Update chemistry domain with 15 ontologies

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
 chebi/chebi.owl filter=lfs diff=lfs merge=lfs -text
+chebi/type_taxonomies.json filter=lfs diff=lfs merge=lfs -text

README.md

@@ -16,7 +16,7 @@ pretty_name: Agricultural
 </div>
 
 ## Overview
-The domain of chemistry ontologies encompasses the structured representation and formalization of chemical knowledge, including entities, reactions, processes, and methodologies. It plays a critical role in facilitating interoperability, data integration, and advanced computational modeling across diverse chemical disciplines. By providing a standardized framework, these ontologies enhance the precision and efficiency of information exchange and support the advancement of research and innovation in the chemical sciences.
+The chemistry domain encompasses the structured representation and formalization of chemical knowledge, including entities, reactions, processes, and methodologies. It plays a critical role in knowledge representation by enabling the integration, sharing, and computational analysis of chemical data across diverse subfields such as organic, inorganic, physical, and computational chemistry. This domain facilitates the advancement of scientific research and innovation by providing a standardized framework for the precise and interoperable exchange of chemical information.
 
 ## Ontologies
 | Ontology ID | Full Name | Classes | Properties | Last Updated |

afo/afo.rst

@@ -48,10 +48,10 @@ Breadth metrics
 Dataset Statistics
 ------------------
 Generated Benchmarks:
-    - **Term Types**: 38
-    - **Taxonomic Relations**: 9889
+    - **Term Types**: 37
+    - **Taxonomic Relations**: 6904
     - **Non-taxonomic Relations**: 34
-    - **Average Terms per Type**: 3.45
+    - **Average Terms per Type**: 3.36
 
 Usage Example
 -------------
@@ -61,7 +61,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = AFO()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.TTL")
 
     # Extract datasets
     data = ontology.extract()

afo/term_typings.json

@@ -0,0 +1,261 @@
+[
+  {
+    "ID": "TT_b44967a5",
+    "term": "copyright",
+    "types": [
+      "RightsStatement"
+    ]
+  },
+  {
+    "ID": "TT_2c135aad",
+    "term": "attribution",
+    "types": [
+      "RightsStatement"
+    ]
+  },
+  {
+    "ID": "TT_2e7abc5d",
+    "term": "iupac-copyright",
+    "types": [
+      "RightsStatement"
+    ]
+  },
+  {
+    "ID": "TT_d786159b",
+    "term": "valid",
+    "types": [
+      "data validity code"
+    ]
+  },
+  {
+    "ID": "TT_bc9a9558",
+    "term": "invalid",
+    "types": [
+      "data validity code"
+    ]
+  },
+  {
+    "ID": "TT_2189dfc1",
+    "term": "negative polarity",
+    "types": [
+      "polarity code"
+    ]
+  },
+  {
+    "ID": "TT_d8fb230b",
+    "term": "positive polarity",
+    "types": [
+      "polarity code"
+    ]
+  },
+  {
+    "ID": "TT_2d119903",
+    "term": "non-hygroscopic",
+    "types": [
+      "hygroscopicity code"
+    ]
+  },
+  {
+    "ID": "TT_de747818",
+    "term": "slightly hygroscopic",
+    "types": [
+      "hygroscopicity code"
+    ]
+  },
+  {
+    "ID": "TT_081f939a",
+    "term": "very hygroscopic",
+    "types": [
+      "hygroscopicity code"
+    ]
+  },
+  {
+    "ID": "TT_287b1e23",
+    "term": "deliquescent",
+    "types": [
+      "hygroscopicity code"
+    ]
+  },
+  {
+    "ID": "TT_cae03c0e",
+    "term": "hygroscopic",
+    "types": [
+      "hygroscopicity code"
+    ]
+  },
+  {
+    "ID": "TT_f6856c9b",
+    "term": "creative-commons-attribution-license",
+    "types": [
+      "LicenseDocument"
+    ]
+  },
+  {
+    "ID": "TT_8f69c203",
+    "term": "iupac-license",
+    "types": [
+      "LicenseDocument"
+    ]
+  },
+  {
+    "ID": "TT_bca90b1b",
+    "term": "fail (calibration)",
+    "types": [
+      "calibration assessment code"
+    ]
+  },
+  {
+    "ID": "TT_58d1099e",
+    "term": "indeterminate (calibration)",
+    "types": [
+      "calibration assessment code"
+    ]
+  },
+  {
+    "ID": "TT_f4de00bc",
+    "term": "pass (calibration)",
+    "types": [
+      "calibration assessment code"
+    ]
+  },
+  {
+    "ID": "TT_27ac5d2a",
+    "term": "machine direction",
+    "types": [
+      "sampling orientation code"
+    ]
+  },
+  {
+    "ID": "TT_0dc6682c",
+    "term": "cross direction",
+    "types": [
+      "sampling orientation code"
+    ]
+  },
+  {
+    "ID": "TT_3fec60be",
+    "term": "below",
+    "types": [
+      "position code"
+    ]
+  },
+  {
+    "ID": "TT_801dd455",
+    "term": "above",
+    "types": [
+      "position code"
+    ]
+  },
+  {
+    "ID": "TT_56ae0f77",
+    "term": "bottom",
+    "types": [
+      "position code"
+    ]
+  },
+  {
+    "ID": "TT_2585483c",
+    "term": "microscopic scale",
+    "types": [
+      "term granularity"
+    ]
+  },
+  {
+    "ID": "TT_37ca2fc0",
+    "term": "atomic scale",
+    "types": [
+      "term granularity"
+    ]
+  },
+  {
+    "ID": "TT_1b055484",
+    "term": "macroscopic scale",
+    "types": [
+      "term granularity"
+    ]
+  },
+  {
+    "ID": "TT_0b43ad69",
+    "term": "mesoscopic scale",
+    "types": [
+      "term granularity"
+    ]
+  },
+  {
+    "ID": "TT_6d79128e",
+    "term": "subatomic scale",
+    "types": [
+      "term granularity"
+    ]
+  },
+  {
+    "ID": "TT_48c0af49",
+    "term": "www.allotrope.org",
+    "types": [
+      "Organization"
+    ]
+  },
+  {
+    "ID": "TT_f1de9255",
+    "term": "www.rsc.org",
+    "types": [
+      "Organization"
+    ]
+  },
+  {
+    "ID": "TT_f89aaa4d",
+    "term": "cohesive peel",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_958cb427",
+    "term": "material elongation",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_c80b88eb",
+    "term": "material break",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_1ab5c4af",
+    "term": "delamination",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_c4c2ea8e",
+    "term": "adhesive peel",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_01d99f39",
+    "term": "material break (remote)",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_285f2a3e",
+    "term": "no seal",
+    "types": [
+      "break code"
+    ]
+  },
+  {
+    "ID": "TT_86247679",
+    "term": "peel with elongation",
+    "types": [
+      "break code"
+    ]
+  }
+]

