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1   /*
2    * Licensed to the Apache Software Foundation (ASF) under one or more
3    * contributor license agreements.  See the NOTICE file distributed with
4    * this work for additional information regarding copyright ownership.
5    * The ASF licenses this file to You under the Apache License, Version 2.0
6    * (the "License"); you may not use this file except in compliance with
7    * the License.  You may obtain a copy of the License at
8    *
9    *  http://www.apache.org/licenses/LICENSE-2.0
10   *
11   * Unless required by applicable law or agreed to in writing, software
12   * distributed under the License is distributed on an "AS IS" BASIS,
13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
14   * See the License for the specific language governing permissions and
15   * limitations under the License.
16   */
17  
18  package org.apache.any23.vocab;
19  
20  import org.eclipse.rdf4j.model.IRI;
21  
22  /**
23   * <p>
24   * The <a href="http://purl.org/ontology/wo/">Wildlife Ontology</a> vocabulary.
25   * </p>
26   * A simple vocabulary for describing biological species and related taxa. The vocabulary defines terms for describing
27   * the names and ranking of taxa, as well as providing support for describing their habitats, conservation status, and
28   * behavioural characteristics, etc
29   * 
30   * @author lewismc
31   * @author Davide Palmisano (dpalmisano@gmail.com)
32   */
33  public class WO extends Vocabulary {
34  
35      /**
36       * The namespace of the vocabulary as a string.
37       */
38      public static final String NS = "http://purl.org/ontology/wo/";
39  
40      private static WO instance;
41  
42      public static WO getInstance() {
43          if (instance == null) {
44              instance = new WO();
45          }
46          return instance;
47      }
48  
49      /**
50       * The namespace of the vocabulary as a IRI.
51       */
52      public final IRI NAMESPACE = createIRI(NS);
53  
54      ////////////////////////////////////////////////////////////////////
55      // CLASSES
56      ////////////////////////////////////////////////////////////////////
57  
58      /**
59       * An adaptation is any feature of an animal or plant which makes it better suited for a particular habitat or to do
60       * a particular task. For instance, being streamlined is an adaptation to swimming fast and being able to survive on
61       * very little water is an adaptation to life in the desert.
62       */
63      public final IRI Adaption = createClass("Adaption");
64  
65      /**
66       * Animal Intelligence or animal cognition is the title given to a modern approach to the mental capacities of
67       * non-human animals. It has developed out of comparative psychology, but has also been strongly influenced by the
68       * approach of ethology, behavioral ecology, and evolutionary psychology.
69       */
70      public final IRI Animal_Intelligence = createClass("AnimalIntelligence");
71  
72      /**
73       * Behavioural pattern describes an animal's dominant way of life. Arboreal animals, for example, live in trees and
74       * nocturnal animals are active at night.
75       */
76      public final IRI BehaviouralPattern = createClass("BehaviouralPattern");
77  
78      /**
79       * A class is a scientific way to group related organisms together, some examples of classes being jellyfish,
80       * reptiles and sea urchins. Classes are big groups and contain within them smaller groupings called orders,
81       * families, genera and species.
82       */
83      public final IRI Class = createClass("Class");
84  
85      /**
86       * A collection of resources, including documents, multimedia files, programme clips and their associated . taxa,
87       * which aims to showcase a particular aspect of natural history film-making, or illustrate aspects of the natural
88       * world. A collection provides an alternate way to organize content over and above the basic taxonomic hierarchy.
89       */
90      public final IRI Collection = createClass("Collection");
91  
92      /**
93       * Communication and senses are how an organism perceives the world - for instance through scent or sight - and how
94       * it sends messages or warnings to others.
95       */
96      public final IRI CommunicationAdaption = createClass("CommunicationAdaption");
97  
98      /**
99       * Conservation status as described by the IUCN Red List. Will typically have a number of properties including an
100      * official IUCN status, population trend, and a year of assessment.
