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Proteomics Standards Initiative (PSI) Protein Modifications Ontology (PSI-MOD)
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Overview
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PSI-MOD is an ontology consisting of terms that describe protein chemical modifications,
logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG).
The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths
for classifying protein modifications either by the molecular structure of the modification,
or by the amino acid residue that is modified.
:Domain: Chemistry
:Category: Protein Modifications
:Current Version: 1.031.6
:Last Updated: 2022-06-13
:Creator: None
:License: Creative Commons Attribution 4.0
:Format: OWL
:Download: `Proteomics Standards Initiative (PSI) Protein Modifications Ontology (PSI-MOD) Homepage <https://github.com/HUPO-PSI/psi-mod-CV>`_
Graph Metrics
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- **Total Nodes**: 28523
- **Total Edges**: 86380
- **Root Nodes**: 9338
- **Leaf Nodes**: 16902
Knowledge coverage
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- Classes: 2098
- Individuals: 0
- Properties: 4
Hierarchical metrics
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- **Maximum Depth**: 4
- **Minimum Depth**: 0
- **Average Depth**: 0.95
- **Depth Variance**: 0.60
Breadth metrics
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- **Maximum Breadth**: 11284
- **Minimum Breadth**: 4
- **Average Breadth**: 5684.00
- **Breadth Variance**: 22690827.20
Dataset Statistics
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Generated Benchmarks:
- **Term Types**: 0
- **Taxonomic Relations**: 8347
- **Non-taxonomic Relations**: 0
- **Average Terms per Type**: 0.00
Usage Example
-------------
.. code-block:: python
from ontolearner.ontology import PSIMOD
# Initialize and load ontology
ontology = PSIMOD()
ontology.load("path/to/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
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