Wildlife Ontology

Latest Version: http://purl.org/ontology/wo/
Created: 2010-01-04
Last Modified: 2010-11-04
Authors: Leigh Dodds; Tom Scott

Abstract

A simple vocabulary for describing biological species and related taxa. The vocabulary defines terms for describing the names and ranking of taxa, as well as providing support for describing their habitats, conservation status, and behavioural characteristics, etc

This work is licensed under a Creative Commons Attribution License. This copyright applies to the Wildlife Ontology and accompanying documentation in RDF. This ontology uses W3C's RDF technology, an open Web standard that can be freely used by anyone.

Introduction

The Wildlife Ontology is a simple lightweight ontology for publishing data about all forms of biological taxa, including phyla, families, and species. The terms in this ontology allow data to be published about:

The relationships between taxa
Their associations with specific habitats, their mode of life, as well as their specific behaviours
Whether a taxon is endangered according to the IUCN terms
Topic relations between web documents and multimedia objects that may feature a taxon
...etc

The Wildlife Ontology was originally designed to support the publishing of data from the BBC Wildlife Finder application. This application provides access to a rich set of information and data about biological species, as well as pointers to BBC broadcast output that relate to these topics. The ontology should therefore complement the existing Programmes Ontology for describing TV programmes.

Whilst it originates in a specific BBC use case, the Wildlife Ontology should be applicable to a wide range of biological data publishing use cases. Care has been taken to try and ensure interoperability with more specialised ontologies used in scientific domains such as taxonomy, ecology, environmental science, and bioinformatics.

Rationale

The Wildlife Ontology has been designed with a particular set of priorities, and it is useful to review these to highlight specific decisions that were made during the modelling process and also to highlight where specific modelling was not done and where it is expected that more specialised ontologies will be used. The primary users of data published using the wildlife ontology are not expected to be taxonomic domain experts, so where necessary some trade-offs have been made to simplify naming and modelling to maximise use of data by the non-specialist. However it is hoped that the data published using this ontology can be easily mixed with data from other sources.

Taxonomic Concepts and Taxonomic Names

Individual species, and other tax, are not clearly defined concepts. The notion of what constitutes the definition of a species may change over time. A species may turn out to be simply a variant of another species, or may be promoted to the level of a genus. The defining characteristics of the members of a species may also similarly change over time. Another point of change is the taxonomic hierarchy: different viewpoints will exist as to the hierarchical organisation of taxa into different ranks; the ranks themselves are often sub-divided and re-grouped, reflecting the viewpoints of different disciplines.

From a modelling perspective this means that there can be no single complete universal description; some trade-offs will always be necessary. In creating this model a decision has been made to use only a simplified taxonomic hierarchy that features the primary ranks. Sub-divisions of ranks, e.g. sub-phylums, etc are not represented. The hierarchical relationship between individual taxa has also not be strictly defined, instead each taxa is linked to its higher ranks through dedicated properties. This potentially allows for some rearrangement in structure, but also supports publishing data in circumstances where data is not readily available about each level in the hierarchy.

In taxonomy, a distinction is also often made between a taxonomic concept and its taxonomic name. Taxonomic names have their own relationships and life-cyle which can be somewhat independent of the concepts to which they are applied. From an RDF perspective this means that taxonomic names should also be modelled as resources: names are not just properties of a taxonomic concept. Preserving this distinction means that data published using the Wildlife Ontology should remain interoperable with external sources. This is especially true when attempting to link to data associated with Life Science Identifiers (LSIDs) which are assigned independently to both taxonomic concepts and names.

Species as Classes vs Species as Instances

One perennial problem associated with modelling biological taxonomies using RDF is whether to attempt to model individual species as Classes, or whether to simply model species as instances of a generic Species class. The latter approach is simpler and avoids creating a huge ontology that attempts to model all biological organisms. Existing ontologies have taken different approaches to resolving this issue, some choosing one style, others another. At present there doesn't seem to be a consensus. With this in mind, the Wildlife Ontology adopts the simpler of the two approaches, i.e. modelling species as instances of a Species class, as this maximises interoperability with many of the existing Linked Data sources, particularly dbpedia, which adopt similar approaches.

