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. For species-specific metadata, use URS_TAXID (for example URS000039ED8D_9606) or pass the same positive integer taxid with a base URS ID; the returned record identity and taxid are verified. A bare URS without taxid is a cross-species sequence record, so species is intentionally empty and publications_count may be null when RNAcentral supplies only a publications URL. Conflicting or nonexistent species identifiers return an error instead of falling back to another organism.

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 with explicit page pagination. m…

miRBase_get_mirna_publications tool specification

Tool Information:

  • Name: miRBase_get_mirna_publications

  • Type: miRNAGetTool

  • Description: Retrieve publications associated with a microRNA from RNAcentral with explicit page pagination. miR-21-5p has hundreds of records; while has_more is true, pass next_page as page. Metadata warns that RNAcentral can repeat a PMID with different source metadata, so total_publications is a source-record count rather than a guaranteed unique-PMID count.

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 per page (1-50).

  • page (integer) (optional) One-based RNAcentral page number. Continue with next_page.

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 for a microRNA from RNAcentral with explicit page pagination. Returns links …

miRBase_get_mirna_xrefs tool specification

Tool Information:

  • Name: miRBase_get_mirna_xrefs

  • Type: miRNAGetTool

  • Description: Get cross-references for a microRNA from RNAcentral with explicit page pagination. Returns links from miRBase, TarBase, ENA, RefSeq, piRBase, LncBase, and other sources. While has_more is true, pass next_page as page so later mappings remain reachable.

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 per page (1-50).

  • page (integer) (optional) One-based RNAcentral page number. Continue with next_page.

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 by name, accession, or keyword using EBI Search over RNAcentral. Results use…

miRBase_search_mirna tool specification

Tool Information:

  • Name: miRBase_search_mirna

  • Type: miRNASearchTool

  • Description: Search for microRNAs by name, accession, or keyword using EBI Search over RNAcentral. Results use exact offset pagination: total_hits reports all matches and, while has_more is true, pass next_start as start with the same query and filters. Returns RNAcentral IDs, descriptions, sequence lengths, and source databases.

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 per page (1-100).

  • start (integer) (optional) Zero-based EBI Search result offset. Continue with next_start.

Example Usage:

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