Design rationale and overview of the African Wildlife tutorial ontologies

(update 30-7-2020: more details are described in the journal article published in the Journal of Biomedical Semantics)

There are several tutorial ontologies, which typically focus on illustrating one or two aspects of ontology development, notably language features and automated reasoning. This may suffice for one’s aims, but for an ontology engineering course, one would need to be able to illustrate a myriad of development factors and devise exercises for a wider range of tasks of ontology development. For instance, to illustrate the use of ontology design patterns, competency questions, foundational ontologies, and science-based modelling practices, neither of which is addressed easily by the popular tutorial ontologies (notably: wine and pizza), perhaps because they predate most of the advances made in ontology engineering research. Also, I have noticed that my students replicate examples from the exercises they carry out and from inspecting popular and easy-to-find ontologies. Marking the practical assignments, I got to see sandwich and ice cream and burger ontologies with toppings and value partitions, and software and mobile phone ontologies where laptop models are instances rather than classes. Not providing good and versatile examples holistically, causes the propagation of sub-optimal ontology development at least in the exercises, which then also may affect negatively the development of an operational domain ontology that the graduates may have to develop later on.

I’ve been exploring alternatives and variants over the past 11 years in the ontology engineering courses that I have taught yearly to about 8-40 students/year. In an attempt to systematise and possibly generalise from that, I’ve identified 22 requirements that contribute to a good tutorial ontology, which concern the suitability of the subject domain (7 factors), the ease of demonstrating logics and reasoning tasks (7), and assistance with demonstrating engineering aspects (8). Its details are described in a technical report [1]. I don’t claim that it’s an exhaustive list, but that it is one that may help someone to develop their own tutorial ontology in a fun or interesting topic if they so wish—after all, not everyone is interested in pizzas, wines, African wildlife, pets, shirts, a small university, or Robert Stevens’ family.

I’ve tried out a variety of extant tutorial ontologies as well as a range of versions of the African Wildlife Ontology (AWO) over the years (early experiences), eventually settling for a set of 14 versions, all the way from the example from the Primer [2] to DOLCE- and BFO-aligned to translated in several languages, and some with possible answers to some of the exercises. A graphical rendering of the main classes and relations is shown in the following figure:

The versions of the AWO are summarised in the following table, which is also mentioned as annotation in the OWL files.

 

The AWO meets a majority of the 22 requirements, is mature by now, and it has been used yearly in an ontology engineering course or tutorial since 2010. Also, it is links up with my ontology engineering textbook with relevant examples and exercises. The AWO provides a wide range of options concerning examples and exercises for ontology engineering well beyond illustrating only logic features and automated reasoning. For instance, it assists in demonstrating tasks about ontology quality, such as alignment to a foundational ontology and satisfying competency questions, versioning, and multilingual ontologies. For instance, it is easier to demonstrate alignment of a class Animal to DOLCE’s (Non-Agentive) Physical Object than, say, debating what Algorithm aligns with or descend into political debates on the gender binary or what constitutes a family. One can use the height or the colours of the plants and animals to discuss how to model attributes as qualities or dependent entities cf. OWL’s data properties or an artificial ValuePartition. Declare, say, de individual lion simba as an instance of Lion, rather than the confusion regarding grape varieties. Use intuitively obvious disjointness between animals and plants, and subsequently easy catches on sensitising modellers to the far-reaching effects of declaring domain and range axioms by first asserting that animals eat animals, and then adding that carnivorous plants eat insects. In addition, it links up easily to topics for ontology integration activities, such as with biodiversity data, wildlife trade, and tourism to create, e.g., an OBDA system with freely available data (e.g., taken from here) or an ontology-enhanced website for an organisation that offers environmentally sustainable safaris. More examples of broad usage options are described in section 2.3 in the tech report.

The AWO is freely available under a CC-BY licence through the textbook’s webpage at https://people.cs.uct.ac.za/~mkeet/OEbook/ in this folder. A more comprehensive description of the requirements, design, and content is described in a technical report [1] for the time being.

 

References

[1] Keet, CM. The African Wildlife Ontology tutorial ontologies: requirements, design, and content. Technical Report 1905.09519. 23 May 2019. https://arxiv.org/abs/1905.09519.

[2] Antoniou, G., van Harmelen, F. A Semantic Web Primer. MIT Press, USA. 2003.

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The TDDonto tool to try out TDD for ontology authoring

Last month I wrote about Test-Driven Development for ontologies, which is described in more detail in the ESWC’16 paper I co-authored with Agnieszka Lawrynowicz [1]. That paper does not describe much about the actual tool implementing the tests, TDDonto, although we have it and used it for the performance evaluation. Some more detail on its design and more experimental results are described in the paper “The TDDonto Tool for Test-Driven Development of DL Knowledge Bases” [2] that has just been published in the proceedings of the 29th International Workshop on Description Logics, which will take place next weekend in Cape Town (22-25 April 2016).

What we couldn’t include there in [2] is multiple screenshots to show how it works, but a blog is a fine medium for that, so I’ll illustrate the tool with some examples in the remainder of the post. It’s an alpha version that works. No usability and HCI evaluations have been done, but at least it’s a Protégé plugin rather than command line :).

First, you need to download the plugin from Agnieszka’s ARISTOTELES project page and place the jar file in the plugins folder of Protégé 5.0. You can then go to the Protégé menu bar, select Windows – Views – Evaluation views – TDDOnto, and place it somewhere on the screen and start using it. For the examples here, I used the African Wildlife Ontology tutorial ontology (AWO v1) from my ontology engineering course.