Existing Work

During the development of the Wildlife Ontology existing work on modelling and publishing RDF data about species descriptions was reviewed. These are summarised below:

These existing vocabularies vary considerably in their approach to modelling species and taxa, particularly around the representation of hierarchies, and differentiation between taxonomic names and concepts. While many of these vocabularies are heavily used within specific research projects, they are in various stages of development and adoption outside of the originating project seems to be low.

The decision was therefore made to create a new lightweight vocabulary, the Wildlife Ontology, to provide a simple, easy to understand vocabulary that could be reused by non-domain experts. This addresses the immediate goals behind opening up the data from the BBC Wildlife Finder application. The approach taken in the design of the vocabulary, as noted in the above rationale, has been to maximise interoperability with these existing vocabularies using Semantic Web infrastructure, e.g. stating equivalencies between classes, properties and instances.

Vocabulary Diagram

The following diagram illustrates the relationships between the key classes in the ontology. A number of classes, e.g. sub classes of TaxonRank, Habitat and Adaptation have been omitted for clarity.

Overview Of Terms

An alphabetical index of the ontology terms, divided into classes, properties and individuals. All the terms are hyperlinked to their detailed description for quick reference.

Ontology Terms

Classes

Class: Adaptation

Label	Adaptation
Status	testing
Sub-Classes	AnimalIntelligence BehaviouralPattern CommunicationAdaptation EcosystemRole ExtremesAdaptation FeedingHabit LifeCycle LocomotionAdaptation MorphologyAdaptation PredationStrategy ReproductionStrategy SurvivalStrategy SocialBehaviour

An adaptation is any feature of an animal or plant which makes it better suited for a particular habitat or to do a particular task. For instance, being streamlined is an adaptation to swimming fast and being able to survive on very little water is an adaptation to life in the desert.

Further Reading:

Class: AnimalIntelligence

Label	Animal Intelligence
Status	testing
Has Parent Class	Adaptation

Animal Intelligence or animal cognition is the title given to a modern approach to the mental capacities of non-human animals. It has developed out of comparative psychology, but has also been strongly influenced by the approach of ethology, behavioral ecology, and evolutionary psychology.

Class: BehaviouralPattern

Label	Behavioural Pattern
Status	testing
Has Parent Class	Adaptation

Behavioural pattern describes an animal's dominant way of life. Arboreal animals, for example, live in trees and nocturnal animals are active at night.

Class: Class

Label	Class
Status	testing
Has Parent Class	TaxonRank

A class is a scientific way to group related organisms together, some examples of classes being jellyfish, reptiles and sea urchins. Classes are big groups and contain within them smaller groupings called orders, families, genera and species.

Further Reading:

Class: Collection

Label	Collection
Status	testing
Has Parent Class	http://purl.org/dc/dcmitype/Collection

A collection of resources, including documents, multimedia files, programme clips and their associated taxa, which aims to showcase a particular aspect of natural history film-making, or illustrate aspects of the natural world. A collection provides an alternate way to organize content over and above the basic taxonomic hierarchy.

Class: CommunicationAdaptation

Label	Communication Adaptation
Status	testing
Has Parent Class	Adaptation

Communication and senses are how an organism perceives the world - for instance through scent or sight - and how it sends messages or warnings to others.

Class: ConservationStatus

Label	Conservation Status
Status	testing

Conservation status as described by the IUCN Red List. Will typically have a number of properties including an official IUCN status, population trend, and a year of assessment.

Class: EcosystemRole

Label	Ecosystem Role
Status	testing
Has Parent Class	Adaptation

Ecosystem roles are about the part an animal or plant plays in sustaining or maintaining the habitat around them. Bees, for example, pollinate flowers, without which those plants would not produce fruits or seeds. Other species, such as dung beetles, play a vital role in keeping grasslands clear of animal waste and recycling valuable resources.

Class: Ecozone

Label	Ecozone
Status	testing

Ecozones are a method of dividing up the Earth's surface. Each ecozone is a large area that contains a number of habitats, which are linked by the evolutionary history of the animals and plants within them. For instance one ecozone is Australasia, because its marsupials evolved in isolation to mammals in the rest of the world.