101      */
102     public final IRI ConservationStatus = createClass("ConservationStatus");
103 
104     /**
105      * Ecosystem roles are about the part an animal or plant plays in sustaining or maintaining the habitat around them.
106      * Bees, for example, pollinate flowers, without which those plants would not produce fruits or seeds. Other
107      * species, such as dung beetles, play a vital role in keeping grasslands clear of animal waste and recycling
108      * valuable resources.
109      */
110     public final IRI EcosystemRole = createClass("EcosystemRole");
111 
112     /**
113      * Ecozones are a method of dividing up the Earth's surface. Each ecozone is a large area that contains a number of
114      * habitats, which are linked by the evolutionary history of the animals and plants within them. For instance one
115      * ecozone is Australasia, because its marsupials evolved in isolation to mammals in the rest of the world.
116      */
117     public final IRI Ecozone = createClass("Ecozone");
118 
119     /**
120      * Organisms that are adapted to extremes (known as Extremophiles) are organisms that thrives in and even may
121      * require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth.
122      */
123     public final IRI ExtremesAdaptiation = createClass("ExtremesAdaptiation");
124 
125     /**
126      * A family is a scientific grouping of closely related organisms. It has smaller groups, called genera and species,
127      * within it. A family can have a lot of members or only a few. Examples of families include the cats (Felidae), the
128      * gulls (Laridae) and the grasses (Poaceae). Further Reading: http://en.wikipedia.org/wiki/Family_%28biology%29
129      * http://www.bbc.co.uk/nature/family
130      */
131     public final IRI Family = createClass("Family");
132 
133     /**
134      * Feeding habits describe the dominant diet of a particular species or group of species, and how they go about
135      * obtaining it.
136      */
137     public final IRI FeedingHabit = createClass("FeedingHabit");
138 
139     /**
140      * Freshwater habitats include bogs, ponds, lakes, rivers and streams. About 3% of Earth's water is freshwater, but
141      * this includes the water locked up in the ice caps and trapped in rocks and soil as groundwater. Only a tiny
142      * fraction (0.014%) is surface water in the form of rivers, lakes and swamps.
143      */
144     public final IRI FreshwaterHabitat = createClass("FreshwaterHabitat");
145 
146     /**
147      * A genus is a scientific way of showing that species are very closed related to each other. In fact the first word
148      * of the species' scientific name is its genus. So for lions (Panthera leo), Panthera is the genus and tells us
149      * that they are closely related to tigers (Panthera tigris), because they share the name. Further Reading:
150      * http://en.wikipedia.org/wiki/Genus http://www.bbc.co.uk/nature/genus
151      */
152     public final IRI Genus = createClass("Genus");
153 
154     /**
155      * A habitat, or biome, is the type of environment in which plant and animals live. Habitat is dictated by what
156      * kinds of plants grow there, the climate and the geography. Rainforest, coral reefs and the tundra are all
157      * habitats where particular kinds of plants and animals might be found. Further Reading:
158      * http://en.wikipedia.org/wiki/Habitat http://www.bbc.co.uk/nature/habitats
159      */
160     public final IRI Habitat = createClass("Habitat");
161 
162     /**
163      * Infraorders are a subdivision of suborders - thus infraorders are an intermediate rank of classification, that
164      * group together related superfamilies and families. The tarsiers are a infraorder of primates, containing a single
165      * extant family, whilst shrimps (Caridea) are an example of an infraorder which encompases many related
166      * superfamiles. Ceratopsia is the infraorder that contains all the horned dinosaurs. Further Reading:
167      * http://en.wikipedia.org/wiki/Infraorder http://www.bbc.co.uk/nature/infraorder
168      */
169     public final IRI Infraorder = createClass("Infraorder");
170 
171     /**
172      * Kingdoms are the major categories into which scientists divide up all living things. The main kingdoms are
173      * animals, plants, fungi and bacteria, although there are others. Each kingdom has its own suite of defining
174      * characteristics - for instance plants have rigid cell walls, whilst animals do not. Further Reading:
175      * http://en.wikipedia.org/wiki/Kingdom_%28biology%29 http://www.bbc.co.uk/nature/kingdom
176      */
177     public final IRI Kingdom = createClass("Kingdom");
178 
179     /**
180      * An organism's Life Cycle describes the stages in an organisms development including metamorphosis, courtship
181      * displays and parental care.
