Ensembl Tools

Configuration File: ensembl_tools.json Tool Type: Local Tools Count: 19

This page contains all tools defined in the ensembl_tools.json configuration file.

Available Tools

ensembl_get_alignment (Type: EnsemblRESTTool)

Get genomic alignments between species for a genomic region. Returns multiple alignments showing …

ensembl_get_alignment tool specification

Tool Information:

  • Name: ensembl_get_alignment

  • Type: EnsemblRESTTool

  • Description: Get genomic alignments between species for a genomic region. Returns multiple alignments showing conserved sequences across species groups. Supports EPO and PECAN alignment methods for predefined species groups (mammals, primates, fish, birds, sauropsids). Useful for studying sequence conservation.

Parameters:

  • species (string) (required) Source species (e.g., ‘human’, ‘homo_sapiens’)

  • region (string) (required) Genomic region in format ‘chromosome:start-end’ (e.g., ‘2:106000000-106100000’)

  • species_set_group (string) (optional) Predefined species group for multiple alignment. Options: ‘mammals’, ‘primates’, ‘fish’, ‘birds’, ‘sauropsids’. Required for EPO method.

  • method (string) (optional) Alignment method: EPO (high quality multiple), EPO_EXTENDED (extended coverage), PECAN (low coverage)

  • compact (boolean) (optional) Compact output format

  • display_species_set (string) (optional) Comma-separated list to filter which species to display in results (optional, e.g., ‘mouse,rat’)

Example Usage:

query = {
    "name": "ensembl_get_alignment",
    "arguments": {
        "species": "example_value",
        "region": "example_value"
    }
}
result = tu.run(query)

ensembl_get_archive (Type: EnsemblRESTTool)

Get historical (archived) gene information by stable ID. Returns gene location and status across …

ensembl_get_archive tool specification

Tool Information:

  • Name: ensembl_get_archive

  • Type: EnsemblRESTTool

  • Description: Get historical (archived) gene information by stable ID. Returns gene location and status across all Ensembl releases. Use this to track gene ID changes, assembly updates, or retrieve information from older Ensembl versions.

Parameters:

  • id (string) (required) Ensembl stable ID (gene, transcript, or protein, e.g., ‘ENSG00000139618’)

Example Usage:

query = {
    "name": "ensembl_get_archive",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_genetree (Type: EnsemblRESTTool)

Get gene tree (phylogenetic tree) for a gene. Returns evolutionary relationships showing ortholog…

ensembl_get_genetree tool specification

Tool Information:

  • Name: ensembl_get_genetree

  • Type: EnsemblRESTTool

  • Description: Get gene tree (phylogenetic tree) for a gene. Returns evolutionary relationships showing orthologues and paralogues across species. Use this to study gene evolution and find related genes in other species. Gene tree IDs can be found in gene lookup responses or by querying the Compara database.

Parameters:

  • id (string) (required) Gene tree ID (e.g., ‘ENSGT00390000003602’). Gene tree IDs can be found in gene lookup responses with expand=1, or by querying Ensembl Compara database.

  • prune_species (string) (optional) Prune tree to specific species (optional, e.g., ‘homo_sapiens,mus_musculus’)

  • prune_taxon (string) (optional) Prune tree to specific taxon (optional)

  • aligned (boolean) (optional) Return aligned sequences

  • sequence (string) (optional) Include sequences in tree (cdna, protein, or none)

Example Usage:

query = {
    "name": "ensembl_get_genetree",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_homology (Type: EnsemblRESTTool)

Get homology (orthologues and paralogues) for a gene by symbol across species. Returns evolutiona…

ensembl_get_homology tool specification

Tool Information:

  • Name: ensembl_get_homology

  • Type: EnsemblRESTTool

  • Description: Get homology (orthologues and paralogues) for a gene by symbol across species. Returns evolutionary relationships with gene IDs, protein IDs, chromosomal locations, and homology types (1-to-1, 1-to-many, etc). Essential for comparative genomics studies.

Parameters:

  • species (string) (required) Source species (e.g., ‘human’, ‘homo_sapiens’)

  • symbol (string) (required) Gene symbol (e.g., ‘BRCA2’, ‘TP53’)

  • target_species (string) (optional) Target species to find homologues in (optional, e.g., ‘mouse’, ‘mus_musculus’). Leave empty to search all species.

