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✨ Add new MDS-Onto and 🐛 bug fixings (PR #303 from sciknoworg/dev)
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‎docs/source/benchmarking/benchmark.rst‎

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@@ -250,6 +250,7 @@ Ontologies related to materials, their structure, properties, processing, and en
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materials_science_and_engineering/vimmp.rst
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materials_science_and_engineering/oiecharacterisation.rst
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materials_science_and_engineering/prima.rst
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materials_science_and_engineering/mdsonto.rst
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Medicine
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==========

‎docs/source/benchmarking/materials_science_and_engineering/mdsonto.rst‎

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The Modular Ontology for Materials and Data Science (MDS-Onto)
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==============================================================================
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.. sidebar::
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.. list-table:: **Ontology Card**
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:header-rows: 0
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* - **Domain**
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- Materials Science and Engineering
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* - **Category**
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- Materials Data Science
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* - **Current Version**
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- 0.3.1.16
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* - **Last Updated**
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- 2026-02-03
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* - **Creator**
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- SDLE Research Center
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* - **License**
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- CC BY-SA 4.0
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* - **Format**
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- owl
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* - **Download**
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- `Download The Modular Ontology for Materials and Data Science (MDS-Onto) <https://cwrusdle.bitbucket.io/files/MDS_Onto/index-en.html>`_
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MDS-Onto is a domain (low) level ontology that describes terms in Materials Data Science. It is divided into six large modules: BuiltEnv, Exposure, Chemistry, Manufacture, Characterization, and Geospatial. Under each module, there are multiple sub-modules such as FTIR, AFM, Chem-Rxn, PV-Module, Accelerated Exposure, etc.
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Metrics & Statistics
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--------------------------
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.. tab:: Graph
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.. list-table:: Graph Statistics
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:widths: 50 50
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:header-rows: 0
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* - **Total Nodes**
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- 4362
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* - **Total Edges**
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- 13095
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* - **Root Nodes**
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- 92
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* - **Leaf Nodes**
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- 2226
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::
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.. tab:: Coverage
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.. list-table:: Knowledge Coverage Statistics
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:widths: 50 50
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:header-rows: 0
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* - **Classes**
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- 1710
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* - **Individuals**
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- 1
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* - **Properties**
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- 169
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::
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.. tab:: Hierarchy
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.. list-table:: Hierarchical Metrics
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:widths: 50 50
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:header-rows: 0
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* - **Maximum Depth**
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- 7
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* - **Minimum Depth**
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- 0
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* - **Average Depth**
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- 1.03
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* - **Depth Variance**
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- 2.01
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::
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.. tab:: Breadth
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.. list-table:: Breadth Metrics
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:widths: 50 50
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:header-rows: 0
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* - **Maximum Breadth**
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- 92
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* - **Minimum Breadth**
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- 1
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* - **Average Breadth**
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- 25.75
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* - **Breadth Variance**
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- 1093.94
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::
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.. tab:: LLMs4OL
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.. list-table:: LLMs4OL Dataset Statistics
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:widths: 50 50
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:header-rows: 0
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* - **Term Types**
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- 1
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* - **Taxonomic Relations**
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- 1648
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* - **Non-taxonomic Relations**
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- 259
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* - **Average Terms per Type**
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- 1.00
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::
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Usage Example
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-------------
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Use the following code to import this ontology programmatically:
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.. code-block:: python
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from ontolearner.ontology import MDSOnto
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ontology = MDSOnto()
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ontology.load("path/to/MDSOnto-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

‎docs/source/ontologizer/new_ontologies.rst‎

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@@ -71,10 +71,10 @@ Each ontology class inherits from ``BaseOntology`` and defines:
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.. code-block:: python
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle ontology-specific blank nodes."""
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if supper()._is_anonymous_id(label):
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return True
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# Add ontology-specific patterns
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# "ontology_data": ...,
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# "documentation": ...
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Once this process is done, you might use the `.save_resource` function to check the constructed files and documentations:
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Once this process is done, you might use the ``.save_resource`` function to check the constructed files and documentations:
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.. code-block:: python
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‎ontolearner/ontology/biology.py‎

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@@ -70,15 +70,14 @@ class GO(BaseOntology):
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format = "OWL"
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download_url = "https://geneontology.org/docs/download-ontology/"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle GO-specific blank nodes."""
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# Check the general patterns from the parent class
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# GO-specific patterns
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if label.startswith('GO_'):
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return True
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False

‎ontolearner/ontology/chemistry.py‎

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@@ -57,15 +57,15 @@ class ChEBI(BaseOntology):
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format = "OWL"
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download_url = "https://www.ebi.ac.uk/chebi/"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle ChEBI-specific blank nodes."""
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# ChEBI-specific patterns
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if re.match(r'^CHEBI_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "OWL"
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download_url = "https://terminology.tib.eu/ts/ontologies/CHEMINF"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle CHEMINF-specific blank nodes."""
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# ChEBI-specific patterns
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if re.match(r'^CHEMINF_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "OWL"
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download_url = "https://github.com/rsc-ontologies/rsc-cmo"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle ChMO-specific blank nodes."""
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# ChEBI-specific patterns
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if re.match(r'^CHMO_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "OWL"
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download_url = "https://terminology.tib.eu/ts/ontologies/MS"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle MassSpectrometry-specific blank nodes."""
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# MassSpectrometry-specific patterns
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if re.match(r'^PEFF_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "OWL"
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download_url = "https://terminology.tib.eu/ts/ontologies/MOP"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle MOP-specific blank nodes."""
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# MOP-specific patterns
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if re.match(r'^MOP_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "OWL"
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download_url = "https://github.com/rsc-ontologies/rxno"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle RXNO-specific blank nodes."""
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# RXNO-specific patterns
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if re.match(r'^RXNO_[0-9]+$', label):
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False

‎ontolearner/ontology/ecology_environment.py‎

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@@ -35,15 +35,14 @@ class ENVO(BaseOntology):
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format = "OWL"
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download_url = "https://obofoundry.org/ontology/envo.html"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle ENVO-specific blank nodes."""
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# ENVO-specific patterns
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if re.match(r'^PATO_[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False

‎ontolearner/ontology/general.py‎

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@@ -53,15 +53,14 @@ class DBpedia(BaseOntology):
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format = "OWL"
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download_url = "https://wiki.dbpedia.org/"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle DBpedia/Wikidata-specific blank nodes."""
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# DBpedia/Wikidata-specific patterns
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if re.match(r'^Q[0-9]+$', label):
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False
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format = "n3"
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download_url = "https://github.com/structureddynamics/UMBEL/tree/master/Ontology"
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@staticmethod
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def _is_anonymous_id(label: str) -> bool:
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def _is_anonymous_id(self, label: str) -> bool:
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"""Override to handle UMBEL-specific blank nodes."""
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# UMBEL-specific patterns
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if re.match(r'^f5295f96ac3e649dcb1740b0d93d3e6c2b[0-9a-f]+$', label): # Long hexadecimal identifiers
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return True
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# Check the general patterns from the parent class
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if BaseOntology._is_anonymous_id(label):
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if super()._is_anonymous_id(label):
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return True
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return False

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