182      */
183     public final IRI Lifecycle = createClass("Lifecycle");
184 
185     /**
186      * Locomotion is how an animal gets around - for instance by swimming, flying or climbing.
187      */
188     public final IRI LocomotionAdaption = createClass("LocomotionAdaption");
189 
190     /**
191      * Approximately 71% of the Earth's surface is covered by the oceans, an area of some 223698816km/sq. Although
192      * marine life evolved around three billion years before life on land, marine habitats are relatively poorly studied
193      * and much of the ocean's depths remains unexplored.
194      */
195     public final IRI MarineHabitat = createClass("MarineHabitat");
196 
197     /**
198      * Morphology is anything to do with what a plant or animal looks like - its size, shape, colour or structure.
199      */
200     public final IRI Morphology = createClass("Morphology");
201 
202     /**
203      * An order is a scientific way to categorise related organisms. An order is a smaller grouping than a class, but
204      * bigger than a family or genus. Examples of orders are willows, cockroaches and primates. Further Reading:
205      * http://en.wikipedia.org/wiki/Order_%28biology%29 http://www.bbc.co.uk/nature/order
206      */
207     public final IRI Order = createClass("Order");
208 
209     /**
210      * A phylum - also known as a division when referring to plants - is a scientfic way of grouping together related
211      * organisms. All the members of a phylum have a common ancestor and anatomical similarities. For instance, all the
212      * arthropods have external skeletons. Phlya are large groups and are further subdivided into classes, orders,
213      * families and so on. Further Reading: http://en.wikipedia.org/wiki/Phylum http://www.bbc.co.uk/nature/phylum
214      */
215     public final IRI Phylum = createClass("Phylum");
216 
217     /**
218      * Predation is catching and killing an animal in order to eat it. The prey can be chased, ambushed or caught in a
219      * trap such as a spider's web.
220      */
221     public final IRI PredationStrategy = createClass("PredationStrategy");
222 
223     /**
224      * A category in the IUCN red list, 2001. Further Reading:
225      * http://www.iucnredlist.org/technical-documents/categories-and-criteria/2001-categories-criteria
226      */
227     public final IRI RedListStatus = createClass("RedListStatus");
228 
229     /**
230      * Reproduction covers all the tactics and behaviours involved in obtaining a mate, conceiving the next generation
231      * and successfully raising them. It includes everything from plants being pollinated, to stags fighting over hinds,
232      * to lionesses babysitting their sisters' cubs.
233      */
234     public final IRI ReproductionStrategy = createClass("ReproductionStrategy");
235 
236     /**
237      * Social behaviour is all about how an animal interacts with members of its own species. For instance, does it live
238      * 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
239      * from its home?
240      */
241     public final IRI SocialBehaviour = createClass("SocialBehaviour");
242 
243     /**
244      * Generic class defining a biological species. Further Reading: http://en.wikipedia.org/wiki/Species
245      * http://www.bbc.co.uk/nature/species
246      */
247     public final IRI Species = createClass("Species");
248 
249     /**
250      * Suborders are an intermediate classification rank - an order can be split into many closely related suborders.