  • target_taxon (string) (optional) Target taxonomic group (optional, e.g., ‘Mammalia’, ‘Primates’)

  • type (string) (optional) Homology type: ‘orthologues’ (different species), ‘paralogues’ (same species), ‘all’ (both)

  • sequence (string) (optional) Include sequences in response

  • aligned (boolean) (optional) Return aligned sequences

Example Usage:

query = {
    "name": "ensembl_get_homology",
    "arguments": {
        "species": "example_value",
        "symbol": "example_value"
    }
}
result = tu.run(query)

ensembl_get_ontology_ancestors (Type: EnsemblRESTTool)

Get ancestor terms for a GO (Gene Ontology) term. Returns parent terms up the ontology hierarchy …

ensembl_get_ontology_ancestors tool specification

Tool Information:

  • Name: ensembl_get_ontology_ancestors

  • Type: EnsemblRESTTool

  • Description: Get ancestor terms for a GO (Gene Ontology) term. Returns parent terms up the ontology hierarchy showing broader biological concepts. Use this to understand term relationships and perform hierarchical analysis.

Parameters:

  • id (string) (required) GO term ID (e.g., ‘GO:0005737’ for cytoplasm)

Example Usage:

query = {
    "name": "ensembl_get_ontology_ancestors",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_ontology_descendants (Type: EnsemblRESTTool)

Get descendant terms for a GO (Gene Ontology) term. Returns child terms down the ontology hierarc…

ensembl_get_ontology_descendants tool specification

Tool Information:

  • Name: ensembl_get_ontology_descendants

  • Type: EnsemblRESTTool

  • Description: Get descendant terms for a GO (Gene Ontology) term. Returns child terms down the ontology hierarchy showing more specific biological concepts. Use this to find related specific terms and expand queries.

Parameters:

  • id (string) (required) GO term ID (e.g., ‘GO:0005737’ for cytoplasm)

  • closest_term (boolean) (optional) Return only immediate children

Example Usage:

query = {
    "name": "ensembl_get_ontology_descendants",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_ontology_term (Type: EnsemblRESTTool)

Get detailed information about a specific ontology term (GO, SO, HPO). Returns term name, definit…

ensembl_get_ontology_term tool specification

Tool Information:

  • Name: ensembl_get_ontology_term

  • Type: EnsemblRESTTool

  • Description: Get detailed information about a specific ontology term (GO, SO, HPO). Returns term name, definition, synonyms, and relationships. Use this to understand biological concepts and validate term usage.

Parameters:

  • id (string) (required) Ontology term ID (e.g., ‘GO:0005737’, ‘SO:0000704’, ‘HP:0001250’)

  • relation (string) (optional) Filter relationships (optional, e.g., ‘is_a’, ‘part_of’, ‘regulates’)

Example Usage:

query = {
    "name": "ensembl_get_ontology_term",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_overlap_features (Type: EnsemblRESTTool)

Get genomic features (genes, transcripts, repeats) overlapping a region. Returns comprehensive an…

ensembl_get_overlap_features tool specification

Tool Information:

  • Name: ensembl_get_overlap_features

  • Type: EnsemblRESTTool

  • Description: Get genomic features (genes, transcripts, repeats) overlapping a region. Returns comprehensive annotations including coding genes, ncRNAs, pseudogenes, and structural features. Use this for genome annotation and feature discovery.

Parameters:

  • species (string) (required) Species (e.g., ‘human’, ‘homo_sapiens’)

  • region (string) (required) Genomic region (e.g., ‘7:140424943-140624564’)

  • feature (string) (optional) Feature type to retrieve

  • biotype (string) (optional) Filter by biotype (optional, e.g., ‘protein_coding’, ‘lincRNA’, ‘miRNA’)

Example Usage:

query = {
    "name": "ensembl_get_overlap_features",
    "arguments": {
        "species": "example_value",
        "region": "example_value"
    }
}
result = tu.run(query)

ensembl_get_regulatory_features (Type: EnsemblRESTTool)

Get regulatory features (promoters, enhancers, transcription factor binding sites) in a genomic r…

ensembl_get_regulatory_features tool specification

Tool Information:

  • Name: ensembl_get_regulatory_features

  • Type: EnsemblRESTTool

  • Description: Get regulatory features (promoters, enhancers, transcription factor binding sites) in a genomic region. Returns regulatory annotations including feature types, positions, and evidence. Use this to identify regulatory elements that may control gene expression.

Parameters:

  • region (string) (required) Genomic region in format ‘chromosome:start-end’ (e.g., ‘1:1000000-2000000’)

  • species (string) (optional) Species name (default ‘human’)

  • feature (string) (required) Feature type (must be ‘regulatory’ for this tool)

Example Usage:

query = {
    "name": "ensembl_get_regulatory_features",
    "arguments": {
        "region": "example_value",
        "feature": "example_value"
    }
}
result = tu.run(query)

ensembl_get_sequence (Type: EnsemblRESTTool)

Get DNA or protein sequence for a gene, transcript, or genomic region. Returns sequence in JSON f…

ensembl_get_sequence tool specification

Tool Information:

  • Name: ensembl_get_sequence

  • Type: EnsemblRESTTool

  • Description: Get DNA or protein sequence for a gene, transcript, or genomic region. Returns sequence in JSON format with metadata. Supports multiple sequence types: genomic, CDS, cDNA, and peptide sequences.