afo/type_non_taxonomic_relations.json

@@ -0,0 +1,267 @@
+{
+  "types": [
+    "Collection",
+    "Concept",
+    "Concept Scheme",
+    "Organization",
+    "anode",
+    "cathode",
+    "chemical substance",
+    "contextual role",
+    "continuant",
+    "continuant fiat boundary",
+    "disposition",
+    "electrical and magnetic quality",
+    "electromagnetic radiation quality",
+    "formal organization",
+    "generically dependent continuant",
+    "height (quality)",
+    "history",
+    "immaterial entity",
+    "independent continuant",
+    "instant",
+    "material entity",
+    "negative charge",
+    "neutral charge",
+    "occurrent",
+    "one-dimensional continuant fiat boundary",
+    "one-dimensional spatial region",
+    "one-dimensional temporal region",
+    "organization",
+    "organizational unit",
+    "portion of bulk stuff",
+    "portion of compound",
+    "portion of element",
+    "portion of water",
+    "positive charge",
+    "process",
+    "process boundary",
+    "process profile",
+    "quality",
+    "realizable entity",
+    "role",
+    "site",
+    "spatial region",
+    "spatiotemporal region",
+    "specifically dependent continuant",
+    "temporal region",
+    "three-dimensional spatial region",
+    "two-dimensional continuant fiat boundary",
+    "two-dimensional spatial region",
+    "water (molecule)",
+    "zero-dimensional continuant fiat boundary",
+    "zero-dimensional spatial region",
+    "zero-dimensional temporal region"
+  ],
+  "relations": [
+    "disjointWith",
+    "equivalentClass",
+    "has close match"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_a83fb754",
+      "head": "material entity",
+      "tail": "immaterial entity",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_958d1ba1",
+      "head": "spatial region",
+      "tail": "site",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_915f5c37",
+      "head": "temporal region",
+      "tail": "spatiotemporal region",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_6cb1537b",
+      "head": "temporal region",
+      "tail": "process",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_5bc5e10c",
+      "head": "continuant",
+      "tail": "occurrent",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ce5fc4f9",
+      "head": "spatial region",
+      "tail": "continuant fiat boundary",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_bcfabe12",
+      "head": "temporal region",
+      "tail": "process boundary",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_75a05eac",
+      "head": "organization",
+      "tail": "Organization",
+      "relation": "has close match"
+    },
+    {
+      "ID": "NR_5524b536",
+      "head": "formal organization",
+      "tail": "organizational unit",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_02bd4574",
+      "head": "zero-dimensional temporal region",
+      "tail": "instant",
+      "relation": "equivalentClass"
+    },
+    {
+      "ID": "NR_9aa23633",
+      "head": "neutral charge",
+      "tail": "negative charge",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_9180b744",
+      "head": "zero-dimensional spatial region",
+      "tail": "three-dimensional spatial region",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_2c83f731",
+      "head": "contextual role",
+      "tail": "role",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_05b3c287",
+      "head": "one-dimensional spatial region",
+      "tail": "three-dimensional spatial region",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ffb481b3",
+      "head": "electrical and magnetic quality",
+      "tail": "electromagnetic radiation quality",
+      "relation": "has close match"
+    },
+    {
+      "ID": "NR_ab6c6ee7",
+      "head": "positive charge",
+      "tail": "negative charge",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_6ecd7b8b",
+      "head": "portion of compound",
+      "tail": "portion of element",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ddbb0a6e",
+      "head": "Collection",
+      "tail": "Concept",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_3f995bfe",
+      "head": "neutral charge",
+      "tail": "positive charge",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_4161b348",
+      "head": "independent continuant",
+      "tail": "specifically dependent continuant",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_16137cda",
+      "head": "one-dimensional continuant fiat boundary",
+      "tail": "zero-dimensional continuant fiat boundary",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ccea6eee",
+      "head": "process profile",
+      "tail": "history",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_6445d71f",
+      "head": "Concept",
+      "tail": "Concept Scheme",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_4763d205",
+      "head": "portion of water",
+      "tail": "water (molecule)",
+      "relation": "has close match"
+    },
+    {
+      "ID": "NR_c812b19f",
+      "head": "portion of bulk stuff",
+      "tail": "chemical substance",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_6bb23b69",
+      "head": "disposition",
+      "tail": "role",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_af278bd4",
+      "head": "two-dimensional spatial region",
+      "tail": "three-dimensional spatial region",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_4ca3f6cf",
+      "head": "one-dimensional continuant fiat boundary",
+      "tail": "two-dimensional continuant fiat boundary",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_b9f1475d",
+      "head": "height (quality)",
+      "tail": "height (quality)",
+      "relation": "has close match"
+    },
+    {
+      "ID": "NR_ad54970a",
+      "head": "anode",
+      "tail": "cathode",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_a3eb819f",
+      "head": "Collection",
+      "tail": "Concept Scheme",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_3e57340a",
+      "head": "independent continuant",
+      "tail": "generically dependent continuant",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_a6c6bb8c",
+      "head": "realizable entity",
+      "tail": "quality",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_9c48bbea",
+      "head": "one-dimensional temporal region",
+      "tail": "zero-dimensional temporal region",
+      "relation": "disjointWith"
+    }
+  ]
+}