251      * Suborders are therefore of lower rank than a order, but higher than a infraorder or a family. All modern snakes
252      * are placed within a suborder (Serpentes). Theropoda is another suborder to which many famous carnivorous
253      * dinosaurs belong. Further Reading: http://en.wikipedia.org/wiki/Suborder http://www.bbc.co.uk/nature/suborder
254      */
255     public final IRI Suborder = createClass("Suborder");
256 
257     /**
258      * Subspecies are a rank of classification that is lower than a species. The differences between subspecies are less
259      * distinct than between species. Generally speaking two subspecies can successfully interbreed but two species
260      * cannot. If a subspecies can be shown to be different enough, then it can be elevated to the status of species.
261      * There are several subspecies of tiger (Panthera tigris) including the Bengal tiger (Panthera tigris tigris),
262      * Sumatran tiger (Panthera tigris sumatrae) and Siberian tiger (Panthera tigris altaica). Further Reading:
263      * http://en.wikipedia.org/wiki/Subspecies http://www.bbc.co.uk/nature/subspecies
264      */
265     public final IRI Subspecies = createClass("Subspecies");
266 
267     /**
268      * Superclass is an intermediate classification rank, or grouping, that sits directly above a class, ranking below a
269      * phylum or subphylum and containing one or more classes. The tetrapods are a superclass encompasing the amphibian,
270      * reptile, bird, mammal and dinosaur classes. Further Reading: http://en.wikipedia.org/wiki/Superclass_(biology)
271      * http://www.bbc.co.uk/nature/superclass
272      */
273     public final IRI Superclass = createClass("Superclass");
274 
275     /**
276      * Superfamilies are an intermediate classification rank, or grouping, that is directly above a family. A
277      * superfamily may contain one or more related families. Dung beetles are a superfamily containing the stag, bess
278      * and scarab beetle families. There is also a superfamily of rodents (muroidea) containing six families of rats,
279      * mice, hamsters and gerbils. Further Reading: http://en.wikipedia.org/wiki/Taxonomic_rank
280      * http://www.bbc.co.uk/nature/superfamily
281      */
282     public final IRI Superfamily = createClass("Superfamily");
283 
284     /**
285      * Superorders are an intermediate classification rank or grouping that sit directly above an order. A superorder
286      * may contain several orders. Sharks are a good example of a superorder, grouping together eight living orders of
287      * shark, as well as, five extinct orders. Perhaps the most famous superorder of them all is Dinosauria - the
288      * dinosaurs! Further Reading: http://en.wikipedia.org/wiki/Superorder http://www.bbc.co.uk/nature/superorder
289      */
290     public final IRI Superorder = createClass("Superorder");
291 
292     /**
293      * Survival strategies include adaptations to changes in . the organisms environment, including: hibernation,
294      * abscission and migration.
295      */
296     public final IRI SurvivalStrategy = createClass("SurvivalStrategy");
297 
298     /** A taxonomic name, describing the structure and provenance of a taxonomic name. */
299     public final IRI TaxonName = createClass("TaxonName");
300 
301     /**
302      * Generic concept for a taxonomic rank such as a Genus or Species. Further Reading:
303      * http://en.wikipedia.org/wiki/Taxonomic_rank
304      */
305     public final IRI TaxonRank = createClass("TaxonRank");
306 
307     /**
308      * Terrestrial habitats include forests, grasslands, deserts and rainforests. They are typically defined by factors
309      * such as plant structure (trees and grasses), leaf types (eg broadleaf and needleleaf), plant spacing (forest,
310      * woodland, savanna) and climate.
