Update agricultural domain with 3 ontologies

.gitattributes

@@ -59,3 +59,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
 agrovoc/agrovoc.rdf filter=lfs diff=lfs merge=lfs -text
 foodon/foodon.owl filter=lfs diff=lfs merge=lfs -text
+foodon/type_taxonomies.json filter=lfs diff=lfs merge=lfs -text

agrovoc/agrovoc.rst

@@ -14,7 +14,7 @@ indexing processes and making searches more efficient.
 :Last Updated: August 12, 2024
 :Creator: Food and Agriculture Organization of the United Nations
 :License: Creative Commons 4.0
-:Format: RDF, SKOS
+:Format: RDF
 :Download: `AGROVOC Multilingual Thesaurus (AGROVOC) Homepage <https://agroportal.lirmm.fr/ontologies/AGROVOC>`_
 
 Graph Metrics
@@ -47,10 +47,10 @@ Breadth metrics
 Dataset Statistics
 ------------------
 Generated Benchmarks:
-    - **Term Types**: 1234769
-    - **Taxonomic Relations**: 13
+    - **Term Types**: 12
+    - **Taxonomic Relations**: 11
     - **Non-taxonomic Relations**: 7
-    - **Average Terms per Type**: 137196.56
+    - **Average Terms per Type**: 3.00
 
 Usage Example
 -------------
@@ -60,7 +60,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = AGROVOC()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.RDF")
 
     # Extract datasets
     data = ontology.extract()
@@ -68,4 +68,4 @@ Usage Example
     # Access specific relations
     term_types = data.term_typings
     taxonomic_relations = data.type_taxonomies
-    non_taxonomic_relations = data.type_non_taxonomic_relations
+    non_taxonomic_relations = data.type_non_taxonomic_relations

agrovoc/term_typings.json

@@ -0,0 +1,86 @@
+[
+  {
+    "ID": "TT_68bce476",
+    "term": "LCSH",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_59e9ed4c",
+    "term": "DDC",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_5ab9855c",
+    "term": "IMT",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_5706ff33",
+    "term": "LCC",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_5181f950",
+    "term": "MeSH",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_0fe6cb03",
+    "term": "NLM",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_1f588b35",
+    "term": "DCMI Type Vocabulary",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_8742af7d",
+    "term": "TGN",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_78af92a9",
+    "term": "UDC",
+    "types": [
+      "VocabularyEncodingScheme"
+    ]
+  },
+  {
+    "ID": "TT_07ae217e",
+    "term": "Agent",
+    "types": [
+      "Agent Class"
+    ]
+  },
+  {
+    "ID": "TT_608bd9a8",
+    "term": "agrontology",
+    "types": [
+      "Vocabulary"
+    ]
+  },
+  {
+    "ID": "TT_d0f36656",
+    "term": "agrovoc",
+    "types": [
+      "Concept Scheme"
+    ]
+  }
+]

agrovoc/type_non_taxonomic_relations.json

@@ -0,0 +1,58 @@
+{
+  "types": [
+    "Agent",
+    "Agent Class",
+    "Collection",
+    "Concept",
+    "Concept Scheme",
+    "Label"
+  ],
+  "relations": [
+    "disjointWith",
+    "type"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_02f44148",
+      "head": "Agent",
+      "tail": "Agent Class",
+      "relation": "type"
+    },
+    {
+      "ID": "NR_7f1e10e8",
+      "head": "Collection",
+      "tail": "Concept Scheme",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_45a0d9a4",
+      "head": "Collection",
+      "tail": "Label",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ab1093a6",
+      "head": "Collection",
+      "tail": "Concept",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_4f2114fe",
+      "head": "Concept Scheme",
+      "tail": "Label",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_473625f4",
+      "head": "Concept",
+      "tail": "Concept Scheme",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_d49edadd",
+      "head": "Concept",
+      "tail": "Label",
+      "relation": "disjointWith"
+    }
+  ]
+}

