Numerical Functions (violin.numeric)

This page details the numeric operators of VIOLIN.

These functions discretize qualitative operations within VIOLIN:

  1. searching for an element in the reading output,

  2. comparing attributes, indentifying whether a given attribute

    • matches exactly an attribute in a corresponding model interaction (MI),

    • is missing where a MI attribute is present,

    • is present where a MI attribute is missing,

    • differs from an attribute in a corresponding MI.

Both functions return numerical values to represent the outcome of the function.

Functions

violin.numeric.get_attributes(A_idx: int, B_idx: int, sign: str, model_df: pandas.core.frame.DataFrame, attrs: list, path: bool = False) → dict[source]

The function gets the attributes of the interaction in model, available attributes includes [Regulator Compartment, Regulator Compartment ID, Regulated Compartment, Regulated Compartment ID, Mechansim, Site, Cell Line, Cell Type, Tissue Type, Organism]. If Regulator Compartment is selected, Regulator Compartment ID will also be selected.

Parameters

  • A_idx (int) – A row index of element A in the input model dataframe.

  • B_idx (int) – A row index of element B in the input model dataframe.

  • sign (str) – A sign of the interaction, available options: ‘positive’ or ‘negative’.

  • model_df (pd.DataFrame) – A DataFrame of a model with BioRECIPE format.

  • attrs (list) – An attributes list for interactions file.

  • path (bool) – An indicator if it is path interaction. Attributes will be empty if only path is found in model.

Returns

model_atts – An dict of attributes for a model interaction.

Return type

dict

violin.numeric.find_element(search_type: str, element_name: str, element_type: str, model_df: pandas.core.frame.DataFrame, id_db: Optional[str] = None) → Union[List, int][source]

This function finds the correct indices of an element within the model. Because elements can exist as multiple types (protein, RNA, gene, etc.), this function checks the element name/ID along with the element type. Function may return a list, if a given element of a specific type exists with varying attributes (such as different locations).

Parameters

  • search_type (str) – An identifier of the element, available options are ‘hgnc’, ‘name’, and ‘id’.

  • element_name (str) – A name (or ID) of the element being searched for.

  • element_type (str) – A type of element (‘protein’, ‘protein family’, etc.)

  • model_df (pd.DataFrame) – A model dataframe within BioRECIPE format.

  • id_db (str) – A database name for provided identifier.

Returns

location – All row indices of the model spreadsheet in which the element is found (returns -1 if not found).

Return type

list|int

violin.numeric.compare(model_atts: dict, reading_atts: dict) → int[source]
Compares a list of model attributes to the corresponding interaction attributes, returns numeric value

  • Attributes are the same (strong corroboration): 0

  • Some or all LEE attributes are missing (weak corroboration): 1

  • Some or all of the model attributes are missing (specification): 2

  • One or more model attribute differs from the LEE attributes (contradiction): 3

Parameters

  • model_atts (dict) – A dictionary of attributes for a model interaction.

  • reading_atts (dict) – A dictionary of attributes for an event from a literactions list.

Returns

value – The numerical representation of comparison outcome.

Return type

int

Dependencies

Python: pandas library

VIOLIN: none

Usage

This example searches for the index of protein family AMPK in the model spreadsheet.:

find_element_index("name","ampk","protein family",model_df)
>> 2

This example compares the location of the reading interaction to the location of its counterpart interaction in the model.:

reading_att = "nan"
model_att = "GO:0005737"
compare(model_att,reading_att)
>> 2