NIH NLM CDE Schema

Overview

The NIH NLM CDE schema represents Common Data Elements from the NIH and National Library of Medicine repositories. This schema covers COVID-19 related data elements.

Schema Details

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

  • Name: NIH_NLM_CDESchema

  • Version: 1.0.0

  • Source: NIH/NLM CDE Repository

Structure

Classes

The schema organizes CDEs into project-specific classes:

Project 5 (COVID-19)

  • Contains COVID-19 related data elements

  • Includes demographic, clinical, and outcome measures

  • Covers complications, treatments, and mental health symptoms

Example Data Elements

  • Address and demographic information (City, State, Postal Code)

  • Age and temporal data

  • COVID-19 case classification and severity

  • Complications and onset dates

  • Mental health and psychosocial symptoms

  • Medications and treatments

  • Discharge disposition

Ontology Bindings

The schema uses standard prefixes:

  • NCIT: NCI Thesaurus for cancer-related terms

  • UMLS: Unified Medical Language System

  • LinkML: Core LinkML types

Usage

from linkml_runtime.utils.schemaview import SchemaView

schema = SchemaView("linkml/nih_nlm_schema.yaml")
classes = schema.all_classes()
for class_name in classes:
    print(f"Class: {class_name}")

Files

  • Schema definition: linkml/nih_nlm_schema.yaml

  • Source data: data/nlm/nlm-cdes.csv