chebi/chebi.rst

@@ -17,7 +17,7 @@ or classes of entities and their parents and/or children are specified.
 :Last Updated: 01/01/2025
 :Creator: None
 :License: Creative Commons 4.0
-:Format: OWL, OBO, JSON
+:Format: OWL
 :Download: `Chemical Entities of Biological Interest (ChEBI) Homepage <https://www.ebi.ac.uk/chebi/>`_
 
 Graph Metrics
@@ -51,8 +51,8 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 1200620
-    - **Non-taxonomic Relations**: 18607
+    - **Taxonomic Relations**: 739967
+    - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
 Usage Example
@@ -63,7 +63,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = ChEBI()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

chebi/term_typings.json

@@ -0,0 +1 @@
+[]

chebi/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

chebi/type_taxonomies.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2df932137641ad65d44f9879201daab8c4c7cb5303f3bac550a61281589df3a8
+size 117880585

cheminf/cheminf.rst

@@ -48,7 +48,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 594
+    - **Taxonomic Relations**: 95
     - **Non-taxonomic Relations**: 1
     - **Average Terms per Type**: 0.00
 
@@ -60,7 +60,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = CHEMINF()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

cheminf/term_typings.json

@@ -0,0 +1 @@
+[]

cheminf/type_non_taxonomic_relations.json

@@ -0,0 +1,17 @@
+{
+  "types": [
+    "numeric data item",
+    "textual data item"
+  ],
+  "relations": [
+    "disjointWith"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_c55a85db",
+      "head": "numeric data item",
+      "tail": "textual data item",
+      "relation": "disjointWith"
+    }
+  ]
+}

