Mass Spectrometry Ontology (MassSpectrometry)

A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.

The Mass Spectrometry Ontology (MassSpectrometry) is a structured controlled vocabulary designed to annotate experiments in the field of proteomics mass spectrometry. It provides a standardized framework for describing experimental setups, instrumentation, data acquisition methods, and analysis workflows. The ontology captures essential concepts such as ionization techniques, mass analyzers, fragmentation methods, and data processing algorithms. By offering a common language for mass spectrometry, it facilitates data sharing, integration, and reproducibility across proteomics studies. The ontology is widely used in bioinformatics pipelines, proteomics databases, and experimental repositories to ensure semantic consistency and interoperability. Researchers can leverage the Mass Spectrometry Ontology to annotate datasets, describe experimental protocols, and enable advanced queries for comparative analyses.

Example Usage: Annotate a proteomics experiment with MassSpectrometry terms to specify the ionization method (e.g., “electrospray ionization”), mass analyzer type (e.g., “time-of-flight”), and data processing software used for peak detection and quantification.

Metrics & Statistics

Graph Statistics

Total Nodes

17851

Total Edges

51814

Root Nodes

3786

Leaf Nodes

7959
Knowledge Coverage Statistics

Classes

3636

Individuals

0

Properties

12
Hierarchical Metrics

Maximum Depth

6

Minimum Depth

0

Average Depth

1.16

Depth Variance

0.58
Breadth Metrics

Maximum Breadth

7345

Minimum Breadth

2

Average Breadth

2534.57

Breadth Variance

9465403.67
LLMs4OL Dataset Statistics

Term Types

0

Taxonomic Relations

7016

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 MassSpectrometry

ontology = MassSpectrometry()
ontology.load("path/to/MassSpectrometry-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