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.

Moret, N., et al. (2018). Cheminformatics tools for analyzing and designing optimized small molecule libraries. BioRxiv, (617), 358978. https://doi.org/10.1101/358978

TAS API (indra.sources.tas.api)

indra.sources.tas.api.process_csv(fname, affinity_class_limit=2, named_only=False, standardized_only=False)[source]

Return a TasProcessor for the contents of a given CSV file..

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

  • fname (str) – The path to a local CSV file containing the TAS data.

  • affinity_class_limit (Optional[int]) – Defines the highest class of binding affinity that is included in the extractions. Default: 2

  • named_only (Optional[bool]) – If True, only chemicals that have a name assigned in some name space (including ones that aren’t fully stanadardized per INDRA’s ontology, e.g., CHEMBL1234) are included. If False, chemicals whose name is assigned based on an ID (e.g., CHEMBL)rather than an actual name are also included. Default: False

  • standardized_only (Optional[bool]) – If True, only chemicals that are fully standardized per INDRA’s ontology (i.e., they have grounding appearing in one of the default_ns_order name spaces, and consequently have any groundings and their name standardized) are extracted. Default: False

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

indra.sources.tas.api.process_from_web(affinity_class_limit=2, named_only=False, standardized_only=False)[source]

Return a TasProcessor for the contents of the TAS dump online.

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

  • named_only (Optional[bool]) – If True, only chemicals that have a name assigned in some name space (including ones that aren’t fully stanadardized per INDRA’s ontology, e.g., CHEMBL1234) are included. If False, chemicals whose name is assigned based on an ID (e.g., CHEMBL)rather than an actual name are also included. Default: False

  • standardized_only (Optional[bool]) – If True, only chemicals that are fully standardized per INDRA’s ontology (i.e., they have grounding appearing in one of the default_ns_order name spaces, and consequently have any groundings and their name standardized) are extracted. Default: False

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=2, named_only=False, standardized_only=False)[source]

A processor for the Target Affinity Spectrum data table.