# Defining ontologies

An ontology defines the entities that a Tracker endpoint can store, as well as their properties and the relationships between different entities.

Tracker internally uses the following ontologies as its base, all ontologies defined by the user of the endpoint are recommended to be build around this base:

- XML Schema (XSD), defining basic types
- Resource Description Framework (RDF), defining classes, properties and inheritance
- Nepomuk Resource Language (NRL), defining resource uniqueness, inheritance and indexes.
- Dublin Core (DC), defining common superproperties for documents

Ontologies are Turtle files with the .ontology extension, Tracker parses all ontology files from the given directory. The individual ontology files may not be self-consistent (i.e. use missing definitions), but all the ontology files as a whole must be.

Tracker loads the ontology files in alphanumeric order, it is advisable that those have a numbered prefix in order to load those at a consistent order despite future additions.

## Creating an ontology

### Defining a namespace

A namespace is the topmost layer of an individual ontology, it will contain all classes and properties defined by it. In order to define a namespace you can do:

    # These prefixes will be used in the definition of the ontology,
    # thus must be explicitly defined
    @prefix nrl: <http://tracker.api.gnome.org/ontology/v3/nrl#> .
    @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
    @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

    # This is our example namespace
    @prefix ex: <http://example.org/#>

    ex: a nrl:Namespace, nrl:Ontology
        nrl:prefix "ex"
        rdfs:comment "example ontology"
        nrl:lastModified "2017-01-01T15:00:00Z"

### Defining classes

Classes are the base of an ontology, all stored resources must define themselves as "being" at least one of these classes. They all derive from the base rdfs:Resource type. To eg. define classes representing animals and plants, you can do:

    ex:Eukaryote a rdfs:Class;
                 rdfs:subClassOf rdfs:Resource;
                 rdfs:comment "An eukaryote".

By convention all classes use CamelCase names, although class names are not restricted. The allowed charset is UTF-8.

Declaring subclasses is possible:

    ex:Animal a rdfs:Class;
              rdfs:subClassOf ex:Eukaryote;
              rdfs:comment "An animal".

    ex:Plant a rdfs:Class;
              rdfs:subClassOf ex:Eukaryote;
              rdfs:comment "A plant".

    ex:Mammal a rdfs:Class;
              rdfs:subClassOf ex:Animal;
              rdfs:comment "A mammal".

With such classes defined, resources may be inserted to the endpoint, eg. with the SPARQL:

    INSERT DATA { <merry> a ex:Mammal }
    INSERT DATA { <treebeard> a ex:Animal, ex:Plant }

Note that multiple inheritance is possible, resources will just inherit all properties from all classes and superclasses.

### Defining properties

Properties relate to a class, so all resources pertaining to that class can define values for these.

    ex:cromosomes a rdf:Property;
                  rdfs:domain ex:Eukaryote;
                  rdfs:range xsd:integer.

    ex:unicellular a rdf:Property;
                   rdfs:domain ex:Eukaryote;
                   rdfs:range xsd:bool;

    ex:dateOfBirth a rdf:Property;
                   rdfs:domain ex:Mammal;
                   rdfs:range xsd:dateTime;

The class the property belongs to is defined by `rdfs:domain`, while the data type contained is defined by `rdfs:range`. By convention all properties use dromedaryCase names, although property names are not restricted. The allowed charset is UTF-8.

The following basic types are supported:

- `xsd:boolean`
- `xsd:string` and `rdf:langString`
- `xsd:integer`, ranging from -2^63 to 2^63-1.
- `xsd:double`, able to store a 8 byte IEEE floating point number.
- `xsd:date` and `xsd:dateTime`, able to store dates and times since January 1st 1 AD, with microsecond resolution.

Of course, properties can also point to resources of the same or other classes, so stored resources can conform a graph:

    ex:parent a rdf:Property;
              rdfs:domain ex:Mammal;
              rdfs:range ex:Mammal;

    ex:pet a rdf:Property;
           rdfs:domain ex:Mammal;
           rdfs:range ex:Eukaryote;

There is also inheritance of properties, an example would be a property in a subclass concretizing a more generic property from a superclass.

    ex:geneticInformation a rdf:Property;
                          rdfs:domain ex:Eukaryote;
                          rdfs:range xsd:string;

    ex:dna a rdf:Property;
           rdfs:domain ex:Mammal;
           rdfs:range xsd:string;
           rdfs:subPropertyOf ex:geneticInformation.

SPARQL queries are expected to provide the same result when queried for a property or one of its superproperties.

    # These two queries should provide the exact same result(s)
    SELECT { ?animal a ex:Animal;
                     ex:geneticInformation "AGCT" }
    SELECT { ?animal a ex:Animal;
                     ex:dna "AGCT" }

### Defining cardinality of properties

By default, properties are multivalued, there are no restrictions in the number of values a property can store.

    INSERT DATA {
      <cat> a ex:Mammal .
      <dog> a ex:Mammal .

      <peter> a ex:Mammal ;
         ex:pets <cat>, <dog>
    }

Wherever this is not desirable, cardinality can be limited on properties through nrl:maxCardinality.

    ex:cromosomes a rdf:Property;
                  rdfs:domain ex:Eukaryote;
                  rdfs:range xsd:integer;
                  nrl:maxCardinality 1.

This will raise an error if the SPARQL updates in the endpoint end up in the property inserted multiple times.

    # This will fail
    INSERT DATA { <cat> a ex:Mammal;
                        ex:cromosomes 38;
                        ex:cromosomes 42 }

    # This will succeed
    INSERT DATA { <donald> a ex:Mammal;
                           ex:cromosomes 47 }

Tracker does not implement support for other maximum cardinalities than 1.