cheminf/type_taxonomies.json

@@ -0,0 +1,556 @@
+{
+  "types": [
+    "numeric parameter",
+    "LexiChem",
+    "GGA Indigo",
+    "CRID registry curation",
+    "ACD/Labs PhysChem software library version 12.01",
+    "RDKit software library version 2015_09_2",
+    "ChemSpider validated synonym",
+    "textual data item",
+    "Cactvs software library version 3.408",
+    "structural standardization information data item",
+    "parameter data item",
+    "CRID devalidation",
+    "cycle count",
+    "polar surface area descriptor calculated by Pipeline Pilot",
+    "rule of three passes calculated by pipeline pilot",
+    "ChemSpider title",
+    "OEChem software library",
+    "PubChem software library version 2.1",
+    "textual parameter",
+    "connection table interpretation information data item",
+    "SwissLipids identifier",
+    "number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01",
+    "software implementation",
+    "RDKit software library",
+    "InChI software library",
+    "chemical name deprecation",
+    "LipidMaps identifier",
+    "medchem friendly descriptor",
+    "molecular species at pH 7.4 calculated by ACD/Labs PhysChem software",
+    "XLogP3 software library",
+    "polar surface area calculated by ACD/Labs PhysChem software library version 12.01",
+    "Unique Ingredient Identifier",
+    "chemical database identifier",
+    "Pipeline Pilot library",
+    "PDB ligand identifier",
+    "information data item",
+    "RTECS identifier",
+    "OEChem software library version 1.7.6",
+    "InChI software library version 1.0.4",
+    "Cactvs software library",
+    "rule of five violations descriptor",
+    "chemical name validation",
+    "LexiChem version 2.2.0",
+    "chemical name devalidation",
+    "CRID deprecation",
+    "rule of five violations calculated by pipeline pilot",
+    "software method",
+    "structural validation information data item",
+    "logD descriptor",
+    "gravitational index",
+    "MolMeDB identifier",
+    "PDB structure identifier",
+    "software application",
+    "software module",
+    "OBI_0000011",
+    "gravitational index (square and cube roots)",
+    "PubChem software library",
+    "numeric data item",
+    "polar surface area descriptor",
+    "number of rule of five violations calculated by RDKit software library version 2015_09_2",
+    "aromatic cycle count",
+    "total polar surface area calculated by RDKit software library version 2015_09_2",
+    "ACD/Labs PhysChem software library",
+    "XLogP3 software library version 3.0",
+    "CRID validation",
+    "logD calculated at pH 7.4 by ACD/Labs PhysChem software",
+    "OEChem software library version 1.9.0",
+    "Pipeline Pilot Server Version 8.5.0",
+    "logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01",
+    "software library",
+    "molecular species at pH 7.4 descriptor",
+    "rule of three passes descriptor",
+    "National Service Center number",
+    "medchem friendly descriptor calculated by pipeline pilot",
+    "validated chemical database identifier"
+  ],
+  "taxonomies": [
+    {
+      "ID": "TR_20665e6c",
+      "parent": "OBI_0000011",
+      "child": "CRID registry curation"
+    },
+    {
+      "ID": "TR_12eb2657",
+      "parent": "software library",
+      "child": "Pipeline Pilot library"
+    },
+    {
+      "ID": "TR_2316a3ef",
+      "parent": "software library",
+      "child": "ACD/Labs PhysChem software library"
+    },
+    {
+      "ID": "TR_adeeb610",
+      "parent": "software library",
+      "child": "PubChem software library"
+    },
+    {
+      "ID": "TR_eb000b3c",
+      "parent": "software library",
+      "child": "RDKit software library"
+    },
+    {
+      "ID": "TR_84bcfb4a",
+      "parent": "software library",
+      "child": "GGA Indigo"
+    },
+    {
+      "ID": "TR_54c1b27b",
+      "parent": "GGA Indigo",
+      "child": "GGA Indigo"
+    },
+    {
+      "ID": "TR_f56cde49",
+      "parent": "software library",
+      "child": "OEChem software library"
+    },
+    {
+      "ID": "TR_ee49f91d",
+      "parent": "software library",
+      "child": "LexiChem"
+    },
+    {
+      "ID": "TR_72910d09",
+      "parent": "software library",
+      "child": "Cactvs software library"
+    },
+    {
+      "ID": "TR_15072d90",
+      "parent": "software library",
+      "child": "XLogP3 software library"
+    },
+    {
+      "ID": "TR_04457e99",
+      "parent": "software library",
+      "child": "InChI software library"
+    },
+    {
+      "ID": "TR_14589cdd",
+      "parent": "chemical database identifier",
+      "child": "validated chemical database identifier"
+    },
+    {
+      "ID": "TR_b81474bc",
+      "parent": "chemical database identifier",
+      "child": "Unique Ingredient Identifier"
+    },
+    {
+      "ID": "TR_e4cd6fb1",
+      "parent": "chemical database identifier",
+      "child": "LipidMaps identifier"
+    },
+    {
+      "ID": "TR_fdc10c48",
+      "parent": "chemical database identifier",
+      "child": "National Service Center number"
+    },
+    {
+      "ID": "TR_ac7e0d70",
+      "parent": "chemical database identifier",
+      "child": "RTECS identifier"
+    },
+    {
+      "ID": "TR_300030c9",
+      "parent": "chemical database identifier",
+      "child": "SwissLipids identifier"
+    },
+    {
+      "ID": "TR_c23b9760",
+      "parent": "chemical database identifier",
+      "child": "MolMeDB identifier"
+    },
+    {
+      "ID": "TR_abad5246",
+      "parent": "chemical database identifier",
+      "child": "PDB ligand identifier"
+    },
+    {
+      "ID": "TR_14b6d872",
+      "parent": "chemical database identifier",
+      "child": "PDB structure identifier"
+    },
+    {
+      "ID": "TR_bfb0a543",
+      "parent": "polar surface area descriptor",
+      "child": "polar surface area descriptor calculated by Pipeline Pilot"
+    },
+    {
+      "ID": "TR_792aa6a9",
+      "parent": "polar surface area descriptor",
+      "child": "total polar surface area calculated by RDKit software library version 2015_09_2"
+    },
+    {
+      "ID": "TR_c9747059",
+      "parent": "polar surface area descriptor",
+      "child": "polar surface area calculated by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_43e76dd0",
+      "parent": "polar surface area descriptor",
+      "child": "polar surface area descriptor calculated by Pipeline Pilot"
+    },
+    {
+      "ID": "TR_6a5564e1",
+      "parent": "rule of five violations descriptor",
+      "child": "rule of five violations calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_c0d55677",
+      "parent": "rule of five violations descriptor",
+      "child": "number of rule of five violations calculated by RDKit software library version 2015_09_2"
+    },
+    {
+      "ID": "TR_e712052b",
+      "parent": "rule of five violations descriptor",
+      "child": "number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_49050c76",
+      "parent": "rule of five violations descriptor",
+      "child": "rule of five violations calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_d3fce240",
+      "parent": "rule of three passes descriptor",
+      "child": "rule of three passes calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_b8c6532e",
+      "parent": "rule of three passes descriptor",
+      "child": "rule of three passes calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_c0eb921f",
+      "parent": "medchem friendly descriptor",
+      "child": "medchem friendly descriptor calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_04ce88ba",
+      "parent": "medchem friendly descriptor",
+      "child": "medchem friendly descriptor calculated by pipeline pilot"
+    },
+    {
+      "ID": "TR_528cbe19",
+      "parent": "logD descriptor",
+      "child": "logD calculated at pH 7.4 by ACD/Labs PhysChem software"
+    },
+    {
+      "ID": "TR_404c7d83",
+      "parent": "logD descriptor",
+      "child": "logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_6c8cf1d6",
