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114 changes: 113 additions & 1 deletion docs/ontologymodeling/metadata.md
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# VBO term Metadata

_Documentation upcoming_
VBO terms have rich metadata, all associated with provenance.

| Metadata | Annotation ID | Description | | |
|---------------------------|--------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------|---|
| VBO ID | http://www.geneontology.org/formats/oboInOwl#id | The unique and permanent identifier of a VBO concept, using the VBO prefix (VBO). | required | |
| VBO Term Label | http://www.w3.org/2000/01/rdf-schema#label | Single, unique label. | required | |
| Most common name | http://purl.obolibrary.org/obo/vbo#most_common_name | Synonym type, indicates the name by which a breed is most commonly referred to. | required | |
| Source | http://www.geneontology.org/formats/oboInOwl#source | Added to an annotation, indicates the annotation provenance. When used as an annotation to the term, “source” represents the provenance of any information about the VBO term. | required | |
| Contributor | dcterms:contributor | ORCID of curators and experts who contributed to the creation/revision of a VBO term. | required | |
| Exact synonym | http://www.geneontology.org/formats/oboInOwl#hasExactSynonym | Name by which a VBO term can be referred to. | required for, “most common name” exact synonym, other exact synonyms are optional | |
| Database cross reference | http://www.geneontology.org/formats/oboInOwl#hasDbXref | Identifier referring to the same VBO concept in another ontology, database, or the source. | optional | |
| Breed code | http://purl.obolibrary.org/obo/vbo#breed_code | Codes used by some communities, international organizations, and/or registration body to refer to the VBO term. | optional | |
| Breed recognition status | http://purl.obolibrary.org/obo/vbo#breed_recognition_status | Refers to the level of recognition by a registration body; may be ‘officially recognized’, ‘in the process of becoming officially recognized’, or ‘not been recognized’. | optional | |
| Domestication status | http://purl.obolibrary.org/obo/vbo#hasdomesticationstatus | Refers to the breed as domestic, feral or wild. | optional | |
| Extinction status | http://purl.obolibrary.org/obo/VBO_0300009 | Breed status referring to the risk of extinction of a breed. | optional | |
| Description of origin | http://purl.obolibrary.org/obo/vbo#origindescription | Free text note that may include the geographical origin and foundation stock of a breed. | optional | |
| Comment | rdfs:comment | Information on specific terms and term usage. | optional | |
| In subset - transboundary | http://www.geneontology.org/formats/oboInOwl#inSubset | Indicate that the term is reported as a “transboundary breed” in DAD-IS | optional DAD-IS only | |


## VBO ID

- Unique and permanent identifiers
- IRI format: http://purl.obolibrary.org/obo/VBO_####### (7-digit)
- OBO ID format: VBO:####### (7-digit)

Example: VBO:0200406 has the unique ID: http://purl.obolibrary.org/obo/VBO_0200406

More information on term ID ranges is provided here [link to VBO developer documentation].


## VBO Term Label

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.

See more explanation in the [term labels and naming conventions](ontologymodeling/term-labels-naming-conventions.md) section.

## Exact synonym

Any name that is provided by breed sources that represents the same concept as the VBO term is added as an exact synonym.

Example: “Teckel” is an exact synonym for 'Dachshund (Dog)' (VBO:0200406)

Notes:
- Source(s) for the exact synonym is(are) required.
- “Exact synonyms” are optional, except for the one representing the ‘most common name’ of the breed (see below) which is required.

## Most Common name

'Most common name' is a ‘synonym_type’ annotation property that is added to an ‘exact synonym’ to indicate that the name is the one most commonly used across sources when refering to the VBO term.

Example, ‘Dachshund’ is the ‘most common name’ for VBO:0200406

## Database cross-reference

- A database cross-reference is an identifier in another ontology, database, or the source that refers to the same concept.
- Database cross-reference is in the CURIE format

Example: ‘Angus (Cattle)’ (VBO:0000104) has database_cross_reference LBO:0000017.

The “source” annotation for the database cross reference is the provenance for this mapping between VBO and the other source. Currently, the provenance is the ORCID of the contributor [link to contributor section] who manually curated this mapping.

## Source

VBO was created based on information available in breed communities, international breed organizations, literature, and personal communication with experts. We keep the provenance of all this information in the “source” annotation. This “source” annotation property can be used to annotate metadata and SubClass axioms. When used as an annotation to the term, “source” represents the provenance of any information about the VBO term.

"Source" can refer to
- a specific record in a database or other ontology
- e.g. 'Abyssinian (Horse)' (VBO:0017087) has source LBO:0000714
- a publication
- e.g. 'Spanish Jennet (Horse)' (VBO:0016895) has source ISBN:9781403966216
- an international breed organization
- e.g. 'Schnauzer, Standard (Dog)' (VBO:0201189) has source https://www.akc.org/dog-breeds/standard-schnauzer/
- individual experts
- e.g. 'Göttingen minipig (Pig)' (VBO:0016899) has source for exact synonym ‘Goettingen miniature pig’ https://orcid.org/0000-0002-5520-6597


## Contributor

Curators and experts who contributed to the creation of a VBO term are recorded by adding their ORCID, using the annotation property “dcterms:contributor”.

Example: 'American Shorthair (Cat)' (VBO:0100018) has dcterms:contributor https://orcid.org/0000-0002-1628-7726

## Breed code

Some breed communities, international breed organizations, and/or registration bodies refer to breeds using codes. These codes are used on registration papers and for competition purposes. Breed codes are therefore of importance for some users. The same codes are often, though not always, reused between communities.

We recorded breed code as annotations using the annotation property “breed code”. Since codes are not always the same across communities, the source for the breed codes are recorded.

Example: 'Abyssinian (Cat)' (VBO:0100000) is known by the breed code, ‘AB’ by TICA and ‘ABY’ by several other cat organizations, FIFe, WCF, GCCF and REFR.

<img src="Screenshot 2024-07-30 at 7.33.45 PM.png" width="400">

## Breed recognition status


## Domestication status


## Extinction status


## Description of origin


## Comment


## in subset - transboundary

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