Class: ExtremesAdaptation

Label	Adapted to Extremes
Status	testing
Has Parent Class	Adaptation

Organisms that are adapted to extremes (known as Extremophiles) are organisms that thrives in and even may require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth.

Class: Family

Label	Family
Status	testing
Has Parent Class	TaxonRank

A family is a scientific grouping of closely related organisms. It has smaller groups, called genera and species, within it. A family can have a lot of members or only a few. Examples of families include the cats (Felidae), the gulls (Laridae) and the grasses (Poaceae).

Further Reading:

Class: FeedingHabit

Label	Feeding Habit
Status	testing
Has Parent Class	Adaptation

Feeding habits describe the dominant diet of a particular species or group of species, and how they go about obtaining it.

Class: FreshwaterHabitat

Label	Freshwater Habitat
Status	testing
Has Parent Class	Habitat

Freshwater habitats include bogs, ponds, lakes, rivers and streams. About 3% of Earth's water is freshwater, but this includes the water locked up in the ice caps and trapped in rocks and soil as groundwater. Only a tiny fraction (0.014%) is surface water in the form of rivers, lakes and swamps.

Class: Genus

Label	Genus
Status	testing
Has Parent Class	TaxonRank

A genus is a scientific way of showing that species are very closed related to each other. In fact the first word of the species' scientific name is its genus. So for lions (Panthera leo), Panthera is the genus and tells us that they are closely related to tigers (Panthera tigris), because they share the name

Further Reading:

Class: Habitat

Label	Habitat
Status	testing
Sub-Classes	TerrestrialHabitat FreshwaterHabitat MarineHabitat

A habitat, or biome, is the type of environment in which plant and animals live. Habitat is dictated by what kinds of plants grow there, the climate and the geography. Rainforest, coral reefs and the tundra are all habitats where particular kinds of plants and animals might be found.

Further Reading:

Class: Infraorder

Label	Infraorder
Status	testing
Has Parent Class	TaxonRank

Infraorders are a subdivision of suborders - thus infraorders are an intermediate rank of classification, that group together related superfamilies and families. The tarsiers are a infraorder of primates, containing a single extant family, whilst shrimps (Caridea) are an example of an infraorder which encompases many related superfamiles. Ceratopsia is the infraorder that contains all the horned dinosaurs.

Further Reading:

Class: Kingdom

Label	Kingdom
Status	testing
Has Parent Class	TaxonRank

Kingdoms are the major categories into which scientists divide up all living things. The main kingdoms are animals, plants, fungi and bacteria, although there are others. Each kingdom has its own suite of defining characteristics - for instance plants have rigid cell walls, whilst animals do not.

Further Reading:

Class: LifeCycle

Label	Life Cycle
Status	testing
Has Parent Class	Adaptation

An organism's Life Cycle describes the stages in an organisms development including metamorphosis, courtship displays and parental care..

Class: LocomotionAdaptation

Label	Locomotion
Status	testing
Has Parent Class	Adaptation

Locomotion is how an animal gets around - for instance by swimming, flying or climbing.

Class: MarineHabitat

Label	Marine Habitat
Status	testing
Has Parent Class	Habitat

Approximately 71% of the Earth's surface is covered by the oceans, an area of some 223698816km/sq. Although marine life evolved around three billion years before life on land, marine habitats are relatively poorly studied and much of the ocean's depths remains unexplored.

Class: MorphologyAdaptation

Label	Morphology
Status	testing
Has Parent Class	Adaptation

Morphology is anything to do with what a plant or animal looks like - its size, shape, colour or structure.

Class: Order

Label	Order
Status	testing
Has Parent Class	TaxonRank

An order is a scientific way to categorise related organisms. An order is a smaller grouping than a class, but bigger than a family or genus. Examples of orders are willows, cockroaches and primates.

Further Reading:

Class: Phylum

Label	Phylum
Status	testing
Has Parent Class	TaxonRank

A phylum - also known as a division when referring to plants - is a scientfic way of grouping together related organisms. All the members of a phylum have a common ancestor and anatomical similarities. For instance, all the arthropods have external skeletons. Phlya are large groups and are further subdivided into classes, orders, families and so on.

