| Authors | |
| Created Date | Date: 2013/12/18 11:33:00 |
| Version | 1.1 |
| Licence | |
| Download | RDF |
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, etcCopyright漏 2010 the British Broadcasting Corporation.
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 taxaTheir associations with specific habitats, their mode of life, as well as their specific behavioursWhether a taxon is endangered according to the IUCN termsTopic 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 大象传媒 Wildlife Finder application. This application provides access to a rich set of information and data about biological species, as well as pointers to 大象传媒 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 大象传媒 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-cycle 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 大象传媒 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.
Ontology Terms
Automatically generated documentation for the ontology terms.
Classes
| Adaptation | |
|---|---|
| URI | |
| Description | 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. |
| Subclasses | ExtremesAdaptation, BehaviouralPattern, CommunicationAdaptation, EcosystemRole, FeedingHabit, LifeCycle, LocomotionAdaptation, MorphologyAdaptation, PredationStrategy, ReproductionStrategy, SocialBehaviour, SurvivalStrategy |
| Properties | adaptation |
| Adapted to Extremes | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Adaptation |
| Behavioural Pattern | |
|---|---|
| URI | |
| Description | Behavioural pattern describes an animal's dominant way of life. Arboreal animals, for example, live in trees and nocturnal animals are active at night. |
| Superclasses | Adaptation |
| Class | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | TaxonRank |
| Properties | class |
| Collection | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | |
| Properties | collection |
| Communication Adaptation | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Adaptation |
| Conservation Status | |
|---|---|
| URI | |
| Description | 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. |
| Properties | conservationStatus, populationTrend, redListStatus, threatDescription, yearAssessed |
| Ecosystem Role | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Adaptation |
| Ecozone | |
|---|---|
| URI | |
| Description | 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. |
| Properties | ecozone |
| Family | |
|---|---|
| URI | |
| Description | 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). |
| Superclasses | TaxonRank |
| Properties | family |
| Feeding Habit | |
|---|---|
| URI | |
| Description | Feeding habits describe the dominant diet of a particular species or group of species, and how they go about obtaining it. |
| Superclasses | Adaptation |
| Freshwater Habitat | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Habitat |
| Genus | |
|---|---|
| URI | |
| Description | 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 |
| Superclasses | TaxonRank |
| Properties | genus |
| Habitat | |
|---|---|
| URI | |
| Description | 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. |
| Subclasses | FreshwaterHabitat, MarineHabitat, TerrestrialHabitat |
| Properties | growsIn, habitat, livesIn |
| Kingdom | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | TaxonRank |
| Properties | kingdom, order |
| Life Cycle | |
|---|---|
| URI | |
| Description | An organism's Life Cycle describes the stages in an organisms development including metamorphosis, courtship displays and parental care.. |
| Superclasses | Adaptation |
| Locomotion | |
|---|---|
| URI | |
| Description | Locomotion is how an animal gets around - for instance by swimming, flying or climbing. |
| Superclasses | Adaptation |
| Marine Habitat | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Habitat |
| Morphology | |
|---|---|
| URI | |
| Description | Morphology is anything to do with what a plant or animal looks like - its size, shape, colour or structure. |
| Superclasses | Adaptation |
| Order | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | TaxonRank |
| Phylum | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | TaxonRank |
| Properties | phylum |
| Predation Strategy | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Adaptation |
| Red List Status | |
|---|---|
| URI | |
| Description | A category in the IUCN red list, 2001. |
| Properties | redListStatus |
| Reproduction Strategy | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Adaptation |
| Social Behaviour | |
|---|---|
| URI | |
| Description | 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? |
| Superclasses | Adaptation |
| Survival Strategy | |
|---|---|
| URI | |
