graph LR
Data_Access_Layer["Data Access Layer"]
Codelist_Management["Codelist Management"]
Data_Transformation_Utilities["Data Transformation & Utilities"]
Phenotype_Engine["Phenotype Engine"]
Reporting_Analytics["Reporting & Analytics"]
Data_Access_Layer -- "provides data to" --> Phenotype_Engine
Phenotype_Engine -- "persists results to" --> Data_Access_Layer
Data_Transformation_Utilities -- "applies transformations to" --> Phenotype_Engine
Codelist_Management -- "supplies criteria to" --> Phenotype_Engine
Phenotype_Engine -- "generates reports for" --> Reporting_Analytics
Data_Transformation_Utilities -- "serializes/deserializes" --> Codelist_Management
Data_Transformation_Utilities -- "serializes/deserializes" --> Phenotype_Engine
click Data_Access_Layer href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/PhenEx/Data Access Layer.md" "Details"
click Codelist_Management href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/PhenEx/Codelist Management.md" "Details"
click Data_Transformation_Utilities href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/PhenEx/Data Transformation & Utilities.md" "Details"
click Phenotype_Engine href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/PhenEx/Phenotype Engine.md" "Details"
click Reporting_Analytics href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/PhenEx/Reporting & Analytics.md" "Details"
The PhenEx system is designed for defining, computing, and reporting on patient phenotypes and cohorts from various database sources. It leverages a Data Access Layer to connect to databases and abstract data tables. The core Phenotype Engine utilizes Codelist Management for criteria and Data Transformation & Utilities for filtering and aggregation to define and execute complex phenotypes and manage cohorts. Finally, the Reporting & Analytics component generates insights from the computed cohorts.
Manages connections to various databases and provides an abstract representation of data tables for querying and manipulation.
Related Classes/Methods:
PhenEx.phenex.ibis_connect.SnowflakeConnector(25:319)PhenEx.phenex.ibis_connect.DuckDBConnector(322:354)PhenEx.phenex.tables.PhenexTable(8:152)PhenEx.phenex.tables.CodeTable(183:195)PhenEx.phenex.tables.MeasurementTable(244:263)PhenEx.phenex.tables.PhenexPersonTable(155:170)PhenEx.phenex.tables.PhenexObservationPeriodTable(230:241)PhenEx.phenex.tables.PhenexVisitOccurrenceTable(198:214)PhenEx.phenex.tables.PhenotypeTable(266:274)PhenEx.phenex.tables.EventTable(173:180)
Provides tools for defining, loading, and manipulating medical codelists from various external sources.
Related Classes/Methods:
PhenEx.phenex.codelists.codelists.Codelist(8:458)PhenEx.phenex.codelists.codelists.LocalCSVCodelistFactory(461:524)PhenEx.phenex.codelists.codelists.MedConBCodelistFactory(527:564)
Offers a framework for filtering and aggregating data, along with utilities for serializing and deserializing PhenEx objects.
Related Classes/Methods:
PhenEx.phenex.aggregators.aggregator.VerticalDateAggregator(7:60)PhenEx.phenex.aggregators.aggregator.Nearest(63:65)PhenEx.phenex.aggregators.aggregator.First(68:70)PhenEx.phenex.aggregators.aggregator.Last(73:75)PhenEx.phenex.aggregators.aggregator.ValueAggregator(78:137)PhenEx.phenex.aggregators.aggregator.Mean(140:142)PhenEx.phenex.aggregators.aggregator.Max(145:147)PhenEx.phenex.aggregators.aggregator.Min(150:152)PhenEx.phenex.aggregators.aggregator.DailyValueAggregator(155:160)PhenEx.phenex.aggregators.aggregator.DailyMean(163:165)PhenEx.phenex.aggregators.aggregator.DailyMedian(168:170)PhenEx.phenex.aggregators.aggregator.DailyMax(173:175)PhenEx.phenex.aggregators.aggregator.DailyMin(178:180)PhenEx.phenex.filters.filter.Filter(7:62)PhenEx.phenex.filters.filter.AndFilter(65:80)PhenEx.phenex.filters.filter.OrFilter(83:100)PhenEx.phenex.filters.filter.NotFilter(103:117)PhenEx.phenex.util.serialization.to_dict.to_dict(5:39)PhenEx.phenex.util.serialization.to_dict.get_phenex_init_params(42:51)
Defines the core logic for creating and executing phenotypes and managing patient cohorts based on defined criteria.
Related Classes/Methods:
PhenEx.phenex.phenotypes.phenotype.Phenotype(15:184)PhenEx.phenex.phenotypes.phenotype.ComputationGraph(194:346)PhenEx.phenex.phenotypes.cohort.Cohort(25:359)PhenEx.phenex.phenotypes.cohort.subset_and_add_index_date(14:22)
Provides tools for generating reports, summaries, and visualizations from processed data and defined cohorts.
Related Classes/Methods: