Ebi Search Tools¶

Configuration File: ebi_search_tools.json Tool Type: Local Tools Count: 7

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

Available Tools¶

ebi_cross_reference_search (Type: EBISearchRESTTool)¶

Search for cross-references between EBI domains. Find entries in one domain that reference entrie


ebi_cross_reference_search tool specification

Tool Information:

  • Name: ebi_cross_reference_search

  • Type: EBISearchRESTTool

  • Description: Search for cross-references between EBI domains. Find entries in one domain that reference entries in another domain (e.g., find UniProt entries referenced by Ensembl genes).

Parameters:

  • domain (string) (required) Source EBI domain to search

  • query (string) (required) Search query. Can include cross-reference filters like ‘xref_uniprot:P04637’

  • size (integer) (optional) Number of results to return

  • format (string) (optional) No description

Example Usage:

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

ebi_get_domain_fields (Type: EBISearchRESTTool)¶

Get list of available searchable fields for a specific EBI domain. Useful for understanding what 


ebi_get_domain_fields tool specification

Tool Information:

  • Name: ebi_get_domain_fields

  • Type: EBISearchRESTTool

  • Description: Get list of available searchable fields for a specific EBI domain. Useful for understanding what fields can be used in queries and field-specific searches.

Parameters:

  • domain (string) (required) EBI domain name

  • format (string) (optional) No description

Example Usage:

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

ebi_get_domain_info (Type: EBISearchRESTTool)¶

Get metadata and field information for a specific EBI domain. Returns domain description, availab


ebi_get_domain_info tool specification

Tool Information:

  • Name: ebi_get_domain_info

  • Type: EBISearchRESTTool

  • Description: Get metadata and field information for a specific EBI domain. Returns domain description, available fields, and search capabilities.

Parameters:

  • domain (string) (required) EBI domain name (e.g., ‘ensembl’, ‘uniprot’, ‘interpro’)

  • format (string) (optional) No description

Example Usage:

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

ebi_get_entry (Type: EBISearchRESTTool)¶

Get detailed information about a specific entry from an EBI domain by its ID. IMPORTANT: EBI Sear


ebi_get_entry tool specification

Tool Information:

  • Name: ebi_get_entry

  • Type: EBISearchRESTTool

  • Description: Get detailed information about a specific entry from an EBI domain by its ID. IMPORTANT: EBI Search requires specific entry ID formats (e.g., ‘P53_HUMAN’ not ‘P04637’). If entry_id doesn’t work, the tool automatically searches for the entry and returns it. For best results, first use ebi_search_domain to find entries, then use the ‘id’ field from search results as entry_id. Returns complete entry data with all available fields.

Parameters:

  • domain (string) (required) EBI domain (e.g., ‘ensembl’, ‘uniprot’, ‘interpro’)

  • entry_id (string) (required) Entry ID in the domain (e.g., Ensembl gene ID, UniProt accession, InterPro accession)

  • fields (string) (optional) Comma-separated list of specific fields to return. If not specified, returns all fields.

  • format (string) (optional) No description

Example Usage:

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

ebi_list_domains (Type: EBISearchRESTTool)¶

List all available EBI Search domains. Returns metadata about all searchable domains including do


ebi_list_domains tool specification

Tool Information:

  • Name: ebi_list_domains

  • Type: EBISearchRESTTool

  • Description: List all available EBI Search domains. Returns metadata about all searchable domains including domain names, descriptions, and field information.

Parameters:

  • format (string) (optional) Response format

Example Usage:

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

ebi_search_domain (Type: EBISearchRESTTool)¶

Search across a specific EBI domain (e.g., ensembl, uniprot, interpro) using the unified EBI Sear


ebi_search_domain tool specification

Tool Information:

  • Name: ebi_search_domain

  • Type: EBISearchRESTTool

  • Description: Search across a specific EBI domain (e.g., ensembl, uniprot, interpro) using the unified EBI Search API. Returns search results with metadata. Use this to search across 160+ EBI data resources.

Parameters:

  • domain (string) (required) EBI domain to search (e.g., ‘ensembl’, ‘uniprot’, ‘interpro’, ‘chembl’, ‘arrayexpress’, ‘metabolights’). See ebi_list_domains for available domains.

  • query (string) (required) Search query string. Supports field-specific queries like ‘name:BRCA1’ or ‘description:cancer’.

  • size (integer) (optional) Number of results to return per page (default: 10, max: 100)

  • start (integer) (optional) Starting position for pagination (default: 0)

  • fields (string) (optional) Comma-separated list of fields to return (e.g., ‘id,name,description’). If not specified, returns all fields.

  • format (string) (optional) Response format: ‘json’ or ‘xml’

Example Usage:

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

ebi_search_with_facets (Type: EBISearchRESTTool)¶

Search EBI domain with faceted filtering and returns facet information. Use facetcount to request


ebi_search_with_facets tool specification

Tool Information:

  • Name: ebi_search_with_facets

  • Type: EBISearchRESTTool

  • Description: Search EBI domain with faceted filtering and returns facet information. Use facetcount to request facets (returned automatically). To filter results BY facet values, use the ‘facets’ parameter with format ‘FACET_NAME:value’ (e.g., ‘TAXONOMY:9606’ for human). First run ebi_search_domain to see available facet IDs in the response, or use ebi_get_domain_info. Returns search results with facet categories for advanced filtering.

Parameters:

  • domain (string) (required) EBI domain to search (e.g., ‘ensembl’, ‘uniprot’, ‘interpro’)

  • query (string) (required) Search query string

  • facets (string) (optional) Optional filter for results using facet values in format ‘FACET_NAME:value’ (e.g., ‘TAXONOMY:9606’ for human, ‘keyword_id:KW-0418’ for kinase). Multiple filters can be comma-separated. IMPORTANT: This is for FILTERING results, not selecting which facets to return. Facets are returned automatically when facetcount > 0.

  • facetcount (integer) (optional) Number of facet values to return per facet category (default: 10). Set to 0 to disable facet return.

  • size (integer) (optional) Number of results to return (default: 10)

  • format (string) (optional) No description

Example Usage:

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