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