Experimental Factor Ontology (EFO)¶
The Experimental Factor Ontology (EFO) is a comprehensive ontology developed to provide systematic, standardized descriptions of experimental variables and factors in biological and biomedical research [1] [2]. EFO integrates terms from multiple biological ontologies in order to support the annotation, analysis, and visualization of experimental data [1] [2]. It provides a semantic framework for describing sample variables and experimental conditions, enabling consistent data annotation and interoperability across diverse datasets [2] [1]. EFO is maintained by EMBL-EBI and serves as an important ontology resource for biological data integration and reuse [1]. By providing a unified framework for describing experimental factors, EFO supports data sharing, discovery, and knowledge integration in genomics, transcriptomics, and related life science domains [1] [2].
Example Usage: Annotate a gene expression or association dataset with EFO terms to specify experimental variables such as tissue type, disease or phenotype, treatment, and assay-related factors, enabling semantic search, cross-study comparison, and meta-analysis across biological datasets [2] [1].
Metrics & Statistics¶
Total Nodes |
948012 |
Total Edges |
2874304 |
Root Nodes |
308011 |
Leaf Nodes |
443836 |
Classes |
88311 |
Individuals |
0 |
Properties |
87 |
Maximum Depth |
13 |
Minimum Depth |
0 |
Average Depth |
1.24 |
Depth Variance |
2.14 |
Maximum Breadth |
308011 |
Minimum Breadth |
5 |
Average Breadth |
62043.14 |
Breadth Variance |
11287110481.98 |
Term Types |
0 |
Taxonomic Relations |
162458 |
Non-taxonomic Relations |
10335 |
Average Terms per Type |
0.00 |
Usage Example¶
Use the following code to import this ontology programmatically:
from ontolearner.ontology import EFO
ontology = EFO()
ontology.load("path/to/EFO-ontology.owl")
# Extract datasets
data = ontology.extract()
# Access specific relations
term_types = data.term_typings
taxonomic_relations = data.type_taxonomies
non_taxonomic_relations = data.type_non_taxonomic_relations