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