Ontology for Biomedical Investigations (OBI)¶
The Ontology for Biomedical Investigations (OBI) provides a comprehensive vocabulary for describing scientific investigations, experimental designs, and biomedical research methodology. It defines over 2500 terms covering assays, devices, protocols, objectives, materials, measurements, and outcomes used in biomedical and life sciences research. OBI enables standardized semantic annotation of experimental workflows, making research methodologies transparent, reproducible, and interoperable across databases and computational systems. The ontology captures hierarchical relationships between experimental concepts, allowing researchers to precisely describe complex experimental designs and data collection procedures. OBI integrates with other biological ontologies (BFO, ChEBI, CHEBI) to provide comprehensive semantic representation of biomedical investigations.
Example Usage: Annotate a microarray experiment with OBI terms such as “assay” for the type of investigation, “microarray device” for equipment, “RNA extraction” for material preparation steps, and measurement-related terms for results.
Metrics & Statistics¶
Total Nodes |
40613 |
Total Edges |
104537 |
Root Nodes |
177 |
Leaf Nodes |
10917 |
Classes |
9703 |
Individuals |
301 |
Properties |
94 |
Maximum Depth |
28 |
Minimum Depth |
0 |
Average Depth |
5.15 |
Depth Variance |
23.70 |
Maximum Breadth |
386 |
Minimum Breadth |
1 |
Average Breadth |
81.62 |
Breadth Variance |
11040.03 |
Term Types |
286 |
Taxonomic Relations |
11843 |
Non-taxonomic Relations |
38 |
Average Terms per Type |
5.61 |
Usage Example¶
Use the following code to import this ontology programmatically:
from ontolearner.ontology import OBI
ontology = OBI()
ontology.load("path/to/OBI-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