agrovoc/type_taxonomies.json

@@ -0,0 +1,77 @@
+{
+  "types": [
+    "Agent Class",
+    "Class",
+    "Size or Duration",
+    "Nothing",
+    "Location",
+    "Rights Statement",
+    "File Format",
+    "Location, Period, or Jurisdiction",
+    "License Document",
+    "Ordered Collection",
+    "Period of Time",
+    "Media Type or Extent",
+    "Media Type",
+    "Collection",
+    "Jurisdiction",
+    "Physical Medium"
+  ],
+  "taxonomies": [
+    {
+      "ID": "TR_7ee717cd",
+      "parent": "Class",
+      "child": "Agent Class"
+    },
+    {
+      "ID": "TR_8629b49e",
+      "parent": "Media Type",
+      "child": "File Format"
+    },
+    {
+      "ID": "TR_21c931d5",
+      "parent": "Media Type",
+      "child": "Physical Medium"
+    },
+    {
+      "ID": "TR_8d29e751",
+      "parent": "Location, Period, or Jurisdiction",
+      "child": "Jurisdiction"
+    },
+    {
+      "ID": "TR_0a804f20",
+      "parent": "Location, Period, or Jurisdiction",
+      "child": "Location"
+    },
+    {
+      "ID": "TR_ba78a5eb",
+      "parent": "Location, Period, or Jurisdiction",
+      "child": "Period of Time"
+    },
+    {
+      "ID": "TR_10be7809",
+      "parent": "Rights Statement",
+      "child": "License Document"
+    },
+    {
+      "ID": "TR_9dbae154",
+      "parent": "Media Type or Extent",
+      "child": "Media Type"
+    },
+    {
+      "ID": "TR_8ebe6099",
+      "parent": "Media Type or Extent",
+      "child": "Size or Duration"
+    },
+    {
+      "ID": "TR_77dcb5ec",
+      "parent": "Nothing",
+      "child": "Nothing"
+    },
+    {
+      "ID": "TR_8f893064",
+      "parent": "Collection",
+      "child": "Ordered Collection"
+    }
+  ]
+}

foodon/foodon.rst

@@ -49,7 +49,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 16
-    - **Taxonomic Relations**: 98513
+    - **Taxonomic Relations**: 76235
     - **Non-taxonomic Relations**: 2072
     - **Average Terms per Type**: 8.00
 
@@ -61,7 +61,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = FoodOn()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()
@@ -69,4 +69,4 @@ Usage Example
     # Access specific relations
     term_types = data.term_typings
     taxonomic_relations = data.type_taxonomies
-    non_taxonomic_relations = data.type_non_taxonomic_relations
+    non_taxonomic_relations = data.type_non_taxonomic_relations

foodon/term_typings.json

@@ -0,0 +1,114 @@
+[
+  {
+    "ID": "TT_541ebb4e",
+    "term": "time:unitHour",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_b28b3070",
+    "term": "time:unitMonth",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_2e5a9086",
+    "term": "time:unitDay",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_2675190c",
+    "term": "time:unitWeek",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_70fa983d",
+    "term": "time:unitYear",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_e8256b04",
+    "term": "time:unitSecond",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_d8f9c586",
+    "term": "time:unitMinute",
+    "types": [
+      "Temporal Unit"
+    ]
+  },
+  {
+    "ID": "TT_98357a96",
+    "term": "uncurated",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_9fd1ff62",
+    "term": "requires discussion",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_81f000a3",
+    "term": "organizational term",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_5c32afe5",
+    "term": "ready for release",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_3aa00569",
+    "term": "example to be eventually removed",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_29ff5d86",
+    "term": "metadata complete",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_d4a73a40",
+    "term": "pending final vetting",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_bc28ce69",
+    "term": "metadata incomplete",
+    "types": [
+      "curation status specification"
+    ]
+  },
+  {
+    "ID": "TT_ba3d9c62",
+    "term": "to be replaced with external ontology term",
+    "types": [
+      "curation status specification"
+    ]
+  }
+]

foodon/type_taxonomies.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1cff380f3fb4cc501fa5cd06deba2e399005c2f52d550c9e38d9bb5ac5606959
+size 10561464

po/po.rst

@@ -12,7 +12,7 @@ morphology and growth and development to plant genomics data.
 :Last Updated: None
 :Creator: None
 :License: Creative Commons 4.0
-:Format: OWL, TTL, CSV, NT
+:Format: OWL
 :Download: `Plant Ontology (PO) Homepage <https://github.com/Planteome/plant-ontology>`_
 
 Graph Metrics
@@ -46,7 +46,7 @@ Dataset Statistics
 ------------------
 Generated Benchmarks:
     - **Term Types**: 0
-    - **Taxonomic Relations**: 5288
+    - **Taxonomic Relations**: 2866
     - **Non-taxonomic Relations**: 36
     - **Average Terms per Type**: 0.00
 
@@ -58,7 +58,7 @@ Usage Example
 
     # Initialize and load ontology
     ontology = PO()
-    ontology.load("path/to/ontology.owl")
+    ontology.load("path/to/ontology.OWL")
 