+      "parent": "logD descriptor",
+      "child": "logD calculated at pH 7.4 by ACD/Labs PhysChem software"
+    },
+    {
+      "ID": "TR_c68a3ae3",
+      "parent": "molecular species at pH 7.4 descriptor",
+      "child": "molecular species at pH 7.4 calculated by ACD/Labs PhysChem software"
+    },
+    {
+      "ID": "TR_9c7b35c1",
+      "parent": "molecular species at pH 7.4 descriptor",
+      "child": "molecular species at pH 7.4 calculated by ACD/Labs PhysChem software"
+    },
+    {
+      "ID": "TR_f21b2d20",
+      "parent": "ACD/Labs PhysChem software library",
+      "child": "ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_67f484ef",
+      "parent": "Pipeline Pilot library",
+      "child": "Pipeline Pilot Server Version 8.5.0"
+    },
+    {
+      "ID": "TR_fb2555a6",
+      "parent": "RDKit software library",
+      "child": "RDKit software library version 2015_09_2"
+    },
+    {
+      "ID": "TR_83026ad2",
+      "parent": "rule of five violations descriptor",
+      "child": "number of rule of five violations calculated by RDKit software library version 2015_09_2"
+    },
+    {
+      "ID": "TR_7111da09",
+      "parent": "polar surface area descriptor",
+      "child": "total polar surface area calculated by RDKit software library version 2015_09_2"
+    },
+    {
+      "ID": "TR_9651d8de",
+      "parent": "PubChem software library",
+      "child": "PubChem software library version 2.1"
+    },
+    {
+      "ID": "TR_875dc147",
+      "parent": "software implementation",
+      "child": "software module"
+    },
+    {
+      "ID": "TR_757ecbb6",
+      "parent": "software implementation",
+      "child": "software method"
+    },
+    {
+      "ID": "TR_dcbb367c",
+      "parent": "software implementation",
+      "child": "software application"
+    },
+    {
+      "ID": "TR_6a556180",
+      "parent": "software implementation",
+      "child": "software module"
+    },
+    {
+      "ID": "TR_e7603ede",
+      "parent": "software implementation",
+      "child": "software method"
+    },
+    {
+      "ID": "TR_f054761b",
+      "parent": "software implementation",
+      "child": "software method"
+    },
+    {
+      "ID": "TR_8642e9d5",
+      "parent": "software implementation",
+      "child": "software method"
+    },
+    {
+      "ID": "TR_b5277e59",
+      "parent": "software application",
+      "child": "software library"
+    },
+    {
+      "ID": "TR_1bba62f0",
+      "parent": "software application",
+      "child": "software library"
+    },
+    {
+      "ID": "TR_19fa2d5f",
+      "parent": "logD descriptor",
+      "child": "logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_70b0cb9b",
+      "parent": "polar surface area descriptor",
+      "child": "polar surface area calculated by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_1d4bed2e",
+      "parent": "software library",
+      "child": "GGA Indigo"
+    },
+    {
+      "ID": "TR_6b6429e2",
+      "parent": "GGA Indigo",
+      "child": "GGA Indigo"
+    },
+    {
+      "ID": "TR_f3a61366",
+      "parent": "rule of five violations descriptor",
+      "child": "number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01"
+    },
+    {
+      "ID": "TR_8add136d",
+      "parent": "OEChem software library",
+      "child": "OEChem software library version 1.9.0"
+    },
+    {
+      "ID": "TR_01e4702a",
+      "parent": "OEChem software library",
+      "child": "OEChem software library version 1.7.6"
+    },
+    {
+      "ID": "TR_33bf86fb",
+      "parent": "cycle count",
+      "child": "aromatic cycle count"
+    },
+    {
+      "ID": "TR_97b89109",
+      "parent": "LexiChem",
+      "child": "LexiChem version 2.2.0"
+    },
+    {
+      "ID": "TR_d7745819",
+      "parent": "Cactvs software library",
+      "child": "Cactvs software library version 3.408"
+    },
+    {
+      "ID": "TR_e5f4ab62",
+      "parent": "XLogP3 software library",
+      "child": "XLogP3 software library version 3.0"
+    },
+    {
+      "ID": "TR_b58cf401",
+      "parent": "InChI software library",
+      "child": "InChI software library version 1.0.4"
+    },
+    {
+      "ID": "TR_6520ba84",
+      "parent": "chemical database identifier",
+      "child": "validated chemical database identifier"
+    },
+    {
+      "ID": "TR_84b55305",
+      "parent": "CRID registry curation",
+      "child": "CRID validation"
+    },
+    {
+      "ID": "TR_cd48363b",
+      "parent": "CRID registry curation",
+      "child": "chemical name devalidation"
+    },
+    {
+      "ID": "TR_479c8ce9",
+      "parent": "CRID registry curation",
+      "child": "chemical name validation"
+    },
+    {
+      "ID": "TR_e9efd877",
+      "parent": "CRID registry curation",
+      "child": "chemical name deprecation"
+    },
+    {
+      "ID": "TR_624de32d",
+      "parent": "CRID registry curation",
+      "child": "CRID deprecation"
+    },
+    {
+      "ID": "TR_b8ac6e5d",
+      "parent": "CRID registry curation",
+      "child": "CRID devalidation"
+    },
+    {
+      "ID": "TR_ee7880a6",
+      "parent": "CRID registry curation",
+      "child": "CRID validation"
+    },
+    {
+      "ID": "TR_98472235",
+      "parent": "CRID registry curation",
+      "child": "chemical name devalidation"
+    },
+    {
+      "ID": "TR_b8a1c53c",
+      "parent": "OBI_0000011",
+      "child": "CRID registry curation"
+    },
+    {
+      "ID": "TR_1bb7301f",
+      "parent": "CRID registry curation",
+      "child": "chemical name validation"
+    },
+    {
+      "ID": "TR_f3d87f4f",
+      "parent": "CRID registry curation",
+      "child": "chemical name deprecation"
+    },
+    {
+      "ID": "TR_61e6a7c0",
+      "parent": "CRID registry curation",
+      "child": "CRID deprecation"
+    },
+    {
+      "ID": "TR_2da79e8a",
+      "parent": "CRID registry curation",
+      "child": "CRID devalidation"
+    },
+    {
+      "ID": "TR_a038b147",
+      "parent": "ChemSpider validated synonym",
+      "child": "ChemSpider title"
+    },
+    {
+      "ID": "TR_6dfaba69",
+      "parent": "parameter data item",
+      "child": "numeric parameter"
+    },
+    {
+      "ID": "TR_234512d8",
+      "parent": "numeric data item",
+      "child": "numeric parameter"
+    },
+    {
+      "ID": "TR_f5c7b1d6",
+      "parent": "parameter data item",
+      "child": "textual parameter"
+    },
+    {
+      "ID": "TR_ddad2a08",
+      "parent": "textual data item",
+      "child": "textual parameter"
+    },
+    {
+      "ID": "TR_c53cc112",
+      "parent": "parameter data item",
+      "child": "numeric parameter"
+    },
+    {
+      "ID": "TR_d67acda2",
+      "parent": "numeric data item",
+      "child": "numeric parameter"
+    },
+    {
+      "ID": "TR_5ea2b2ad",
+      "parent": "parameter data item",
+      "child": "textual parameter"
+    },
+    {
+      "ID": "TR_667190ec",
+      "parent": "textual data item",
+      "child": "textual parameter"
+    },
+    {
+      "ID": "TR_01e5ef11",
+      "parent": "information data item",
+      "child": "connection table interpretation information data item"
+    },
+    {
+      "ID": "TR_c02ab9db",
+      "parent": "information data item",
+      "child": "structural standardization information data item"
+    },
+    {
+      "ID": "TR_3ff0b444",
+      "parent": "information data item",
+      "child": "structural validation information data item"
+    },
+    {
+      "ID": "TR_f00db8f0",
+      "parent": "information data item",
+      "child": "connection table interpretation information data item"
+    },
+    {
+      "ID": "TR_fb35736f",
+      "parent": "information data item",
+      "child": "structural standardization information data item"
+    },
+    {
+      "ID": "TR_f04430df",
+      "parent": "information data item",
+      "child": "structural validation information data item"
+    },
+    {
+      "ID": "TR_a2f8be80",
+      "parent": "gravitational index",
+      "child": "gravitational index (square and cube roots)"
+    }
+  ]
+}