Parameters:

  • id (string) (required) Ensembl gene/transcript ID (e.g., ‘ENSG00000139618’ or ‘ENST00000380152’)

  • type (string) (optional) Sequence type: ‘genomic’ (genomic DNA), ‘cds’ (coding sequence), ‘cdna’ (cDNA), ‘peptide’ (protein sequence)

  • species (string) (optional) Species name (optional, defaults to human)

  • multiple_sequences (boolean) (optional) Return multiple sequences if available (e.g., all transcripts)

Example Usage:

query = {
    "name": "ensembl_get_sequence",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_species (Type: EnsemblRESTTool)

Get information about a species or list all available species in Ensembl. Returns scientific name…

ensembl_get_species tool specification

Tool Information:

  • Name: ensembl_get_species

  • Type: EnsemblRESTTool

  • Description: Get information about a species or list all available species in Ensembl. Returns scientific name, common name, assembly details, and database version. Use without ID to list all species (200+ available).

Parameters:

  • division (string) (optional) Filter by Ensembl division (optional)

Example Usage:

query = {
    "name": "ensembl_get_species",
    "arguments": {
    }
}
result = tu.run(query)

ensembl_get_taxonomy (Type: EnsemblRESTTool)

Get taxonomic classification for a species. Returns complete lineage from kingdom to species leve…

ensembl_get_taxonomy tool specification

Tool Information:

  • Name: ensembl_get_taxonomy

  • Type: EnsemblRESTTool

  • Description: Get taxonomic classification for a species. Returns complete lineage from kingdom to species level with scientific names and taxonomy IDs. Useful for understanding species relationships and filtering by taxonomic groups.

Parameters:

  • id (string) (required) NCBI Taxonomy ID (e.g., ‘9606’ for human, ‘10090’ for mouse) or species name (e.g., ‘homo_sapiens’)

Example Usage:

query = {
    "name": "ensembl_get_taxonomy",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_variants (Type: EnsemblRESTTool)

Get genetic variants (SNPs, indels) in a genomic region. Returns variant information including po…

ensembl_get_variants tool specification

Tool Information:

  • Name: ensembl_get_variants

  • Type: EnsemblRESTTool

  • Description: Get genetic variants (SNPs, indels) in a genomic region. Returns variant information including positions, alleles, and consequences. Use this to find variants overlapping a specific genomic region.

Parameters:

  • region (string) (required) Genomic region in format ‘chromosome:start-end’ (e.g., ‘13:32315086-32400268’ or ‘1:1000000-2000000’)

  • species (string) (optional) Species name (default ‘human’). Examples: ‘human’, ‘mouse’, ‘rat’

  • feature (string) (optional) Feature type to retrieve (default ‘variation’)

Example Usage:

query = {
    "name": "ensembl_get_variants",
    "arguments": {
        "region": "example_value"
    }
}
result = tu.run(query)

ensembl_get_variation (Type: EnsemblRESTTool)

Get detailed information about a specific genetic variation by its ID (e.g., rs699). Returns vari…

ensembl_get_variation tool specification

Tool Information:

  • Name: ensembl_get_variation

  • Type: EnsemblRESTTool

  • Description: Get detailed information about a specific genetic variation by its ID (e.g., rs699). Returns variation details including alleles, frequencies, consequences, and evidence. Use ensembl_get_variants to find variant IDs in a region.

Parameters:

  • id (string) (required) Variation ID (e.g., ‘rs699’, ‘rs1421085’). Use ensembl_get_variants to find variant IDs in a genomic region.

  • species (string) (optional) Species name (default ‘human’)

  • phenotypes (integer) (optional) Include phenotype associations (0=no, 1=yes)

Example Usage:

query = {
    "name": "ensembl_get_variation",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_variation_phenotypes (Type: EnsemblRESTTool)

Get phenotype associations for a specific genetic variation. Returns detailed phenotype informati…

ensembl_get_variation_phenotypes tool specification

Tool Information:

  • Name: ensembl_get_variation_phenotypes

  • Type: EnsemblRESTTool

  • Description: Get phenotype associations for a specific genetic variation. Returns detailed phenotype information including traits, studies, and effect sizes. Use this to understand the phenotypic consequences of a variant.

Parameters:

  • id (string) (required) Variation ID (e.g., ‘rs699’). Use ensembl_get_variants to find variant IDs in a genomic region.

