Rnacentral Tools

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

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

Available Tools

RNAcentral_get_by_accession (Type: RNAcentralGetTool)

Retrieve a single RNAcentral entry by accession for detailed annotations and source cross-referen…

RNAcentral_get_by_accession tool specification

Tool Information:

  • Name: RNAcentral_get_by_accession

  • Type: RNAcentralGetTool

  • Description: Retrieve a single RNAcentral entry by accession for detailed annotations and source cross-references. Use for cross-database ID mapping and metadata.

Parameters:

  • accession (string) (required) RNAcentral accession (e.g., ‘URS000075C808’).

Example Usage:

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

RNAcentral_get_region_ncRNAs (Type: RNAcentralGetTool)

List all RNAcentral non-coding RNAs overlapping a genome locus, aggregated from 50+ member databa…

RNAcentral_get_region_ncRNAs tool specification

Tool Information:

  • Name: RNAcentral_get_region_ncRNAs

  • Type: RNAcentralGetTool

  • Description: List all RNAcentral non-coding RNAs overlapping a genome locus, aggregated from 50+ member databases (miRBase, snoRNA, tRNA, lncRNA, piRNA, etc.). Provide a species (default ‘homo_sapiens’) and either a ‘region’ string (‘2:39745816-39826679’) or discrete ‘chromosome’/’start’/’end’. Returns overlapping ncRNA transcripts and their exon features with biotype, strand and coordinates, split into data.transcripts and data.exons. Use to annotate what ncRNAs sit in a region of interest. Public, no authentication.

Parameters:

  • region ([‘string’, ‘null’]) (optional) Locus as ‘chr:start-end’ (1-based), e.g. ‘2:39745816-39826679’. Omit if giving chromosome/start/end.

  • species ([‘string’, ‘null’]) (optional) Ensembl species slug (default ‘homo_sapiens’). E.g. ‘mus_musculus’, ‘danio_rerio’.

  • chromosome ([‘string’, ‘null’]) (optional) Chromosome name without ‘chr’ prefix, e.g. ‘2’. Used with start/end when ‘region’ is omitted.

  • start ([‘integer’, ‘null’]) (optional) Region start (1-based). Used with chromosome/end when ‘region’ is omitted.

  • end ([‘integer’, ‘null’]) (optional) Region end (1-based). Used with chromosome/start when ‘region’ is omitted.

Example Usage:

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

RNAcentral_get_xrefs_and_pubs (Type: RNAcentralGetTool)

Get the resolved per-source cross-references AND literature for an RNAcentral entry in one call. …

RNAcentral_get_xrefs_and_pubs tool specification

Tool Information:

  • Name: RNAcentral_get_xrefs_and_pubs

  • Type: RNAcentralGetTool

  • Description: Get the resolved per-source cross-references AND literature for an RNAcentral entry in one call. Returns the full xref list (with database name, taxid, accession id, NCBI gene id, miRBase mature/precursor products, Ensembl/GENCODE transcript ids, RefSeq, etc.) under data.xrefs, and the publications list (title, authors, PMID, DOI) under data.publications. Use after RNAcentral_search or RNAcentral_get_by_accession to map an URS id to external databases and supporting papers. Example: URS000063A371 returns 8 xrefs (database=Rfam, taxid=7955, accession id ‘CR381647.10:84955..85035:rfam’) and 8 publications (e.g. PMID 12844358, DOI 10.1186/gb-2003-4-7-r42).

Parameters:

  • accession (string) (required) RNAcentral URS identifier (e.g., ‘URS000063A371’, ‘URS000075C808’).

Example Usage:

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

RNAcentral_search (Type: RNAcentralSearchTool)

Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to…

RNAcentral_search tool specification

Tool Information:

  • Name: RNAcentral_search

  • Type: RNAcentralSearchTool

  • Description: Search aggregated ncRNA records (miRNA, rRNA, lncRNA, etc.) across sources via RNAcentral. Use to find accessions, types, species, and descriptions for ncRNA analysis.

Parameters:

  • query (string) (required) Keyword, accession, or sequence-based query (per RNAcentral API).

  • page_size (integer) (optional) Number of records per page (1–100).

Example Usage:

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