Further Reading:

Class: PredationStrategy

Label	Predation Strategy
Status	testing
Has Parent Class	Adaptation

Predation is catching and killing an animal in order to eat it. The prey can be chased, ambushed or caught in a trap such as a spider's web.

Class: RedListStatus

Label	Red List Status
Status	testing
Has Parent Class	http://www.w3.org/2004/02/skos/core#Category

A category in the IUCN red list, 2001.

Further Reading:

http://www.iucnredlist.org/technical-documents/categories-and-criteria/2001-categories-criteria

Class: ReproductionStrategy

Label	Reproduction Strategy
Status	testing
Has Parent Class	Adaptation

Reproduction covers all the tactics and behaviours involved in obtaining a mate, conceiving the next generation and successfully raising them. It includes everything from plants being pollinated, to stags fighting over hinds, to lionesses babysitting their sisters' cubs.

Class: SocialBehaviour

Label	Social Behaviour
Status	testing
Has Parent Class	Adaptation

Social behaviour is all about how an animal interacts with members of its own species. For instance, does it live in a colony or on its own, does it fight to be top of the pecking order, or does it try to keep strangers away from its home?

Class: Species

Label	species
Status	testing
Has Parent Class	TaxonRank

Generic class defining a biological species

Further Reading:

Class: Suborder

Label	Suborder
Status	testing
Has Parent Class	TaxonRank

Suborders are an intermediate classification rank - an order can be split into many closely related suborders. Suborders are therefore of lower rank than a order, but higher than a infraorder or a family. All modern snakes are placed within a suborder (Serpentes). Theropoda is another suborder to which many famous carnivorous dinosaurs belong.

Further Reading:

Class: Subspecies

Label	Subspecies
Status	testing
Has Parent Class	TaxonRank

Subspecies are a rank of classification that is lower than a species. The differences between subspecies are less distinct than between species. Generally speaking two subspecies can successfully interbreed but two species cannot. If a subspecies can be shown to be different enough, then it can be elevated to the status of species. There are several subspecies of tiger (Panthera tigris) including the Bengal tiger (Panthera tigris tigris), Sumatran tiger (Panthera tigris sumatrae) and Siberian tiger (Panthera tigris altaica).

Further Reading:

Class: Superclass

Label	Superclass
Status	testing
Has Parent Class	TaxonRank

Superclass is an intermediate classification rank, or grouping, that sits directly above a class, ranking below a phylum or subphylum and containing one or more classes. The tetrapods are a superclass encompasing the amphibian, reptile, bird, mammal and dinosaur classes.

Further Reading:

Class: Superfamily

Label	Superfamily
Status	testing
Has Parent Class	TaxonRank

Superfamilies are an intermediate classification rank, or grouping, that is directly above a family. A superfamily may contain one or more related families. Dung beetles are a superfamily containing the stag, bess and scarab beetle families. There is also a superfamily of rodents (muroidea) containing six families of rats, mice, hamsters and gerbils.

Further Reading:

Class: Superorder

Label	Superorder
Status	testing
Has Parent Class	TaxonRank

Superorders are an intermediate classification rank or grouping that sit directly above an order. A superorder may contain several orders. Sharks are a good example of a superorder, grouping together eight living orders of shark, as well as, five extinct orders. Perhaps the most famous superorder of them all is Dinosauria - the dinosaurs!

Further Reading:

Class: SurvivalStrategy

Label	Survival Strategy
Status	testing
Has Parent Class	Adaptation

Survival strategies include adaptations to changes in the organisms environment, including: hibernation, abscission and migration.

Class: TaxonName

Label	Taxon Name
Status	testing

A taxonomic name, describing the structure and provenance of a taxonomic name.

Class: TaxonRank

Label	Taxonomic Rank
Status	testing
Sub-Classes	Kingdom Phylum Superclass Class Superorder Infraorder Suborder Order Superfamily Family Tribe Genus Species Subspecies

Generic concept for a taxonomic rank such as a Genus or Species.

