Lncrna Tools#

Configuration File: lncrna_tools.json Tool Type: Local Tools Count: 5

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

Available Tools#

LNCipedia_get_lncrna (Type: miRNAGetTool)#

Get detailed lncRNA information from RNAcentral including full RNA sequence, species, gene associ…

LNCipedia_get_lncrna tool specification

Tool Information:

  • Name: LNCipedia_get_lncrna

  • Type: miRNAGetTool

  • Description: Get detailed lncRNA information from RNAcentral including full RNA sequence, species, gene associations, publication count, and source databases. For species-specific metadata, use URS_TAXID 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. Example human IDs include URS0002A146E4_9606 (MALAT1), URS00026A23F2_9606 (HOTAIR), and URS000075DAEC_9606 (NEAT1).

Parameters:

  • rnacentral_id (string) (required) RNAcentral URS identifier. Use species-specific format ‘URS_TAXID’ (e.g., ‘URS0002A146E4_9606’ for human MALAT1) or base URS ID with taxid parameter.

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

Example Usage:

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

LNCipedia_get_lncrna_publications (Type: miRNAGetTool)#

Retrieve publications associated with a long non-coding RNA from RNAcentral with explicit page pa…

LNCipedia_get_lncrna_publications tool specification

Tool Information:

  • Name: LNCipedia_get_lncrna_publications

  • Type: miRNAGetTool

  • Description: Retrieve publications associated with a long non-coding RNA from RNAcentral with explicit page pagination. 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., ‘URS0002A146E4’ for MALAT1). 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": "LNCipedia_get_lncrna_publications",
    "arguments": {
        "rnacentral_id": "example_value"
    }
}
result = tu.run(query)

LNCipedia_get_lncrna_xrefs (Type: miRNAGetTool)#

Get cross-references for a long non-coding RNA from RNAcentral with explicit page pagination. Whi…

LNCipedia_get_lncrna_xrefs tool specification

Tool Information:

  • Name: LNCipedia_get_lncrna_xrefs

  • Type: miRNAGetTool

  • Description: Get cross-references for a long non-coding RNA from RNAcentral with explicit page pagination. While has_more is true, pass next_page as page so later database mappings remain reachable.

Parameters:

  • rnacentral_id (string) (required) RNAcentral URS identifier (e.g., ‘URS0002A146E4’ for MALAT1). 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": "LNCipedia_get_lncrna_xrefs",
    "arguments": {
        "rnacentral_id": "example_value"
    }
}
result = tu.run(query)

LNCipedia_search_lncrna (Type: miRNASearchTool)#

Search long non-coding RNAs by name, accession, or keyword using EBI Search over RNAcentral. Resu…

LNCipedia_search_lncrna tool specification

Tool Information:

  • Name: LNCipedia_search_lncrna

  • Type: miRNASearchTool

  • Description: Search long non-coding RNAs by name, accession, or keyword using EBI Search over RNAcentral. Results use exact offset pagination: while has_more is true, pass next_start as start with the same query and species filter.

Parameters:

  • query (string) (required) Search query: lncRNA name (e.g., ‘MALAT1’, ‘HOTAIR’), gene symbol, accession, or keyword. Supports AND/OR operators.

  • species (string) (optional) Species name filter (e.g., ‘Homo sapiens’, ‘Mus musculus’). 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": "LNCipedia_search_lncrna",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)

LNCipedia_search_ncrna_by_type (Type: miRNASearchTool)#

Search any RNAcentral non-coding RNA type with exact offset pagination. Supports miRNA, lncRNA, r…

LNCipedia_search_ncrna_by_type tool specification

Tool Information:

  • Name: LNCipedia_search_ncrna_by_type

  • Type: miRNASearchTool

  • Description: Search any RNAcentral non-coding RNA type with exact offset pagination. Supports miRNA, lncRNA, rRNA, tRNA, snRNA, snoRNA, piRNA and others; while has_more is true, continue with next_start.

Parameters:

  • query (string) (required) Search query: gene name, keyword, or accession. Use ‘*’ for all entries of the specified RNA type.

  • rna_type (string) (optional) RNA type filter: miRNA, lncRNA, rRNA, tRNA, snRNA, snoRNA, piRNA, pre_miRNA, SRP_RNA, RNase_P_RNA, antisense_RNA, ribozyme, etc.

  • species (string) (optional) Species name filter (e.g., ‘Homo sapiens’). 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": "LNCipedia_search_ncrna_by_type",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)