Microscopy Ontology (MO)¶
The Microscopy Ontology (MO) is a domain ontology developed to provide a structured framework for describing microscopy and microanalysis experiments, data, and equipment. It extends the PMD Core Ontology (PMDco) and was developed within the Platform MaterialDigital ecosystem to support semantic integration and interoperability of microscopy data [2] [1]. The ontology covers microscopy-specific concepts and relationships needed to describe processes, equipment, and parameters in microscopy and microanalysis workflows [1] [3]. MO is intended to improve the semantic representation of microscopy knowledge and support better query results and logical linking among related terms and data objects [1] [2]. By providing a standardized vocabulary grounded in PMDco, the ontology supports interoperable data description and integration across materials-science microscopy datasets and related digital research infrastructures [3] [4].
Example Usage: Annotate a microscopy dataset with MO terms to specify the imaging modality (for example scanning electron microscopy or transmission electron microscopy), relevant equipment and parameters, sample-related descriptors, and analysis-related concepts, enabling semantic search, interoperable data integration, and improved querying across microscopy data sources [1] [2].
Metrics & Statistics¶
Total Nodes |
931 |
Total Edges |
1776 |
Root Nodes |
10 |
Leaf Nodes |
693 |
Classes |
217 |
Individuals |
0 |
Properties |
3 |
Maximum Depth |
1 |
Minimum Depth |
0 |
Average Depth |
0.09 |
Depth Variance |
0.08 |
Maximum Breadth |
10 |
Minimum Breadth |
1 |
Average Breadth |
5.50 |
Breadth Variance |
20.25 |
Term Types |
0 |
Taxonomic Relations |
130 |
Non-taxonomic Relations |
0 |
Average Terms per Type |
0.00 |
Usage Example¶
Use the following code to import this ontology programmatically:
from ontolearner.ontology import MO
ontology = MO()
ontology.load("path/to/MO-ontology.ttl")
# 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