| Description | Survival strategies include adaptations to changes in the organisms environment, including: hibernation, abscission and migration. |
| Superclasses | Adaptation |
| Taxon Name | |
|---|---|
| URI | |
| Description | A taxonomic name, describing the structure and provenance of a taxonomic name. |
| Properties | commonName, genusName, name, scientificName, speciesName, taxonomicName |
| Taxonomic Rank | |
|---|---|
| URI | |
| Description | Generic concept for a taxonomic rank such as a Genus or Species. |
| Subclasses | Class, Family, Genus, Kingdom, Order, Phylum, Species |
| Properties | adaptation, class, conservationStatus, family, genus, growsIn, habitat, kingdom, livesIn, name, order, phylum, species |
| Terrestrial Habitat | |
|---|---|
| URI | |
| Description | 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. |
| Superclasses | Habitat |
| Species | |
|---|---|
| URI | |
| Description | Generic class defining a biological species |
| Superclasses | TaxonRank |
| Properties | species |
Properties
| adaptation | |
|---|---|
| URI | |
| Description | associates a taxon rank with an adaptation which it displays |
| Domain | TaxonRank |
| Range | Adaptation |
| class name | |
|---|---|
| URI | |
| Description | Used to specify the name of a class as part of a Taxon Name |
| Superproperties | taxonomicName |
| collection | |
|---|---|
| URI | |
| Description | associates a taxon rank, habitat, species, clip with a collection of which it is a member |
| Superproperties | |
| Range | Collection |
| common name | |
|---|---|
| URI | |
| Description | 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 |
| Domain | TaxonName |
| Range |
| conservation status | |
|---|---|
| URI | |
| Description | associates a taxon rank with a description of a recent assessment of its conservation status |
| Domain | TaxonRank |
| Range | ConservationStatus |
| distribution map | |
|---|---|
| URI | |
| Description | associates a habitat, ecozone, or taxon rank with a map depicting its distribution or location |
| Range |
| ecozone | |
|---|---|
| URI | |
| Description | indicates that a habitat or a taxon rank can be found within an ecozone |
| Range | Ecozone |
| family name | |
|---|---|
| URI | |
| Description | Used to specify the name of a family as part of a Taxon Name |
| Superproperties | taxonomicName |
| genus name | |
|---|---|
| URI | |
| Description | 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. |
| Superproperties | taxonomicName |
| Domain | TaxonName |
| grows in | |
|---|---|
| URI | |
| Description | associates a taxon rank with a habitat in which it grows. Sub-property of wo:habitat to be used for plants, fungi, etc |
| Domain | TaxonRank |
| Range | Habitat |
| habitat | |
|---|---|
| URI | |
| Description | associates a taxon rank with a habitat in which it may typically be found |
| Domain | TaxonRank |
| Range | Habitat |
| kingdom name | |
|---|---|
| URI | |
| Description | Used to specify the name of a kingdom as part of a Taxon Name |
| Superproperties | taxonomicName |
| lives in | |
|---|---|
| URI | |
| Description | 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 |
| Domain | TaxonRank |
| Range | Habitat |
| order name | |
|---|---|
| URI | |
| Description | Used to specify the name of an order as part of a Taxon Name |
| Superproperties | taxonomicName |
| phylum name | |
|---|---|
| URI | |
| Description | Used to specify the name of a phylum as part of a Taxon Name |
| Superproperties | taxonomicName |
| population trend | |
|---|---|
| URI | |
| Description | 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. |
| Domain | ConservationStatus |
| Range |
| red list status | |
|---|---|
| URI | |
| Description | associates a Conservation Status with a category in the IUCN Red List |
| Domain | ConservationStatus |
| Range | RedListStatus |
| scientific name | |
|---|---|
| URI | |
| Description | 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). |
| Domain | TaxonName |
| Range |
| species name | |
|---|---|
| URI | |
| Description | 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. |
| Superproperties | taxonomicName |
| Domain | TaxonName |
| Range |
| taxonomic name | |
|---|---|
| URI | |
| Description | 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. |
| Subproperty | className, familyName, genusName, kingdomName, orderName, phylum_name, speciesName |
| Domain | TaxonName |
| Range |
| threatDescription | |
|---|---|
| URI | |
| Description | description of the threat(s) that have been identified as part of the assessment of the Conservation Status of a taxon |
| Domain | ConservationStatus |
| Range |
| year assessed | |
|---|---|
| URI | |
| Description | the year in which the conservation status was assessed. |
| Domain | ConservationStatus |
| Range |