311      */
312     public final IRI TerrestrialHabitat = createClass("TerrestrialHabitat");
313 
314     /**
315      * Tribes are a taxonomic rank that fall between family and genus. Tribes can also be split in to smaller related
316      * groups called subtribes. Tribes are mainly, but not always, used in botany to classify plants. The true grass
317      * family is divided up into many subfamiles and then into tribes, one of which is bamboo. The insect world also
318      * uses tribes as a classification rank, for example, bombini is the tribe of bumblebees. Further Reading:
319      * http://en.wikipedia.org/wiki/Tribe_(biology) http://www.bbc.co.uk/nature/tribe
320      */
321     public final IRI Tribe = createClass("Tribe");
322 
323     //////////////////////////////////////////////////////////
324     // PROPERTIES
325     //////////////////////////////////////////////////////////
326     /**
327      * associates a taxon rank with an adaptation which it displays
328      */
329     public final IRI adaptation = createProperty("adaptation");
330 
331     /**
332      * associates a taxon rank with a class
333      */
334     public final IRI clazz = createProperty("class");
335 
336     /**
337      * associates a taxon rank, habitat, species, clip with a collection of which it is a member
338      */
339     public final IRI collection = createProperty("collection");
340 
341     /**
342      * associates a taxon rank with a description of a recent assessment of its conservation status
343      */
344     public final IRI conservationStatus = createProperty("conservationStatus");
345 
346     /**
347      * associates a habitat, ecozone, or taxon rank with a map depicting its distribution or location
348      */
349     public final IRI distributionMap = createProperty("distributionMap");
350 
351     /** indicates that a habitat or a taxon rank can be found within an ecozone */
352     public final IRI ecozone = createProperty("ecozone");
353 
354     /** associates a taxon rank with a family */
355     public final IRI family = createProperty("family");
356 
357     /** associates a taxon rank with a genus */
358     public final IRI genus = createProperty("genus");
359 
360     /**
361      * associates a taxon rank with a habitat in which it grows. Sub-property of wo:habitat to be used for plants,
362      * fungi, etc
363      */
364     public final IRI growsIn = createProperty("growsIn");
365 
366     /** associates a taxon rank with a habitat in which it may typically be found */
367     public final IRI habitat = createProperty("habitat");
368 
369     /** associates a taxon rank with a infraorder */
370     public final IRI infraorder = createProperty("infraorder");
371 
372     /** associates a taxon rank with a kingdom */
373     public final IRI kingdom = createProperty("kingdom");
374 
375     /**
376      * associates a taxon rank with a habitat in which it lives. Sub-property of wo:habitat to be used for members of
377      * the animal kingdom
378      */
379     public final IRI livesIn = createProperty("livesIn");
380 
381     /** associates a taxon rank with a taxon name */
382     public final IRI name = createProperty("name");
383 
384     /** associates a taxon rank with an order */
385     public final IRI order = createProperty("order");
386 
387     /** associates a taxon rank with a phylum */
388     public final IRI phylum = createProperty("phylum");
389 
390     /** associates a Conservation Status with a category in the IUCN Red List */
391     public final IRI redListStatus = createProperty("redListStatus");
392 
393     /** associates a taxon rank with a species */
394     public final IRI species = createProperty("species");
395 
396     /** associates a taxon rank with a subspecies */
397     public final IRI subspecies = createProperty("subspecies");
398 
399     /** associates a taxon rank with a suborder */
400     public final IRI suborder = createProperty("suborder");
401 
402     /** associates a taxon rank with a superclass */
403     public final IRI superclass = createProperty("superclass");
404 
405     /** associates a taxon rank with a superfamily */
406     public final IRI superfamily = createProperty("superfamily");
407 
408     /** associates a taxon rank with a superorder */
409     public final IRI superorder = createProperty("superorder");
410 
411     /** associates a taxon rank with a tribe */
412     public final IRI tribe = createProperty("tribe");
413 
414     //////////////////////////////////////////////////////////////
415     // DATATYPE PROPERTIES
416     //////////////////////////////////////////////////////////////
417 
418     /** Used to specify the name of a class as part of a Taxon Name */
419     public final IRI clazzName = createProperty("className");
420 
421     /**
422      * associates a formal taxon name with a common version. E.g. Panthera leo might be associated with a common name of
423      * 'Lion'. A given taxon name may have several common names
424      */
425     public final IRI commonName = createProperty("commonName");
426 
427     /** Used to specify the name of a family as part of a Taxon Name */
428     public final IRI familyName = createProperty("familyName");
429 
430     /**
431      * specifies the genus part of a binomial name, allowing this portion of the name to be explicitly described.
