Merge pull request #192 from monarch-initiative/240730-doc

VBO classification documentation

docs/ontologymodeling/classification.md

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 # VBO Classification
 
-_Documentation upcoming_
+## High-level classification
+VBO breed terms are classified under the general term ‘Vertebrate breed’ (VBO:0400000) and grouped based on specific animal species (e.g., ‘Dog breed’) or group of animals of the same genus (‘Cattle breed’) based on community and expert usage and jargon. 
+
+**VBO high-level classification:** 
+
+<img src="image.png" width="300">
+
+
+## VBO is integrated within the NCBITaxon hierarchy.
+Breeds are identified as distinctive groups within a family, genus, or species. Therefore, in the ontology, breeds are subclasses of family/genus/species represented by NCBITaxon entities. 
+Based on the broad definition of vertebrate breed, “a group of animals that share specific characteristics that distinguish it from other organisms of the same family/genus/species (...)”, breeds were created as subclasses of family/genus/species, which are represented by the NCBITaxon entities. Hence VBO terms are integrated within the NCBITaxon hierarchy using the is_a relation. 
+One of the advantages is that VBO terms can be autoclassified based on the NCBITaxon hierarchy.
+
+**Example:** ‘Cattle breed’ (VBO:0400020) is defined as: ‘Vertebrate breed’ **and** Bos (NCBITaxon:9903). Bos indicus (zebu cattle, NCBITaxon:9915), Bos taurus (cattle, NCBITaxon:9913), Bos indicus × Bos taurus (hybrid cattle, NCBITaxon:30522), and Bos grunniens (yak, NCBITaxon:30521), are all autoclassified as ‘Cattle breed’ via the NCBITaxon hierarchy.
+
+<img src="Screenshot 2024-07-30 at 12.52.48 PM.png" width="800">
+
+## Sub-breeds, strains, variety, etc
+Distinguishable sub-breeds, strains, or varieties are also included in VBO and are related to the ontological parent breed using an is_a relation.17–19 For example, 'Chihuahua, Long-Haired (Dog)' (VBO:0200339) and 'Chihuahua, Smooth-Haired (Dog)' (VBO:0200340) are subclasses of 'Chihuahua (Dog)' (VBO:0200338).
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+<img src="Screenshot 2024-07-30 at 12.49.22 PM.png" width="350">
+
+## DAD-IS Breeds reported in a specific country
+Breeds defined as having been reported in a specific country by National Coordinators in DAD-IS are either 
+- direct subclasses of their corresponding NCBITaxon (see cattle breeds above: 'Guraghe, Ethiopia (Cattle)', subclass of _Bos indicus_)
+- subclasses of other breeds (see cattle breeds above: 'Aberdeen Angus, Brazil (Cattle)', subclass of 'Aberdeen-Angus (Cattle)')