Protein Modifications Ontology (PSIMOD)¶
The Protein Modifications Ontology (PSIMOD) is a comprehensive ontology developed by the Proteomics Standards Initiative (PSI) to describe chemical modifications of proteins. It organizes protein modifications into a directed acyclic graph (DAG) structure, enabling hierarchical classification based on molecular structure or the modified amino acid residue. PSIMOD captures a wide range of protein modifications, including phosphorylation, acetylation, ubiquitination, and glycosylation, providing detailed descriptions of their chemical nature and biological significance. The ontology supports semantic annotation of proteomics datasets, facilitating data integration, analysis, and sharing across proteomics studies. By providing a standardized vocabulary, PSIMOD enhances the reproducibility and interoperability of proteomics research, enabling advanced queries and comparative analyses.
Example Usage: Annotate a proteomics dataset with PSIMOD terms to specify protein modifications, such as “PSI-MOD:00046 (phosphorylation)” or “PSI-MOD:00048 (acetylation),” and link these modifications to their respective biological pathways.
Metrics & Statistics¶
Total Nodes |
28523 |
Total Edges |
86380 |
Root Nodes |
9338 |
Leaf Nodes |
16902 |
Classes |
2098 |
Individuals |
0 |
Properties |
4 |
Maximum Depth |
4 |
Minimum Depth |
0 |
Average Depth |
0.95 |
Depth Variance |
0.60 |
Maximum Breadth |
11284 |
Minimum Breadth |
4 |
Average Breadth |
5684.00 |
Breadth Variance |
22690827.20 |
Term Types |
0 |
Taxonomic Relations |
7913 |
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 PSIMOD
ontology = PSIMOD()
ontology.load("path/to/PSIMOD-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