Target Affinity Spectrum (indra.sources.tas)

This module provides and API and processor to the Target Affinity Spectrum data set compiled by N. Moret in the Laboratory of Systems Pharmacology at HMS. This data set is based on experiments as opposed to the manually curated drug-target relationships provided in the LINCS small molecule dataset.

TAS API (indra.sources.tas.api)

indra.sources.tas.api.process_csv(affinity_class_limit=2)[source]

Return a TasProcessor for the contents of the csv contained in data.

Interactions are classified into the following classes based on affinity:
1 – Kd < 100nM
2 – 100nM < Kd < 1uM
3 – 1uM < Kd < 10uM
10 – Kd > 10uM

By default, only classes 1 and 2 are extracted but the affinity_class_limit parameter can be used to change the upper limit of extracted classes.

Parameters:affinity_class_limit (Optional[int]) – Defines the highest class of binding affinity that is included in the extractions. Default: 2
Returns:A TasProcessor object which has a list of INDRA Statements extracted from the CSV file representing drug-target inhibitions in its statements attribute.
Return type:TasProcessor

TAS Processor (indra.sources.tas.processor)

class indra.sources.tas.processor.TasProcessor(data, affinity_class_limit)[source]

A processor for the Target Affinity Spectrum data table.