.. sidebar::

    .. list-table:: **Ontology Card**
       :header-rows: 0

       * - **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**
         - `Download Protein Modifications Ontology (PSIMOD) <https://github.com/HUPO-PSI/psi-mod-CV>`_

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
--------------------------

.. tab:: Graph


    .. list-table:: Graph Statistics
        :widths: 50 50
        :header-rows: 0

        * - **Total Nodes**
          - 28523
        * - **Total Edges**
          - 86380
        * - **Root Nodes**
          - 9338
        * - **Leaf Nodes**
          - 16902
    ::


.. tab:: Coverage


    .. list-table:: Knowledge Coverage Statistics
        :widths: 50 50
        :header-rows: 0

        * - **Classes**
          - 2098
        * - **Individuals**
          - 0
        * - **Properties**
          - 4

    ::

.. tab:: Hierarchy


    .. list-table:: Hierarchical Metrics
        :widths: 50 50
        :header-rows: 0

        * - **Maximum Depth**
          - 4
        * - **Minimum Depth**
          - 0
        * - **Average Depth**
          - 0.95
        * - **Depth Variance**
          - 0.60
    ::


.. tab:: Breadth


    .. list-table:: Breadth Metrics
        :widths: 50 50
        :header-rows: 0

        * - **Maximum Breadth**
          - 11284
        * - **Minimum Breadth**
          - 4
        * - **Average Breadth**
          - 5684.00
        * - **Breadth Variance**
          - 22690827.20
    ::

.. tab:: LLMs4OL


    .. list-table:: LLMs4OL Dataset Statistics
        :widths: 50 50
        :header-rows: 0

        * - **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:

.. code-block:: python

    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