treatment

ACTIN-Treatment

ACTIN-Treatment creates a database of potential treatments for ACTIN-Algo to match against.
The application takes in a set of configuration files and writes a database in JSON format to a specified output directory.

This application requires Java 11+ and can be run as follows:

java -cp actin.jar com.hartwig.actin.treatment.TreatmentCreatorApplication \
   -trial_config_directory /path/to/trial_config_dir \
   -doid_json /path/to/full_doid_tree_json_file \
   -output_directory /path/to/where/treatment_json_files/are/written

Configuration of trials in the treatment database

Trials are read from the trial_config_directory. The following files are expected to be present in this directory:

• trial_definition.tsv defining all trials that can be matched against.
• cohort_definition.tsv defining all cohorts within the set of trials that can be matched against.
• inclusion_criteria.tsv defining all inclusion criteria for the trials and cohorts
• inclusion_criteria_reference.tsv providing (external) reference texts for the inclusion criteria.

The treatment database will only be created if the trial config is entirely consistent and can be resolved to interpretable rules. In case of any configuration issue, this application will crash while providing details on how to solve the configuration issue(s).

An example trial configuration database can be found here

Trial Definition

Field	Example
trialId	ACTN 2021
open	1
acronym	ACTIN
title	ACTIN is a study to evaluate a new treatment decision system

The following checks are done on the level of trial definitions:

• Every trial ID must be unique
• Every file identifier generated for any trial must be unique. The file identifier is the trial ID with spaces replaced by underscores.

Cohort Definition

Field	Example
trialId	ACTN 2021
cohortId	A
open	1
slotsAvailable	1
blacklist	0
description	First evaluation phase

The following checks are done on the level of cohort definitions:

• Every trial ID referenced from a cohort must be defined in the trial definitions file
• Every cohort ID must be unique within the context of a specific trial

Inclusion Criteria

Field	Example
trialId	ACTN 2021
referenceIds	I-01, I-02
appliesToCohorts	all
inclusionRule	AND(IS_AT_LEAST_X_YEARS_OLD[18], HAS_METASTATIC_CANCER)

The following checks are done on the level of inclusion criteria:

• Every trial ID referenced in an inclusion criterion must be defined in the trial definition file
• Every reference ID must be defined in the inclusion criteria reference file.
• Every cohort ID in the comma-separated list of cohorts must be defined in the cohort definition file, unless this field has been set to all cohorts.
• The inclusion rule has to be valid according to inclusion rule configuration

Inclusion Criteria Reference

Field	Example
trialId	ACTN 2021
referenceId	I-01
referenceText	Patient has to be 18 years old

The following checks are done on the level of inclusion criteria references:

• Every trial ID referenced in a criteria reference must be defined in the trial definition file.
• Every reference ID must be unique within the context of a specific trial.

Inclusion rule configuration

An inclusion rule has to be either a specific rule or a composite rule combining specific rules defined in ACTIN-Algo.

• Inputs to composite rules are expected to be enclosed in parentheses (for example NOT(SPECIFIC_RULE)).
• Inputs to specific rules are expected to be enclosed in brackets (for example SPECIFIC_RULE_WITH_ONE_PARAM[2]).
• A list of inputs to rules are expected to be separated by semicolons (for example HAS_TOXICITY_OF_AT_LEAST_GRADE_X_IGNORING_Y[2, NEUROPATHY;THYROID]).

An inclusion rule is configured validly only if the expected number of inputs is provided in the config and the inputs can be resolved to the type of input expected by the function.

Some examples:

Human readable rule	How to configure as a inclusion rule
Patient has to be an adult	IS_AT_LEAST_X_YEARS_OLD[18]
Has a maximum total bilirubin of 2.5 ULN, or 5.0 ULN in case patient has Gilbert's disease	OR(HAS_TOTAL_BILIRUBIN_ULN_AT_MOST_X[2.5], AND(HAS_GILBERT_DISEASE, HAS_TOTAL_BILIRUBIN_ULN_AT_MOST_X[5]))
Patient has no active CNS metastases	NOT(HAS_ACTIVE_CNS_METASTASES)

Version History and Download Links

• Upcoming (first release)