chiro/chiro.rst

@@ -48,7 +48,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 27299
+    - **Taxonomic Relations**: 25262
     - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
@@ -60,7 +60,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = CHIRO()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

chiro/term_typings.json

@@ -0,0 +1 @@
+[]

chiro/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

chmo/chmo.rst

@@ -15,7 +15,7 @@ The Chemical Methods Ontology contains more than 3000 classes and describes meth
 :Last Updated: 2022-04-19
 :Creator: None
 :License: Creative Commons 4.0
-:Format: OWL, TTL, CSV, NT
+:Format: OWL
 :Download: `Chemical Methods Ontology (ChMO) Homepage <https://github.com/rsc-ontologies/rsc-cmo>`_
 
 Graph Metrics
@@ -49,8 +49,8 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 4268
-    - **Non-taxonomic Relations**: 114
+    - **Taxonomic Relations**: 3601
+    - **Non-taxonomic Relations**: 1
     - **Average Terms per Type**: 0.00
 
 Usage Example
@@ -61,7 +61,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = ChMO()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

chmo/term_typings.json

@@ -0,0 +1 @@
+[]

chmo/type_non_taxonomic_relations.json

@@ -0,0 +1,17 @@
+{
+  "types": [
+    "analyte role",
+    "matrix role"
+  ],
+  "relations": [
+    "disjointWith"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_722d17e4",
+      "head": "analyte role",
+      "tail": "matrix role",
+      "relation": "disjointWith"
+    }
+  ]
+}

fix/fix.rst

@@ -45,7 +45,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 2978
+    - **Taxonomic Relations**: 2751
     - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
@@ -57,7 +57,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = FIX()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

fix/term_typings.json

@@ -0,0 +1 @@
+[]

fix/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

massspectrometry/massspectrometry.rst

@@ -45,8 +45,8 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 16046
-    - **Non-taxonomic Relations**: 2
+    - **Taxonomic Relations**: 7016
+    - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
 Usage Example
@@ -57,7 +57,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = MassSpectrometry()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

massspectrometry/term_typings.json

@@ -0,0 +1 @@
+[]

massspectrometry/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

mop/mop.rst

@@ -46,8 +46,8 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 4171
-    - **Non-taxonomic Relations**: 47
+    - **Taxonomic Relations**: 3840
+    - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
 Usage Example
@@ -58,7 +58,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = MOP()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

mop/term_typings.json

@@ -0,0 +1 @@
+[]

mop/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

nmrcv/nmrcv.rst

@@ -71,7 +71,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = NMRCV()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

nmrcv/term_typings.json

@@ -0,0 +1 @@
+[]

nmrcv/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}

ontokin/ontokin.rst

@@ -45,7 +45,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 138
+    - **Taxonomic Relations**: 51
     - **Non-taxonomic Relations**: 1
     - **Average Terms per Type**: 0.00
 