Further Reading:

http://en.wikipedia.org/wiki/Taxonomic_rank

Class: TerrestrialHabitat

Label	Terrestrial Habitat
Status	testing
Has Parent Class	Habitat

Terrestrial habitats include forests, grasslands, deserts and rainforests. They are typically defined by factors such as plant structure (trees and grasses), leaf types (eg broadleaf and needleleaf), plant spacing (forest, woodland, savanna) and climate.

Class: Tribe

Label	Tribe
Status	testing
Has Parent Class	TaxonRank

Tribes are a taxonomic rank that fall between family and genus. Tribes can also be split in to smaller related groups called subtribes. Tribes are mainly, but not always, used in botany to classify plants. The true grass family is divided up into many subfamiles and then into tribes, one of which is bamboo. The insect world also uses tribes as a classification rank, for example, bombini is the tribe of bumblebees.

Further Reading:

Object Properties

Property: adaptation

Label	adaptation
Status	testing
Range	Adaptation
Domain	TaxonRank

associates a taxon rank with an adaptation which it displays

Property: class

Label	class
Status	testing
Range	Class
Domain	TaxonRank

associates a taxon rank with a class

Property: collection

Label	collection
Status	testing
Has Parent Property	http://purl.org/dc/terms/isPartOf
Range	Collection

associates a taxon rank, habitat, species, clip with a collection of which it is a member

Property: conservationStatus

Label	conservation status
Status	testing
Range	ConservationStatus
Domain	TaxonRank

associates a taxon rank with a description of a recent assessment of its conservation status

Property: distributionMap

Label	distribution map
Status	unstable
Range	http://xmlns.com/foaf/0.1/Image

associates a habitat, ecozone, or taxon rank with a map depicting its distribution or location

Property: ecozone

Label	ecozone
Status	testing
Range	Ecozone

indicates that a habitat or a taxon rank can be found within an ecozone

Property: family

Label	family
Status	testing
Range	Family
Domain	TaxonRank

associates a taxon rank with a family

Property: genus

Label	genus
Status	testing
Range	Genus
Domain	TaxonRank

associates a taxon rank with a genus

Property: growsIn

Label	lives in
Status	testing
Range	Habitat
Domain	TaxonRank

associates a taxon rank with a habitat in which it grows. Sub-property of wo:habitat to be used for plants, fungi, etc

Property: habitat

Label	habitat
Status	testing
Range	Habitat
Domain	TaxonRank

associates a taxon rank with a habitat in which it may typically be found

Property: infraorder

Label	infraorder
Status	testing
Range	infraorder
Domain	TaxonRank

associates a taxon rank with a infraorder

Property: kingdom

Label	kingdom
Status	testing
Range	Kingdom
Domain	TaxonRank

associates a taxon rank with a kingdom

Property: livesIn

Label	lives in
Status	testing
Range	Habitat
Domain	TaxonRank

associates a taxon rank with a habitat in which it lives. Sub-property of wo:habitat to be used for members of the animal kingdom

Property: name

Label	name
Status	testing
Range	TaxonName
Domain	TaxonRank

associates a taxon rank with a taxon name

Property: order

Label	order
Status	testing
Range	Kingdom
Domain	TaxonRank

associates a taxon rank with an order

Property: phylum

Label	phylum
Status	testing
Range	Phylum
Domain	TaxonRank

associates a taxon rank with a phylum

Property: redListStatus

Label	red list status
Status	testing
Range	RedListStatus
Domain	ConservationStatus

associates a Conservation Status with a category in the IUCN Red List

Property: species

Label	genus
Status	testing
Range	Species
Domain	TaxonRank

associates a taxon rank with a species

Property: subspecies

Label	subspecies
Status	testing
Range	subspecies
Domain	TaxonRank

associates a taxon rank with a subspecies

Property: suborder

Label	suborder
Status	testing
Range	suborder
Domain	TaxonRank

associates a taxon rank with a suborder

Property: superclass

Label	superclass
Status	testing
Range	superclass
Domain	TaxonRank

associates a taxon rank with a superclass

Property: superfamily

Label	superfamily
Status	testing
Range	superfamily
Domain	TaxonRank

associates a taxon rank with a superfamily

Property: superorder

Label	superorder
Status	testing
Range	superorder
Domain	TaxonRank

associates a taxon rank with a superorder

Property: tribe

Label	tribe
Status	testing
Range	tribe
Domain	TaxonRank

associates a taxon rank with a tribe

Datatype Properties

Property: className

Label	class name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a class as part of a Taxon Name