### Defining uniqueness

It is desirable for certain properties to keep their values unique across all resources, this can be expressed by defining the properties as being a nrl:InverseFunctionalProperty.

    ex:geneticInformation a rdf:Property, nrl:InverseFunctionalProperty;
                          rdfs:domain ex:Eukaryote;
                          rdfs:range xsd:string;

With that in place, no two resources can have the same value on the property.

    # First insertion, this will succeed
    INSERT DATA { <drosophila> a ex:Eukariote;
                               ex:geneticInformation "AGCT" }

    # This will fail
    INSERT DATA { <melanogaster> a ex:Eukariote;
                                 ex:geneticInformation "AGCT" }

### Defining indexes

It may be the case that SPARQL queries performed on the endpoint are known to match, sort, or filter on certain properties more often than others. In this case, the ontology may use nrl:domainIndex in the class definition:

    # Make queries on ex:dateOfBirth faster
    ex:Mammal a rdfs:Class;
              rdfs:subClassOf ex:Animal;
              rdfs:comment "A mammal";
              nrl:domainIndex ex:dateOfBirth.

Classes may define multiple domain indexes.

Note: Be frugal with indexes, do not add these proactively. An index in the wrong place might not affect query performance positively, but all indexes come at a cost in disk size.

### Defining full-text search properties

Tracker provides nonstandard full-text search capabilities, in order to use these, the string properties can use nrl:fulltextIndexed:

    ex:name a rdf:Property;
            rdfs:domain ex:Mammal;
            rdfs:range xsd:string;
            nrl:fulltextIndexed true;
            nrl:weight 10.

Weighting can also be applied, so certain properties rank higher than others in full-text search queries. With nrl:fulltextIndexed in place, sparql queries may use full-text search capabilities:

    SELECT { ?mammal a ex:Mammal;
                     fts:match "timmy" }

### Predefined elements

It may be desirable for the ontology to offer predefined elements of a certain class, which can then be used by the endpoint.

    ex:self a ex:Mammal.

Usage does not differ in use from the elements of that same class that could be inserted in the endpoint.

    INSERT DATA { ex:self ex:pets <cat> .
                  <cat> ex:pets ex:self }

### Accompanying metadata

Ontology files are optionally accompanied by description files, those have the same basename, but the ".description" extension.

    @prefix dsc: <http://tracker.api.gnome.org/ontology/v3/dsc#> .

    <virtual-ontology-uri:30-nie.ontology> a dsc:Ontology ;
    	dsc:title "Example ontology" ;
    	dsc:description "A little bit of this and that." ;
    	dsc:upstream "http://www.example.org/ontologies";
    	dsc:author "John doe, &lt;john@example.org&gt;";
    	dsc:editor "Jane doe, &lt;jane@example.org&gt;";
    	dsc:gitlog "http://git.example.org/cgit/tracker/log/example.ontology";
    	dsc:contributor "someone else, &lt;some1@example.org&gt;";

    	dsc:localPrefix "ex" ;
    	dsc:baseUrl "http://www.example.org/ontologies/ex#";
    	dsc:relativePath "./10-ex.ontology" ;

    	dsc:copyright "All rights given away".

## Updating an ontology

As software evolves, sometimes changes in the ontology are unavoidable. Tracker can transparently handle certain ontology changes on existing databases.

1. Adding a class.

2. Removing a class. All resources will be removed from this class, and all related properties will disappear.

3. Adding a property.

4. Removing a property. The property will disappear from all elements pertaining to the class in domain of the property.

5. Changing rdfs:range of a property. The following conversions are allowed:

   - `xsd:integer` to `xsd:bool`, `xsd:double` and `xsd:string`
   - `xsd:double` to `xsd:bool`, `xsd:integer` and `xsd:string`
   - `xsd:string` to `xsd:bool`, `xsd:integer` and `xsd:double`

6. Adding and removing `nrl:domainIndex` from a class.

7. Adding and removing `nrl:fulltextIndexed` from a property.

8. Changing the `nrl:weight` on a property.

9. Removing `nrl:maxCardinality` from a property.

However, there are certain ontology changes that Tracker will find incompatible. Either because they are incoherent or resulting into situations where it can not deterministically satisfy the change in the stored data. Tracker will error out and refuse to do any data changes in these situations:

- Properties with rdfs:range being `xsd:bool`, `xsd:date`, `xsd:dateTime`, or any other custom class are not convertible. Only conversions covered in the list above are accepted.
- You can not add `rdfs:subClassOf` in classes that are not being newly added. You can not remove `rdfs:subClassOf` from classes. The only allowed change to `rdfs:subClassOf` is to correct subclasses when deleting a class, so they point a common superclass.
- You can not add `rdfs:subPropertyOf` to properties that are not being newly added. You can not change an existing `rdfs:subPropertyOf` unless it is made to point to a common superproperty. You can however remove `rdfs:subPropertyOf` from non-new properties.
- Properties can not move across classes, thus any change in `rdfs:domain` is forbidden.
- You can not add `nrl:maxCardinality` restrictions on properties that are not being newly added.
- You can not add nor remove `nrl:InverseFunctionalProperty` from a property that is not being newly added.

The recommendation to bypass these situations is the same for all, use different property and class names and use SPARQL to manually migrate the old data to the new format if necessary.

High level code is in a better position to solve the possible incoherences (e.g. picking a single value if a property changes from multiple values to single value). After the manual data migration has been completed, the old classes and properties can be dropped.

The results of the search are