Merge pull request #196 from monarch-initiative/240812-documentation

Axiom documentation

docs/ontologymodeling/axioms.md

@@ -1,3 +1,52 @@
 # Axioms in VBO
 
-_Documentation upcoming_
+Logical axioms are relational information about classes that are primarily aimed at machines. They relate terms within the same ontology and across ontologies. They provide context, allow reasoners to assist in and verify classification, and support complex computational queries. 
+Read more information about logical axiomatization [here](https://oboacademy.github.io/obook/explanation/logical-axiomatization/).
+
+
+## “has foundation stock” axioms
+
+Breeds are often created by crossing other breeds whose traits and/or pedigrees are desirable. The animals that are the progenitors, or foundation, of a breed are called “foundation stock”; they provide part of the underlying genetic base for a new distinct population. (https://en.wikipedia.org/wiki/Foundation_stock). Knowing the “foundation stock(s)” of a breed is often of great interest for example in breeding programs to understand the frequency of a disease allele in a population.  
+
+**Object**: VBO term representing a breed
+“has foundation stock” axiom is added to a VBO term representing a breed (it should be noted that there is no indication in the ontology whether a term represents a breed, a sub-breed, a variety, etc). The following terms should not have a “has foundation stock” SubClassOf annotation: 
+- NCBITaxom term representing a species, genus, family, etc
+- VBO term representing a grouping class (e.g. “dog breed”, “cattle breed”, etc)
+
+**Relation**: has_foundation_stock
+
+- ‘has_foundation_stock’ (VBO:0300019). 
+It should be noted that this relation is currently created in VBO. We plan on submitting it to the Relation Ontology (RO). If in scope, new relations are created in RO, the RO term will replace the current VBO relation.
+- Definition: “a relation between two distinct material entities (breeds or species), a descendant entity and an ancestor entity, in which the descendant entity is the result of mating, manipulation, or geographical or cultural isolation of the ancestor entity, therefore inheriting some of the ancestor’s genetic material.” 
+
+**Target**: VBO term or NCBITaxon term
+Targets allowed includes: 
+- VBO term representing a breed
+   - example: ‘Cymric (Cat)’ VBO:0100080 has_foundation_stock ‘Manx (Cat)’ VBO:0100156
+- NCBITaxon representing species
+   - Breed created by crossing with “wild” animals of the same species. 
+   - Breed created by crossing with a group of animal from another species (where no actual breed of this another species is recorded): 
+        - example: ‘Kanaani (Cat)’ VBO:0100137 has_foundation_stock ‘African Wildcat’ NCBITaxon:61377
+
+**Notes**:
+- A term can have multiple “has foundation stock” SubClassOf 
+   - example: 'Himalayan (Cat)' (VBO:0100117) was created from a cross of individuals from 'Siamese (Cat)' (VBO:0100221) and 'Persian (Cat)' (VBO:0100188) 
+- A lot of the information about “foundation stock” is provided in breed descriptions and histories issued by the breed sources. These sources are recorded as “source” annotation of the SubClassOf axiom. 
+- Currently, a lot of “foundation stock” information is available in the “description of origin” annotation, and not yet as “SubClassOf” annotation. Ongoing work extract this information from the free text note to create these “SubClassOf” annotations.
+
+## “located_in some Country” axioms
+
+Most breeds in DAD-IS [link to DAD-IS source] represent breed populations that exist in a specific country as reported by officially nominated National Coordinators. Therefore the concept of these DAD-IS breeds specifically represent a “breed that exists in a specific country”. This concept is unique to DAD-IS and its goals. (LINK) 
+
+**Object**: VBO term representing a DAD-IS “local breeds” or “national breed population” 
+- “national breed population” refers to the existence of a particular breed in a particular country. For example, a breed of chicken called “Alatau” reported to exist in Kyrgyzstan (VBO:0007427)
+- “local breed” refers to a country specific instance of a same breed that exists in each of several countries (itself called “transboundary” breed). (see example below)
+
+**Relation**: located_in (RO:0001025)
+
+**Target**: Country (Wikidata ID for country)
+
+**Notes**: 
+- This SubClassOf should **only** be used for breeds reported from DAD-IS, i.e. representing a breed defined as existing in a country. This concept will rarely exists outside of DAD-IS.
+   - example: ‘Jersey Giant, Canada; Chicken’ (VBO:0006068)
+