Mirna Tools

Configuration File: mirna_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

miRBase_get_mirna (Type: miRNAGetTool)

Get detailed miRNA information from RNAcentral including full RNA sequence, species, RNA type, ge…

miRBase_get_mirna tool specification

Tool Information:

  • Name: miRBase_get_mirna

  • Type: miRNAGetTool

  • Description: Get detailed miRNA information from RNAcentral including full RNA sequence, species, RNA type, gene associations, publication count, and source databases. Use a species-specific RNAcentral ID (format: URS_TAXID, e.g., ‘URS000039ED8D_9606’ for human hsa-miR-21-5p) or a base URS ID with optional taxid parameter. Key miRNA IDs: URS000039ED8D_9606 (hsa-miR-21-5p), URS0000D54CAD_9606 (hsa-miR-155-5p), URS0000416056_9606 (hsa-let-7a-5p), URS000039ED8D_10090 (mmu-miR-21a-5p).

Parameters:

  • rnacentral_id (string) (required) RNAcentral URS identifier. Use species-specific format ‘URS_TAXID’ (e.g., ‘URS000039ED8D_9606’) or base URS ID (e.g., ‘URS000039ED8D’) with taxid parameter.

  • taxid (integer) (optional) NCBI Taxonomy ID for species-specific lookup (e.g., 9606 for human, 10090 for mouse). Optional if rnacentral_id already includes taxid.

Example Usage:

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

miRBase_get_mirna_publications (Type: miRNAGetTool)

Retrieve publications associated with a microRNA from RNAcentral. Returns publication titles, aut…

miRBase_get_mirna_publications tool specification

Tool Information:

  • Name: miRBase_get_mirna_publications

  • Type: miRNAGetTool

  • Description: Retrieve publications associated with a microRNA from RNAcentral. Returns publication titles, authors, PubMed IDs, DOIs, and journal information. miR-21-5p (URS000039ED8D) has 344+ publications, making it one of the most-studied miRNAs. Use after miRBase_search_mirna to get the RNAcentral ID, then retrieve associated literature.

Parameters:

  • rnacentral_id (string) (required) RNAcentral URS identifier (e.g., ‘URS000039ED8D’ for hsa-miR-21-5p). Use base URS ID without taxid suffix.

  • page_size (integer) (optional) Number of publications to return (1-50). Default: 10.

Example Usage:

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

miRBase_get_mirna_xrefs (Type: miRNAGetTool)

Get cross-references (xrefs) for a microRNA from RNAcentral. Returns database links from miRBase,…

miRBase_get_mirna_xrefs tool specification

Tool Information:

  • Name: miRBase_get_mirna_xrefs

  • Type: miRNAGetTool

  • Description: Get cross-references (xrefs) for a microRNA from RNAcentral. Returns database links from miRBase, TarBase, ENA, RefSeq, piRBase, LncBase, and other sources. Includes external accession IDs, expert database URLs, species information, and miRBase-specific fields (mature products, precursor links). Essential for mapping miRNA IDs across databases and finding target interaction data.

Parameters:

  • rnacentral_id (string) (required) RNAcentral URS identifier (e.g., ‘URS000039ED8D’ for hsa-miR-21-5p). Use base URS ID without taxid suffix.

  • page_size (integer) (optional) Number of cross-references to return (1-50). Default: 10.

Example Usage:

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

miRBase_search_mirna (Type: miRNASearchTool)

Search for microRNAs (miRNAs) by name, accession, or keyword using EBI Search over RNAcentral. RN…

miRBase_search_mirna tool specification

Tool Information:

  • Name: miRBase_search_mirna

  • Type: miRNASearchTool

  • Description: Search for microRNAs (miRNAs) by name, accession, or keyword using EBI Search over RNAcentral. RNAcentral aggregates miRNA data from miRBase, TarBase, LncBase, and 50+ other databases. Supports filtering by species (e.g., ‘Homo sapiens’, ‘Mus musculus’) and RNA type. Returns RNAcentral IDs, descriptions, sequence lengths, and source databases. Use this to find miRNAs like hsa-miR-21-5p, let-7, miR-155, or search by miRBase accession (e.g., MIMAT0000076). Examples: search ‘hsa-miR-21’ for human miR-21 family, ‘let-7 AND TAXONOMY:Homo sapiens’ for human let-7 family members.

Parameters:

  • query (string) (required) Search query: miRNA name (e.g., ‘hsa-miR-21-5p’), miRBase accession (e.g., ‘MIMAT0000076’), gene name, or keyword. Supports AND/OR operators.

  • species (string) (optional) Species name filter (e.g., ‘Homo sapiens’, ‘Mus musculus’, ‘Drosophila melanogaster’). Leave empty for all species.

  • size (integer) (optional) Number of results to return (1-100). Default: 10.

Example Usage:

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