ensembl Mapping | gene2ensembl.gz (269.7 MB) | MappingProduct | tsv | Gene to Ensembl mapping data providin... |
| pheknowlator.graph | PheKnowLator graph | knowledge_graphs?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&inv=1&invt=Ab5_1Q&project=pheknowlator | GraphProduct | owl | PheKnowLator graph files, including s... |
| omim.mim2gene | OMIM mim2gene.txt | mim2gene.txt (951.6 KB) | MappingProduct | tsv | Public mapping of MIM numbers to NCBI... |
| rna-kg.kg.neo4j | RNA-KG Neo4j Dump | rnakgv20.dump (3.7 GB) | GraphProduct | neo4j | RNA-KG as a Neo4j Dump |
| rna-kg.kg.nodes | RNA-KG Nodes | nodes.csv (4.1 GB) | GraphProduct | csv | RNA-KG Nodes in CSV format |
| rna-kg.kg.edges | RNA-KG Edges | edges.csv (17.1 GB) | GraphProduct | csv | RNA-KG Edges in CSV format |
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | GraphProduct | neo4j | Integrated graph knowledge base combi... |
| aop-db.data | AOP-DB Data | adverse-outcome-pathway-database-aop-db-version-2 | Product | ❔ | The EPA has developed the Adverse Out... |
| rnacentral.portal | RNAcentral Portal | rnacentral.org | GraphicalInterface | http | Web portal for searching and browsing... |
| rnacentral.api | RNAcentral REST API | api | ProgrammingInterface | http | REST API for programmatic access to R... |
| rnacentral.ftp | RNAcentral FTP Archive | RNAcentral | Product | http | FTP archive with current and archived... |
| rnacentral.public-db | RNAcentral Public Postgres Database | public-database | DataModelProduct | postgres | Public PostgreSQL database for direct... |
| genecards.gene.annotations ⚠ | GeneCards Gene Annotations | www.genecards.org | Product | http | Integrated gene annotation data aggre... |
| string.protein.links | STRING Protein Links | protein.links.v12.0.txt.gz (128.7 GB) | GraphProduct | txt | protein network data (full network, s... |
| string.protein.links.detailed | STRING Protein Links Detailed | protein.links.detailed.v12.0.txt.gz (189.6 GB) | GraphProduct | txt | protein network data (full network, i... |
| string.protein.links.full | STRING Protein Links Full | protein.links.full.v12.0.txt.gz (199.6 GB) | GraphProduct | txt | protein network data (full network, i... |
| string.protein.physical.links | STRING Protein Physical Links | protein.physical.links.v12.0.txt.gz (11.1 GB) | GraphProduct | txt | protein network data (physical subnet... |
| string.protein.physical.links.detailed | STRING Protein Physical Links Detailed | protein.physical.links.detailed.v12.0.txt.gz (13.8 GB) | GraphProduct | txt | protein network data (physical subnet... |
| string.protein.physical.links.full | STRING Protein Physical Links Full | protein.physical.links.full.v12.0.txt.gz (14.5 GB) | GraphProduct | txt | protein network data (physical subnet... |
| string.cog.links | STRING COG Links | COG.links.v12.0.txt.gz (176.8 MB) | GraphProduct | txt | association scores between orthologou... |
| string.cog.links.detailed | STRING COG Links Detailed | COG.links.detailed.v12.0.txt.gz (238.7 MB) | GraphProduct | txt | association scores (incl. subscores p... |
| string.database | STRING Database Network Schema | network_schema.v12.0.sql.gz (262.2 GB) | GraphProduct | ❔ | full database, part II: the networks ... |
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation, and transcriptional regulation. It provides comprehensive annotation of genes, computes multiple alignments, predicts regulatory function, and collects disease data.
Ensembl annotates genes, computes multiple alignments, predicts regulatory function, and collects disease data across a wide range of vertebrate species. The project is based at EMBL-EBI (European Molecular Biology Laboratory’s European Bioinformatics Institute) and its software and data are freely available.
BioMart is a highly customizable data mining tool that allows extraction of data without any programming knowledge. Users can create complex queries to extract specific datasets across various Ensembl databases.
VEP analyzes variants and predicts their functional consequences. It can be used both through a web interface and as a command-line tool for larger datasets. VEP supports various input formats and provides detailed annotations for variants.
Tools for searching Ensembl genomes with DNA or protein sequences to identify similar regions or homologs.
A RESTful API that provides programmatic access to Ensembl data, allowing developers to integrate Ensembl data into their own applications using any programming language.
A comprehensive set of Perl modules for programmatic access to all Ensembl data, enabling complex queries and data manipulation.
Ensembl has several specialized sister resources focused on specific taxonomic groups:
Ensembl data can be accessed through:
Ensembl follows a regular release cycle, with each release bringing updated genome assemblies, gene annotations, and new features. Archives of previous releases are maintained to ensure reproducibility of research based on specific versions.
Created: May 30, 2025 | Last modified: February 20, 2026