     # Extract datasets
     data = ontology.extract()
@@ -66,4 +66,4 @@ Usage Example
     # Access specific relations
     term_types = data.term_typings
     taxonomic_relations = data.type_taxonomies
-    non_taxonomic_relations = data.type_non_taxonomic_relations
+    non_taxonomic_relations = data.type_non_taxonomic_relations

po/term_typings.json

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

po/type_non_taxonomic_relations.json

@@ -0,0 +1,260 @@
+{
+  "types": [
+    "cambial initial cell",
+    "cardinal organ part",
+    "collective organ part structure",
+    "collective plant organ structure",
+    "free tepal",
+    "fruit operculum",
+    "fused tepal",
+    "gametophyte perianth",
+    "guard cell",
+    "hydroid",
+    "hydrome",
+    "leptoid",
+    "leptome",
+    "perianth",
+    "phloem",
+    "plant cell",
+    "plant epidermal initial cell",
+    "plant organ",
+    "portion of plant tissue",
+    "protonema side branch initial cell",
+    "protonema sub-apical initial cell",
+    "protosporangium endothecium",
+    "root initial cell",
+    "root system",
+    "shoot epidermal pavement cell",
+    "shoot system",
+    "sieve element",
+    "socket cell",
+    "sporangium wall endothecium",
+    "spore capsule operculum",
+    "subsidiary cell",
+    "tracheary element",
+    "trichome cell",
+    "vascular system",
+    "xylem"
+  ],
+  "relations": [
+    "disjointWith"
+  ],
+  "non_taxonomies": [
+    {
+      "ID": "NR_fc1c1f6e",
+      "head": "portion of plant tissue",
+      "tail": "cardinal organ part",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_b8401239",
+      "head": "cambial initial cell",
+      "tail": "protonema side branch initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_3ecc9a05",
+      "head": "sporangium wall endothecium",
+      "tail": "protosporangium endothecium",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_217f2139",
+      "head": "root initial cell",
+      "tail": "protonema side branch initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_b07d960e",
+      "head": "plant cell",
+      "tail": "cardinal organ part",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_980203d6",
+      "head": "portion of plant tissue",
+      "tail": "plant organ",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_a4ed6df0",
+      "head": "cambial initial cell",
+      "tail": "protonema sub-apical initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_b7286c34",
+      "head": "guard cell",
+      "tail": "shoot epidermal pavement cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_938760aa",
+      "head": "free tepal",
+      "tail": "fused tepal",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_009bfaf1",
+      "head": "root initial cell",
+      "tail": "protonema sub-apical initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_6dac801c",
+      "head": "plant cell",
+      "tail": "plant organ",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_e62ba919",
+      "head": "xylem",
+      "tail": "hydrome",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_20f4e164",
+      "head": "root initial cell",
+      "tail": "cambial initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_e1ed5709",
+      "head": "portion of plant tissue",
+      "tail": "collective plant organ structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_4e25c715",
+      "head": "portion of plant tissue",
+      "tail": "collective organ part structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_1784788a",
+      "head": "subsidiary cell",
+      "tail": "shoot epidermal pavement cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_68f5f320",
+      "head": "shoot epidermal pavement cell",
+      "tail": "trichome cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_559fe1ca",
+      "head": "vascular system",
+      "tail": "plant cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_7ed4aab0",
+      "head": "plant cell",
+      "tail": "collective organ part structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_cece7ddd",
+      "head": "leptoid",
+      "tail": "sieve element",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_619baffb",
+      "head": "socket cell",
+      "tail": "shoot epidermal pavement cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_0d41dd6f",
+      "head": "plant cell",
+      "tail": "collective plant organ structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_52417536",
+      "head": "perianth",
+      "tail": "gametophyte perianth",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_e51a9670",
+      "head": "vascular system",
+      "tail": "cardinal organ part",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_22a39a29",
+      "head": "cambial initial cell",
+      "tail": "plant epidermal initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_384de60b",
+      "head": "phloem",
+      "tail": "leptome",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_bde5ba2d",
+      "head": "tracheary element",
+      "tail": "hydroid",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_ed6fce6c",
+      "head": "root initial cell",
+      "tail": "plant epidermal initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_5661a1dd",
+      "head": "vascular system",
+      "tail": "plant organ",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_bf5638fe",
+      "head": "plant epidermal initial cell",
+      "tail": "protonema side branch initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_b7625d54",
+      "head": "vascular system",
+      "tail": "collective organ part structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_628857d9",
+      "head": "plant cell",
+      "tail": "portion of plant tissue",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_a4e425e0",
+      "head": "plant epidermal initial cell",
+      "tail": "protonema sub-apical initial cell",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_341c5b3c",
+      "head": "vascular system",
+      "tail": "collective plant organ structure",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_7c29bb1a",
+      "head": "shoot system",
+      "tail": "root system",
+      "relation": "disjointWith"
+    },
+    {
+      "ID": "NR_7cfd5334",
+      "head": "fruit operculum",
+      "tail": "spore capsule operculum",
+      "relation": "disjointWith"
+    }
+  ]
+}