8. Investigations, Studies And Assays: the ISA format

This module contains the core functionality for converting a batch of PTMD data to ISA-Tab format.

class ptmd.lib.isa.core.Batch2ISA(file: File)

Bases: object

Class for converting a batch of PTMD data to ISA-json format.

Parameters

file – The file to convert.

convert() → list[dict]

Convert the file to ISA format.

Returns

A list of dictionaries containing the ISA investigations.

static create_blank_source() → Source

Create a blank source.

Returns

A blank source.

static create_characteristic(box_id: str, position: str, replicate: int) → list[isatools.model.characteristic.Characteristic]

Create characteristics for a sample.

Parameters

  • box_id – The box id of the sample.

  • position – The position of the sample.

  • replicate – The replicate of the sample.

Returns

A list of characteristics.

create_factor_values(timepoint: str, dose: str, compound: str | None) → list[FactorValue]

Create factor values for a sample.

Parameters

  • timepoint – The timepoint of the sample.

  • dose – The dose of the sample.

  • compound – The compound of the sample.

Returns

A list of factor values.

create_factors() → None

Create the factors for the study.

create_parameter_values(values: dict) → list[isatools.model.parameter_value.ParameterValue]

Create parameter values for a sample.

Parameters

values – The values of the parameters.

create_protocol() → Protocol

Create a protocol for the study.

Returns

A protocol.

create_protocol_parameters(parameter_names: list[str]) → None

Create protocol parameters for the study.

Parameters

parameter_names – The names of the parameters.

create_sample(info: dict, study: Study) → Sample

Create a sample from a dictionary

Parameters

  • info – The dictionary containing the sample information.

  • study – The study to add the sample to.

Returns

A sample.

create_samples(study: Study) → None

Create a sample from a dictionary

Parameters

study – The study to add the samples to.

create_source(sample_identifier: str) → Source

Create a source for a sample.

Parameters

sample_identifier – The identifier of the sample.

Returns

A source.

create_treatment_process(inputs: list, outputs: list, protocol: Protocol, values: dict) → Process

Create a treatment process for a sample.

Parameters

  • inputs – The inputs of the process.

  • outputs – The outputs of the process.

  • protocol – The protocol of the process.

  • values – The values of the parameters.

Returns

A process.

Ontology annotations and sources to create the ISA investigations.