@@ -57,7 +57,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = OntoKin()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

ontokin/term_typings.json

@@ -0,0 +1 @@
+[]

ontokin/type_non_taxonomic_relations.json

@@ -0,0 +1,17 @@
+{
+  "types": [
+    "RateCoefficient",
+    "ReactionRateCoefficient"
+  ],
+  "relations": [
+    "equivalentClass"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_f297f7c2",
+      "head": "ReactionRateCoefficient",
+      "tail": "RateCoefficient",
+      "relation": "equivalentClass"
+    }
+  ]
+}

ontokin/type_taxonomies.json

@@ -0,0 +1,303 @@
+{
+  "types": [
+    "SurfaceCoverageReaction",
+    "PLOGReaction",
+    "FallOffModelCoefficient",
+    "GasPhase",
+    "CHEBReaction",
+    "LindemannReaction",
+    "ArrheniusReaction",
+    "LiquidPhase",
+    "Phase",
+    "PublicationSpecification",
+    "ThermoModel",
+    "Species",
+    "Organization",
+    "SitePhase",
+    "Product",
+    "ThreeBodyReaction",
+    "LandauTellerReaction",
+    "ReverseReaction",
+    "GasPhaseReaction",
+    "BulkPhase",
+    "SolidPhase",
+    "FallOffReaction",
+    "RateCoefficient",
+    "SurfaceReaction",
+    "Reactant",
+    "PressureDependentReaction",
+    "SRIReaction",
+    "JournalSpecification",
+    "LandauTellerRateCoefficient",
+    "ArrheniusCoefficient",
+    "ForwardReaction",
+    "TroeReaction",
+    "CHEBRateCoefficient",
+    "Person",
+    "CoverageDependency",
+    "ProceedingsSpecification",
+    "Agent",
+    "ChemicalReaction",
+    "PreprintSpecification",
+    "StickingCoefficient",
+    "StickingCoefficientReaction",
+    "NASA"
+  ],
+  "taxonomies": [
+    {
+      "ID": "TR_1f7634a6",
+      "parent": "RateCoefficient",
+      "child": "ArrheniusCoefficient"
+    },
+    {
+      "ID": "TR_823ad696",
+      "parent": "RateCoefficient",
+      "child": "CHEBRateCoefficient"
+    },
+    {
+      "ID": "TR_68438d1b",
+      "parent": "RateCoefficient",
+      "child": "CoverageDependency"
+    },
+    {
+      "ID": "TR_8f81ca01",
+      "parent": "RateCoefficient",
+      "child": "FallOffModelCoefficient"
+    },
+    {
+      "ID": "TR_356d27ba",
+      "parent": "RateCoefficient",
+      "child": "LandauTellerRateCoefficient"
+    },
+    {
+      "ID": "TR_03f6b9c4",
+      "parent": "RateCoefficient",
+      "child": "StickingCoefficient"
+    },
+    {
+      "ID": "TR_280e684b",
+      "parent": "GasPhaseReaction",
+      "child": "ArrheniusReaction"
+    },
+    {
+      "ID": "TR_3c3c24ce",
+      "parent": "GasPhaseReaction",
+      "child": "LandauTellerReaction"
+    },
+    {
+      "ID": "TR_91acfbd7",
+      "parent": "GasPhaseReaction",
+      "child": "ThreeBodyReaction"
+    },
+    {
+      "ID": "TR_a27ea2eb",
+      "parent": "GasPhaseReaction",
+      "child": "ArrheniusReaction"
+    },
+    {
+      "ID": "TR_accbbe35",
+      "parent": "Phase",
+      "child": "BulkPhase"
+    },
+    {
+      "ID": "TR_9ce5340a",
+      "parent": "Phase",
+      "child": "GasPhase"
+    },
+    {
+      "ID": "TR_975004ab",
+      "parent": "Phase",
+      "child": "LiquidPhase"
+    },
+    {
+      "ID": "TR_ce0ea4ad",
+      "parent": "Phase",
+      "child": "SitePhase"
+    },
+    {
+      "ID": "TR_133ff331",
+      "parent": "Phase",
+      "child": "SolidPhase"
+    },
+    {
+      "ID": "TR_102d01b0",
+      "parent": "Phase",
+      "child": "BulkPhase"
+    },
+    {
+      "ID": "TR_6aaafa5c",
+      "parent": "PressureDependentReaction",
+      "child": "CHEBReaction"
+    },
+    {
+      "ID": "TR_58ad5a5b",
+      "parent": "PressureDependentReaction",
+      "child": "FallOffReaction"
+    },
+    {
+      "ID": "TR_3950dee9",
+      "parent": "PressureDependentReaction",
+      "child": "PLOGReaction"
+    },
+    {
+      "ID": "TR_4aa511ff",
+      "parent": "PressureDependentReaction",
+      "child": "CHEBReaction"
+    },
+    {
+      "ID": "TR_924d0543",
+      "parent": "PressureDependentReaction",
+      "child": "FallOffReaction"
+    },
+    {
+      "ID": "TR_5eabdf25",
+      "parent": "ChemicalReaction",
+      "child": "ForwardReaction"
+    },
+    {
+      "ID": "TR_a7d4926c",
+      "parent": "ChemicalReaction",
+      "child": "GasPhaseReaction"
+    },
+    {
+      "ID": "TR_713d7caa",
+      "parent": "ChemicalReaction",
+      "child": "ReverseReaction"
+    },
+    {
+      "ID": "TR_da313262",
+      "parent": "ChemicalReaction",
+      "child": "SurfaceReaction"
+    },
+    {
+      "ID": "TR_321ce714",
+      "parent": "Phase",
+      "child": "GasPhase"
+    },
+    {
+      "ID": "TR_443ce512",
+      "parent": "ChemicalReaction",
+      "child": "GasPhaseReaction"
+    },
+    {
+      "ID": "TR_9289a34c",
+      "parent": "PublicationSpecification",
+      "child": "JournalSpecification"
+    },
+    {
+      "ID": "TR_22044d89",
+      "parent": "PublicationSpecification",
+      "child": "PreprintSpecification"
+    },
+    {
+      "ID": "TR_aac0a117",
+      "parent": "PublicationSpecification",
+      "child": "ProceedingsSpecification"
+    },
+    {
+      "ID": "TR_20f1d783",
+      "parent": "PublicationSpecification",
+      "child": "JournalSpecification"
+    },
+    {
+      "ID": "TR_c153b953",
+      "parent": "GasPhaseReaction",
+      "child": "LandauTellerReaction"
+    },
+    {
+      "ID": "TR_40deca64",
+      "parent": "FallOffReaction",
+      "child": "LindemannReaction"
+    },
+    {
+      "ID": "TR_daf3b45c",
+      "parent": "FallOffReaction",
+      "child": "SRIReaction"
+    },
+    {
+      "ID": "TR_3c84565f",
+      "parent": "FallOffReaction",
+      "child": "TroeReaction"
+    },
+    {
+      "ID": "TR_0991a9a8",
+      "parent": "ThermoModel",
+      "child": "NASA"
+    },
+    {
+      "ID": "TR_e6a0d1eb",
+      "parent": "ThreeBodyReaction",
+      "child": "PressureDependentReaction"
+    },
+    {
+      "ID": "TR_72c4d1b5",
+      "parent": "Species",
+      "child": "Product"
+    },
+    {
+      "ID": "TR_2480a0dc",
+      "parent": "Species",
+      "child": "Reactant"
+    },
+    {
+      "ID": "TR_dc42261b",
+      "parent": "Species",
+      "child": "Reactant"
+    },
+    {
+      "ID": "TR_79e48739",
+      "parent": "Phase",
+      "child": "SitePhase"
+    },
+    {
+      "ID": "TR_c04e1cd1",
+      "parent": "SurfaceReaction",
+      "child": "StickingCoefficientReaction"
+    },
+    {
+      "ID": "TR_89926111",
+      "parent": "SurfaceReaction",
+      "child": "SurfaceCoverageReaction"
+    },
+    {
+      "ID": "TR_fc5d4be4",
+      "parent": "SurfaceReaction",
+      "child": "StickingCoefficientReaction"
+    },
+    {
+      "ID": "TR_5c368894",
+      "parent": "SurfaceReaction",
+      "child": "SurfaceCoverageReaction"
+    },
+    {
+      "ID": "TR_5648ee1e",
+      "parent": "ChemicalReaction",
+      "child": "SurfaceReaction"
+    },
+    {
+      "ID": "TR_ddc75aa8",
+      "parent": "ChemicalReaction",
+      "child": "SurfaceReaction"
+    },
+    {
+      "ID": "TR_134bc011",
+      "parent": "GasPhaseReaction",
+      "child": "ThreeBodyReaction"
+    },
+    {
+      "ID": "TR_d332c5a5",
+      "parent": "GasPhaseReaction",
+      "child": "ThreeBodyReaction"
+    },
+    {
+      "ID": "TR_60f36e19",
+      "parent": "Agent",
+      "child": "Organization"
+    },
+    {
+      "ID": "TR_1a83797f",
+      "parent": "Agent",
+      "child": "Person"
+    }
+  ]
+}

