PhenX CDE Schema

Overview

The PhenX CDE schema represents Common Data Elements from the PhenX Toolkit, which provides standard measures for phenotype and exposure assessment in genomic research.

Schema Details

  • ID: https://example.org/schemas/phenx_cde

  • Name: PhenX_CDESchema

  • Version: 1.0.0

  • Source: PhenX Toolkit

Structure

Classes

The schema organizes PhenX measures into classes based on assessment instruments. Classes are typically named after the data dictionary version (e.g., DD_120902_finalized).

Example Measures

The schema includes measures such as:

  • Social preference assessments

  • Imagination and creativity indicators

  • Sensory sensitivity measures

  • Social interaction patterns

  • Communication styles

  • Behavioral preferences

  • Interest patterns

Data Elements

Example data elements include:

  • Preference for doing things with others

  • Ability to imagine story characters

  • Notice of small sounds or details

  • Social situation comfort

  • Conversation abilities

  • Fascination with patterns, dates, or numbers

Usage

from linkml_runtime.utils.schemaview import SchemaView

schema = SchemaView("linkml/phenx_schema.yaml")
slots = schema.all_slots()
for slot_name in list(slots.keys())[:10]:
    print(f"Slot: {slot_name}")

Files

  • Schema definition: linkml/phenx_schema.yaml

  • Source data: data/phenx-redcap/ (REDCap format)