Modomics Tools#

Configuration File: modomics_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

MODOMICS_get_modification (Type: MODOMICSTool)#

Get one RNA modification by exact numeric ID from the complete MODOMICS catalog. The apparent /mo…

MODOMICS_get_modification tool specification

Tool Information:

  • Name: MODOMICS_get_modification

  • Type: MODOMICSTool

  • Description: Get one RNA modification by exact numeric ID from the complete MODOMICS catalog. The apparent /modifications/{id} route currently ignores the ID and returns all 433 records, so this wrapper deliberately fetches the complete catalog, validates every catalog-key/embedded-ID pair, and selects only the exact key. Unknown IDs are explicit errors rather than silently returning the first catalog entry. Returns chemical structure, formula, masses, reference moiety, abbreviations, product ions, and LC elution data.

Parameters:

  • modification_id (integer) (required) Current MODOMICS modification numeric ID. Live catalog examples: 118 (pseudouridine/Y), 96 (N6-methyladenosine/m6A), 18 (5-methylcytidine/m5C), 2 (5,2’-O-dimethylcytidine/m5Cm). IDs 78 and 58 represent different modifications and must not be used as aliases for these compounds.

Example Usage:

query = {
    "name": "MODOMICS_get_modification",
    "arguments": {
        "modification_id": 10
    }
}
result = tu.run(query)

MODOMICS_list_modifications (Type: MODOMICSTool)#

List known RNA modifications from MODOMICS with chemical properties. The complete catalog is reco…

MODOMICS_list_modifications tool specification

Tool Information:

  • Name: MODOMICS_list_modifications

  • Type: MODOMICSTool

  • Description: List known RNA modifications from MODOMICS with chemical properties. The complete catalog is recoverably paginated: start at offset=0 and continue with data.next_offset while data.has_more is true; data.total is the complete count.

Parameters:

  • limit (integer) (optional) Maximum number of modifications to return (default: 50, max: 500)

  • offset (integer) (optional) Zero-based catalog offset. Continue with data.next_offset.

Example Usage:

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

MODOMICS_search_modifications (Type: MODOMICSTool)#

Search the full MODOMICS catalog by name, short name, or chemical formula. Matches are recoverabl…

MODOMICS_search_modifications tool specification

Tool Information:

  • Name: MODOMICS_search_modifications

  • Type: MODOMICSTool

  • Description: Search the full MODOMICS catalog by name, short name, or chemical formula. Matches are recoverably paginated: start at offset=0 and continue with data.next_offset while data.has_more is true.

Parameters:

  • query (string) (required) Search term to match against modification name, short name, or formula. Examples: ‘pseudouridine’, ‘methyl’, ‘m6A’, ‘inosine’, ‘thio’

  • limit (integer) (optional) Maximum number of results to return (default: 20)

  • offset (integer) (optional) Zero-based match offset. Continue with data.next_offset.

Example Usage:

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