proco/proco.rst

@@ -46,7 +46,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 14
-    - **Taxonomic Relations**: 2975
+    - **Taxonomic Relations**: 1757
     - **Non-taxonomic Relations**: 1
     - **Average Terms per Type**: 7.00
 
@@ -58,7 +58,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = PROCO()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

proco/term_typings.json

@@ -0,0 +1,100 @@
+[
+  {
+    "ID": "TT_298e6b51",
+    "term": "terms merged",
+    "types": [
+      "obsolescence reason specification"
+    ]
+  },
+  {
+    "ID": "TT_6c871fb5",
+    "term": "term split",
+    "types": [
+      "obsolescence reason specification"
+    ]
+  },
+  {
+    "ID": "TT_67bdb31f",
+    "term": "term imported",
+    "types": [
+      "obsolescence reason specification"
+    ]
+  },
+  {
+    "ID": "TT_1a09c3cb",
+    "term": "placeholder removed",
+    "types": [
+      "obsolescence reason specification"
+    ]
+  },
+  {
+    "ID": "TT_92d7cb81",
+    "term": "failed exploratory term",
+    "types": [
+      "obsolescence reason specification"
+    ]
+  },
+  {
+    "ID": "TT_d375489a",
+    "term": "uncurated",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_eb571099",
+    "term": "organizational term",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_0f2a1d2c",
+    "term": "requires discussion",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_0ad6e94c",
+    "term": "pending final vetting",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_3201dd7b",
+    "term": "metadata complete",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_7bbc6475",
+    "term": "metadata incomplete",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_9a3cd7d5",
+    "term": "ready for release",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_0b5dd5cd",
+    "term": "example to be eventually removed",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_f7943604",
+    "term": "to be replaced with external ontology term",
+    "types": [
+      "curation status specification"
+    ]
+  }
+]

proco/type_non_taxonomic_relations.json

@@ -0,0 +1,17 @@
+{
+  "types": [
+    "Graham condensor",
+    "coil condenser"
+  ],
+  "relations": [
+    "disjointWith"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_3825244e",
+      "head": "Graham condensor",
+      "tail": "coil condenser",
+      "relation": "disjointWith"
+    }
+  ]
+}

psimod/psimod.rst

@@ -49,7 +49,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 8347
+    - **Taxonomic Relations**: 7913
     - **Non-taxonomic Relations**: 0
     - **Average Terms per Type**: 0.00
 
@@ -61,7 +61,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = PSIMOD()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()

psimod/term_typings.json

@@ -0,0 +1 @@
+[]

psimod/type_non_taxonomic_relations.json

@@ -0,0 +1,5 @@
+{
+  "types": [],
+  "relations": [],
+  "non_taxonomies": []
+}