  • species (string) (optional) Species name (default ‘human’)

  • phenotypes (integer) (optional) Include phenotype associations (must be 1 for this tool)

Example Usage:

query = {
    "name": "ensembl_get_variation_phenotypes",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_xrefs (Type: EnsemblRESTTool)

Get cross-references (external database IDs) for an Ensembl gene, transcript, or protein. Returns…

ensembl_get_xrefs tool specification

Tool Information:

  • Name: ensembl_get_xrefs

  • Type: EnsemblRESTTool

  • Description: Get cross-references (external database IDs) for an Ensembl gene, transcript, or protein. Returns mappings to databases like UniProt, RefSeq, HGNC, MGI, and many others. Use this to convert between different database identifiers.

Parameters:

  • id (string) (required) Ensembl ID (gene, transcript, or protein ID, e.g., ‘ENSG00000139618’, ‘ENST00000380152’, ‘ENSP00000369497’)

  • external_db (string) (optional) Filter by external database name (optional, e.g., ‘UniProt’, ‘RefSeq’, ‘HGNC’)

  • object_type (string) (optional) Object type filter (optional, e.g., ‘gene’, ‘transcript’, ‘translation’)

Example Usage:

query = {
    "name": "ensembl_get_xrefs",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

ensembl_get_xrefs_by_name (Type: EnsemblRESTTool)

Get cross-references for an Ensembl object by its name/symbol. Returns mappings to external datab…

ensembl_get_xrefs_by_name tool specification

Tool Information:

  • Name: ensembl_get_xrefs_by_name

  • Type: EnsemblRESTTool

  • Description: Get cross-references for an Ensembl object by its name/symbol. Returns mappings to external databases. Use this when you have a gene symbol or name instead of an Ensembl ID.

Parameters:

  • name (string) (required) Gene symbol or name (e.g., ‘BRCA1’, ‘TP53’)

  • species (string) (optional) Species name (default ‘homo_sapiens’)

  • external_db (string) (optional) Filter by external database name (optional)

Example Usage:

query = {
    "name": "ensembl_get_xrefs_by_name",
    "arguments": {
        "name": "example_value"
    }
}
result = tu.run(query)

ensembl_lookup_gene (Type: EnsemblRESTTool)

Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, de…

ensembl_lookup_gene tool specification

Tool Information:

  • Name: ensembl_lookup_gene

  • Type: EnsemblRESTTool

  • Description: Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, description, and external references. Supports both stable IDs (e.g., ENSG00000139618) and gene symbols (e.g., BRCA1). For gene symbols, species parameter is required.

Parameters:

  • gene_id (string) (required) Ensembl gene ID or symbol (e.g., ‘ENSG00000139618’ or ‘BRCA1’). If using a stable ID, the tool will automatically route to /lookup/id endpoint.

  • species (string) (optional) Species name required for gene symbols (default ‘homo_sapiens’). Examples: ‘homo_sapiens’, ‘mus_musculus’, ‘rattus_norvegicus’

Example Usage:

query = {
    "name": "ensembl_lookup_gene",
    "arguments": {
        "gene_id": "example_value"
    }
}
result = tu.run(query)

ensembl_vep_region (Type: EnsemblRESTTool)

Variant Effect Predictor (VEP) for genomic variants. Predicts functional consequences of variants…

ensembl_vep_region tool specification

Tool Information:

  • Name: ensembl_vep_region

  • Type: EnsemblRESTTool

  • Description: Variant Effect Predictor (VEP) for genomic variants. Predicts functional consequences of variants including impact on genes, transcripts, and proteins. Returns SIFT/PolyPhen scores, consequence types, and affected transcripts. Essential for variant interpretation.

Parameters:

  • species (string) (required) Species (e.g., ‘human’, ‘homo_sapiens’)

  • region (string) (required) Genomic region with variant (e.g., ‘21:25891796-25891796’)

  • allele (string) (required) Alternative allele (e.g., ‘T’, ‘C’)

  • AncestralAllele (integer) (optional) Include ancestral allele information

  • Blosum62 (integer) (optional) Include BLOSUM62 protein conservation score

  • CADD (integer) (optional) Include CADD scores

  • Conservation (integer) (optional) Include conservation scores

  • DisGeNET (integer) (optional) Include DisGeNET disease associations

  • GeneSplicer (integer) (optional) Include GeneSplicer predictions

  • GO (integer) (optional) Include Gene Ontology terms

  • LoF (integer) (optional) Include Loss-of-Function predictions

  • MaxEntScan (integer) (optional) Include MaxEntScan splice predictions

  • Phenotypes (integer) (optional) Include phenotype annotations

  • SIFT (string) (optional) SIFT prediction: p=prediction, s=score, b=both

  • PolyPhen (string) (optional) PolyPhen prediction: p=prediction, s=score, b=both

Example Usage:

query = {
    "name": "ensembl_vep_region",
    "arguments": {
        "species": "example_value",
        "region": "example_value",
        "allele": "example_value"
    }
}
result = tu.run(query)