Update documentation

docs/cite.md

@@ -1,4 +1,4 @@
 # How to cite VBO
 
 Use the following DOI to cite VBO:
-doi: https://doi.org/10.5281/zenodo.7996674
+doi: https://doi.org/10.48550/arXiv.2406.02623

docs/general/general.md

@@ -8,7 +8,7 @@ VBO serves as a single, computable resource for vertebrate breed names. It is us
 VBO is restricted to non-human vertebrate animal species. It covers breeds and breed populations for livestock, companion animals, and laboratory animals.
 
 ## What is a breed in VBO?  
-Maybe definitions of 'breed' exist in the literature and in different communities. In VBO, a 'breed' is defined as : a group of animals that share specific characteristics (such as traits, behavior,...) that distinguish it from other organisms of the same species, and/or which cultural or geographical separation has led to the general acceptance of its separate identity.
+Many definitions of 'breed' exist in the literature and in different communities. In VBO, a 'breed' is defined as: A taxonomic entity representing a population of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) and/or for which cultural or geographical separation has led to the general acceptance of its separate identity.
 
 Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature (see table below).
 

docs/ontologymodeling/axioms.md

@@ -4,49 +4,52 @@ Logical axioms are relational information about classes that are primarily aimed
 Read more information about logical axiomatization [here](https://oboacademy.github.io/obook/explanation/logical-axiomatization/).
 
 
-## “has foundation stock” axioms
+## “has foundation stock” axiom
 
-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.  
+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] (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)
+- 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
+**Relation**: has foundation stock
 
-- ‘has_foundation_stock’ (VBO:0300019). 
+- ‘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
+   - 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
+   - Breed created by crossing with a group of animals 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.
+- Currently, a lot of “foundation stock” information is available in the “description of origin” annotation, and not yet as “SubClassOf” annotation. Work is underway to extract this information from the free text note to create these “SubClassOf” annotations.
 
-## “located_in some Country” axioms
+## “breed reported in geographic location” axiom
 
-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) 
+Most breeds in [DAD-IS] (https://www.fao.org/dad-is/en/) 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 [https://www.fao.org/dad-is/en/] (https://www.fao.org/dad-is/en/).
 
 **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)
+- “local breed” refers to a country specific instance of a same breed that exists in each of several countries (itself called “transboundary” breed). (Example: ‘Jersey Giant, Canada (Chicken)’ (VBO:0006068) and 'Jersey Giant, Ireland (Chicken)' (VBO:0006071) are local breeds with the transboundary parent term 'Jersey Giant (Chicken)' (VBO:0000547))
 
-**Relation**: located_in (RO:0001025)
+**Relation**: breed reported in geographic location
+
+- ‘breed reported in geographic location’ (VBO:0300020). 
+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 a breed and the geographic location where the breed was reported to exist by country-nominated FAO National Coordinators.” 
 
 **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)
-
+- 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.
+- VBO terms with this SubClassOf axiom should have the following rdfs:comment, "The concept of “breed reported in geographic location by FAO National Coordinators” is unique to DAD-IS [https://www.fao.org/dad-is/en/] (https://www.fao.org/dad-is/en/). This VBO term should therefore be used specifically for the breed conforming to this concept."

docs/ontologymodeling/classification.md

@@ -1,28 +1,27 @@
 # VBO Classification
 
 ## 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 breed terms are classified under the general term ‘Vertebrate breed’ (VBO:0400000) and grouped, for example, based on specific animal species (e.g., ‘Horse breed’) or 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. 
+Breeds are identified as distinctive entities within a family, genus, species or subspecies. Therefore, in the ontology, breeds are subclasses of family/genus/species represented by NCBITaxon entities. Based on the broad definition of vertebrate breed, “a taxonomic entity representing a population of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) and/or for which cultural or geographical separation has led to the general acceptance of its separate identity,” breeds were created as subclasses of family/genus/species/subspecies, 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).
+Distinguishable sub-breeds, strains, or varieties are also included in VBO and are related to the ontological parent breed using an is_a relation. For example, 'Chihuahua, Long-Haired (Dog)' (VBO:0200339) and 'Chihuahua, Smooth-Haired (Dog)' (VBO:0200340) are subclasses of 'Chihuahua (Dog)' (VBO:0200338).
 
 <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)')
+- subclasses of other breeds (see cattle breeds above: 'Aberdeen Angus, Brazil (Cattle)', subclass of 'Aberdeen-Angus (Cattle)')

docs/ontologymodeling/metadata.md

@@ -37,7 +37,7 @@ Term labels are unique and follow the format:
 - **'Most common name (Species)’**
 in which Species is the English name (e.g. 'Chihuahua (Dog)' (VBO:0200338)). 
 - **'Most common name, Country; (Species)'**
-in which Country and Species are the English names. (e.g., ‘Jersey Giant, Canada; Chicken’ (VBO:0006068)). This format is used for breeds defined by their country of existence as reported by FAO National Coordinators in DAD-IS.
+in which Country and Species are the English names. (e.g., ‘Jersey Giant, Canada (Chicken)’ (VBO:0006068)). This format is used for breeds defined by their country of existence as reported by FAO National Coordinators in DAD-IS.
 
 See more explanation in the [term labels and naming conventions](ontologymodeling/term-labels-naming-conventions.md) section.
 

docs/ontologymodeling/term-labels-naming-conventions.md

@@ -7,7 +7,7 @@ To create unique VBO term labels, we concatenated the breed’s most common name
 
 The “Most common name” represents the breed name that is most often used to refer to the breed, as determined by the information found in the sources (_LINK to be added_). This ‘most common name’ is also recorded as an “exact synonym” [_LINK to be added_]. All breed names, including the one that are shared between breeds, are available as synonyms in VBO. For example, an exact synonym of Tibetan (Goat) VBO:0000845 is Tibetan. 
 
-Including the ‘Species’ in the term label could be controversial. Breeds have a is_a relationship to a species, and therefore repeating the species name (ie ontological parentage) in the label is a break with standard ontology practices.  While we recognize that this solution is not ideal, we were unable to ensure term label uniqueness without including the species name in the term label. As exemplified above, breeds from different species can share the same name, and some breeds can share identical name with other types of entities such as countries. 
+Including the ‘Species’ in the term label could be controversial. Breeds have a is_a relationship to a species, and therefore repeating the species name (i.e., ontological parentage) in the label is a break with standard ontology practices.  While we recognize that this solution is not ideal, we were unable to ensure term label uniqueness without including the species name in the term label. As exemplified above, breeds from different species can share the same name, and some breeds can share identical name with other types of entities such as countries. 
 
 
 **The case of DAD-IS “national breed population” and “local breeds”.** 
@@ -20,5 +20,5 @@ As a consequence, it is very common to find breeds in DAD-IS with the same commo
 The naming convention reported above, based on “most common name” and “species” is therefore not sufficient to ensure term label uniqueness for DAD-IS “national breed population” and “local breed”. The country where the breed has been reported by the National Coordinators had to be included to the VBO term label, following the format: 
 `**'Most common name’, Country (Species)'**`, in which country and species are the English names (e.g ‘Jersey Giant, Canada (Chicken)’ VBO:0006068).
 
-We recognize that adding the Ccuntry of existence in the term name, in addition to the species, is not ideal and is unusual to ontology practices, but this concatenation of attributes was the only viable solution to ensure term uniqueness. 
+We recognize that adding the country of existence in the term name, in addition to the species, is not ideal and is unusual to ontology practices, but this concatenation of attributes was the only viable solution to ensure term uniqueness.