Property: commonName

Label	common name
Status	testing
Range	http://www.w3.org/2001/XMLSchema#string
Domain	TaxonName

associates a formal taxon name with a common version. E.g. Panthera leo might be associated with a common name of 'Lion'. A given taxon name may have several common names

Property: familyName

Label	family name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a family as part of a Taxon Name

Property: genusName

Label	genus name
Status	testing
Has Parent Property	taxonomicName

specifies the genus part of a binomial name, allowing this portion of the name to be explicitly described. Therefore this property will typically only be used in TaxonNames associated with species. The property is largely provided as a convenience to avoid applications having to parse the binomial name.

Property: infraorderName

Label	infraorder name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a infraorder as part of a Taxon Name

Property: kingdomName

Label	kingdom name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a kingdom as part of a Taxon Name

Property: orderName

Label	order name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of an order as part of a Taxon Name

Property: phylumName

Label	phylum name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a phylum as part of a Taxon Name

Property: populationTrend

Label	population trend
Status	unstable
Range	http://www.w3.org/2001/XMLSchema#string
Domain	ConservationStatus

provides some indication of the population trend associated with an assessment of a taxon's conversation status. The value of this property is a simple literal, and is recommended to be one of: Decreasing, Increasing, Stable, Unknown.

Property: scientificName

Label	scientific name
Status	testing
Range	http://www.w3.org/2001/XMLSchema#string
Domain	TaxonName

associates a taxon name with its formal scientific name. This may be a binomial name (e.g. Panthera leo) in the case of a species name, or a uninomial (e.g. Panthera) name in the case of a name associated with another taxon rank. In formal taxonomic naming conventions, the scientific name is often qualified with the source of the name, e.g. Panthera leo (Linnaeus, 1758).

Property: shortDescription

Label	short description
Status	testing
Range	http://www.w3.org/2001/XMLSchema#string

associates a short description with a Collection.

Property: speciesName

Label	species name
Status	testing
Has Parent Property	taxonomicName
Range	http://www.w3.org/2001/XMLSchema#string
Domain	TaxonName

specifies the species part of a binomial name, allowing this portion of the name to be explicitly described. Therefore this property will typically only be used in TaxonNames associated with species. The property is largely provided as a convenience to avoid applications having to parse the binomial name.

Property: suborderName

Label	suborder name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a suborder as part of a Taxon Name

Property: subspeciesName

Label	subspecies name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a subspecies as part of a Taxon Name

Property: superspeciesName

Label	superspecies name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a superspecies as part of a Taxon Name

Property: superclassName

Label	superclass name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a superclass as part of a Taxon Name

Property: superfamilyName

Label	superfamily name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a superfamily as part of a Taxon Name

Property: superorderName

Label	superorder name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a superorder as part of a Taxon Name

Property: taxonomicName

Label	taxonomic name
Status	testing
Sub-Properties	kingdomName phylumName className orderName familyName genusName speciesName
Range	http://www.w3.org/2001/XMLSchema#string
Domain	TaxonName

a naming property, associating a formal taxonomic name with a Taxon Name instance. This property is a parent of a number of sub-properties that provide more specific terms for denoting names of families, phyla, species, etc.

Property: threatDescription

Label	threatDescription
Status	testing
Range	http://www.w3.org/2001/XMLSchema#string
Domain	ConservationStatus

description of the threat(s) that have been identified as part of the assessment of the Conservation Status of a taxon

Property: tribeName

Label	tribe name
Status	testing
Has Parent Property	taxonomicName

Used to specify the name of a tribe as part of a Taxon Name

Property: yearAssessed

Label	year assessed
Status	testing
Range	http://www.w3.org/2001/XMLSchema#string
Domain	ConservationStatus

the year in which the conservation status was assessed.