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
Unknown
| 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 | Relation | 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 | had primary source | 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 | had primary source | Edges for KGX distribution of the RTX... |
| rtx-kg2.neo4j | RTX-KG2 Neo4j | arax.ncats.io | ProgrammingInterface | ❔ | had primary source | Neo4j distribution of the RTX-KG2 as ... |
| ncbigene.gene2ensembl | Gene to Ensembl Mapping | gene2ensembl.gz (269.7 MB) | MappingProduct | tsv | had primary source | 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 | had primary source | PheKnowLator graph files, including s... |
| omim.mim2gene | OMIM mim2gene.txt | mim2gene.txt (951.6 KB) | MappingProduct | tsv | had primary source | Public mapping of MIM numbers to NCBI... |
| rna-kg.kg.neo4j | RNA-KG Neo4j Dump | rnakgv20.dump (3.7 GB) | GraphProduct | neo4j | had primary source | RNA-KG as a Neo4j Dump |
| rna-kg.kg.nodes | RNA-KG Nodes | nodes.csv (4.1 GB) | GraphProduct | csv | had primary source | RNA-KG Nodes in CSV format |
| rna-kg.kg.edges | RNA-KG Edges | edges.csv (17.1 GB) | GraphProduct | csv | had primary source | RNA-KG Edges in CSV format |
| epigraphdb.graph | EpiGraphDB Graph Database | graph-database | GraphProduct | neo4j | had primary source | Integrated graph knowledge base combi... |
| aop-db.data | AOP-DB Data | adverse-outcome-pathway-database-aop-db-version-2 | Product | ❔ | had primary source | The EPA has developed the Adverse Out... |
| rnacentral.portal | RNAcentral Portal | rnacentral.org | GraphicalInterface | http | had primary source | Web portal for searching and browsing... |
| rnacentral.api | RNAcentral REST API | api | ProgrammingInterface | http | had primary source | REST API for programmatic access to R... |
| rnacentral.ftp | RNAcentral FTP Archive | RNAcentral | Product | http | had primary source | FTP archive with current and archived... |
| rnacentral.public-db | RNAcentral Public Postgres Database | public-database | DataModelProduct | postgres | had primary source | Public PostgreSQL database for direct... |
| genecards.gene.annotations ⚠ | GeneCards Gene Annotations | www.genecards.org | Product | http | had primary source | Integrated gene annotation data aggre... |
| string.protein.links | STRING Protein Links | protein.links.v12.0.txt.gz (128.7 GB) | GraphProduct | txt | had primary source | 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 | had primary source | 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 | had primary source | 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 | had primary source | 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 | had primary source | 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 | had primary source | protein network data (physical subnet... |
| string.cog.links | STRING COG Links | COG.links.v12.0.txt.gz (176.8 MB) | GraphProduct | txt | had primary source | association scores between orthologou... |
| string.cog.links.detailed | STRING COG Links Detailed | COG.links.detailed.v12.0.txt.gz (238.7 MB) | GraphProduct | txt | had primary source | association scores (incl. subscores p... |
| string.database | STRING Database Network Schema | network_schema.v12.0.sql.gz (262.2 GB) | GraphProduct | ❔ | had primary source | full database, part II: the networks ... |
| archs4.human.gene_counts | ARCHS4 Human Gene Counts | human_gene_v2.latest.h5 (57.6 GB) | Product | hdf5 | was derived from | Latest human gene-level ARCHS4 expres... |
| archs4.mouse.gene_counts | ARCHS4 Mouse Gene Counts | mouse_gene_v2.latest.h5 (45.7 GB) | Product | hdf5 | was derived from | Latest mouse gene-level ARCHS4 expres... |
| archs4.human.transcript_counts | ARCHS4 Human Transcript Counts | human_transcript_v2.latest.h5 (178.8 GB) | Product | hdf5 | was derived from | Latest human transcript-level ARCHS4 ... |
| archs4.mouse.transcript_counts | ARCHS4 Mouse Transcript Counts | mouse_transcript_v2.latest.h5 (105.8 GB) | Product | hdf5 | was derived from | Latest mouse transcript-level ARCHS4 ... |
| archs4.zoo | ARCHS4 Zoo Downloads | zoo | Product | hdf5 | was derived from | Collection page for ARCHS4 Zoo downlo... |
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