432      * Therefore this property will typically only be used in TaxonNames associated with species. The property is
433      * largely provided as a convenience to avoid applications having to parse the binomial name.
434      */
435     public final IRI genusName = createProperty("genusName");
436 
437     /** Used to specify the name of a infraorder as part of a Taxon Name */
438     public final IRI infraorderName = createProperty("infraorderName");
439 
440     /** Used to specify the name of a kingdom as part of a Taxon Name */
441     public final IRI kingdomName = createProperty("kingdomName");
442 
443     /** Used to specify the name of an order as part of a Taxon Name */
444     public final IRI orderName = createProperty("orderName");
445 
446     /** Used to specify the name of a phylum as part of a Taxon Name */
447     public final IRI phylumName = createProperty("phylumName");
448 
449     /**
450      * provides some indication of the population trend associated with an assessment of a taxon's conversation status.
451      * The value of this property is a simple literal, and is recommended to be one of: Decreasing, Increasing, Stable,
452      * Unknown.
453      */
454     public final IRI populationTrend = createProperty("populationTrend");
455 
456     /**
457      * associates a taxon name with its formal scientific name. This may be a binomial name (e.g. Panthera leo) in the
458      * case of a species name, or a uninomial (e.g. Panthera) name in the case of a name associated with another taxon
459      * rank. In formal taxonomic naming conventions, the scientific name is often qualified with the source of the name,
460      * e.g. Panthera leo (Linnaeus, 1758).
461      */
462     public final IRI scientificName = createProperty("scientificName");
463 
464     /** associates a short description with a Collection. */
465     public final IRI shortDescription = createProperty("shortDescription");
466 
467     /**
468      * specifies the species part of a binomial name, allowing this portion of the name to be explicitly described.
469      * Therefore this property will typically only be used in TaxonNames associated with species. The property is
470      * largely provided as a convenience to avoid applications having to parse the binomial name.
471      */
472     public final IRI speciesName = createProperty("speciesName");
473 
474     /** Used to specify the name of a suborder as part of a Taxon Name */
475     public final IRI suborderName = createProperty("suborderName");
476 
477     /** Used to specify the name of a subspecies as part of a Taxon Name */
478     public final IRI subspeciesName = createProperty("subspeciesName");
479 
480     /** Used to specify the name of a superspecies as part of a Taxon Name */
481     public final IRI superspeciesName = createProperty("superspeciesName");
482 
483     /** Used to specify the name of a superclass as part of a Taxon Name */
484     public final IRI superclassName = createProperty("superclassName");
485 
486     /** Used to specify the name of a superfamily as part of a Taxon Name */
487     public final IRI superfamilyName = createProperty("superfamilyName");
488 
489     /** Used to specify the name of a superorder as part of a Taxon Name */
490     public final IRI superorderName = createProperty("superorderName");
491 
492     /**
493      * a naming property, associating a formal taxonomic name with a Taxon Name instance. This property is a parent of a
494      * number of sub-properties that provide more specific terms for denoting names of families, phyla, species, etc.
495      */
496     public final IRI taxonomicName = createProperty("taxonomicName");
497 
498     /**
499      * description of the threat(s) that have been identified as part of the assessment of the Conservation Status of a
500      * taxon
501      */
502     public final IRI threatDescription = createProperty("threatDescription");
503 
504     /** Used to specify the name of a tribe as part of a Taxon Name */
505     public final IRI tribeName = createProperty("tribeName");
506 
507     /** the year in which the conservation status was assessed. */
508     public final IRI yearAssessed = createProperty("yearAssessed");
509 
510     private IRI createClass(String name) {
511         return createClass(NS, name);
512     }
513 
514     private IRI createProperty(String name) {
515         return createProperty(NS, name);
516     }
517 
518     private WO() {
519         super(NS);
520     }
521 
522 }