Make sure to have selected an automated reasoner, and classify your ontology. Now, type a new test in the “New test” field at the top, e.g. carnivore DisjointWith: herbivore, click “Add test”, select the checkbox of the test to execute, and click the “Execute test”: the status will be returned, as shown in the screenshot below. In this case, the “OK” says that the disjointness is already asserted or entailed in the ontology.

Now let’s do a TDD test that is going to fail (you won’t know upfront, of course); e.g., testing whether impalas are herbivores:

The TDD test failed because the subsumption is neither asserted nor entailed in the ontology. One can then click “add to ontology”, which updates the ontology:

Note that the reasoner has to be run again after a change in the ontology.

Lets do two more: testing whether lion is a carnivore and that flower is a plan part. The output of the tests is as follows:

It returns “OK” for the lion, because it is entailed in the ontology: a carnivore is an entity that eats only animals or parts thereof, and lions eat only herbivore and eats some impala (which are animals). The other one, Flower SubClassOf: PlantParts fails as “undefined”, because Flower is not in the ontology.

Ontologies do not have only subsumption and disjointness axioms, so let’s assume that impalas eat leaves and we want check whether that is in the ontology, as well as whether lions eat animals:

The former failed because there are no properties for the impala in the AWO v1, the latter passed, because a lion eats impala, and impala is an animal. Or: the TDDOnto tool indeed behaves as expected.

Currently, only a subset of all the specified tests have been implemented, due to some limitations of existing tools, but we’re working on implementing those as well.

If you have any feedback on TDDOnto, please don’t hesitate to tell us. I hope to be seeing you later in the week at DL’16, where I’ll be presenting the paper on Sunday afternoon (24th) and I also can give a live demo any time during the workshop (or afterwards, if you stay for KR’16).

 

References

[1] Keet, C.M., Lawrynowicz, A. Test-Driven Development of Ontologies. 13th Extended Semantic Web Conference (ESWC’16). Springer LNCS. 29 May – 2 June, 2016, Crete, Greece. (in print)

[2] Lawrynowicz, A., Keet, C.M. The TDDonto Tool for Test-Driven Development of DL Knowledge bases. 29th International Workshop on Description Logics (DL’16). April 22-25, Cape Town, South Africa. CEUR WS vol. 1577.

Nontransitive vs. intransitive direct part-whole relations in OWL

Confusing is-a with part-of is known to be a common mistake by novice ontology developers. Each time I taught the ontology engineering course, I had included a session of 1-2 hours to explain some basic aspects of part-whole relations and, lo and behold, none of the participants made that mistake in the labs or mini-projects! One awkward thing did pop-up there and at other occasions, though, which had to do with modelling direct parthood that does not go well at the moment, to say the least, for a plethora of reasons. Inclusion of direct parthood is not without philosophical quarrels, and the more I think of it, the more I dislike the relation, but somehow the issue appears often in the context of part-whole relations in ontologies. The observed underlying modelling issue—representing intransitivity versus nontransitivity—holds for any OWL object property anyway, so I will proceed with the general case with an example about giraffes.

Preliminaries

First of all, to clarify terms in the post’s title: INtransitive means that for all x, y, z, if Rxy and Ryz then Rxz does not hold; formally and an option to state this in a Description Logic is to use role chaining: .  NONtransitive means that we cannot say either way if the property is transitive or intransitive, i.e., in some cases is may be transitive but not in other occasions. Direct parthood is to be understood as follows: if some part x is a direct part of a y, then there is no other object z such that x is a part of z and z is a part of y; formally, . If direct parthood is in- or non-transitive is beside the point at this stage, so let us look now at what happens with it in an OWL ontology when one tries to model it one way or another.

The OWL ontology and the reasoner

Given that I used the African Wildlife Ontology as a tutorial ontology earlier and the theme appeals to people, I will use it again here. Depending on what we do with the direct parthood relation in the ontology, Giraffe is, or is not, classified automatically as a subclass of Herbivore. Herbivore is a defined class, equivalent to, in Protégé 4.1 notation, (eats only plant) or (eats only (is-part-of some plant)), and Giraffe is a subclass of both Animal and eats only (leaf or Twig). Leaves are part of a twig, twigs of a branch, and branches of a tree that in turn is a subclass of plant. The is-part-of is, correctly according to mereology, included in the ontology as being transitive. Instead of all the is-part-of and is-proper-part-of between plant parts and plants in the AfricanWildlifeOntology1.owl, we model them using direct-part. AfricanWildlifeOntology4a.owl has direct-part as sister object property to is-part-of, AfricanWildlifeOntology4b.owl has it as sub-object property of is-part-of, and neither ontology has any “characteristics” (relational properties) checked for direct-part. Before running the reasoner to classify the taxonomy, what do you think will happen with our Giraffe in both cases?

In AfricanWildlifeOntology4a.owl, Giraffe is still a mere direct subclass of Animal, whereas with AfricanWildlifeOntology4b.owl, we do obtain the (desired) deduction that Giraffe is a Herbivore. That is, we obtain different results depending on where we put the uncharacterized direct-part object property in the RBox. Why is this so?

By not clicking the checkbox “transitive”, an object property is non­-transitive, but not in-transitive. In fact, we cannot represent explicitly that an object property is intransitive in OWL (see OWL guide and related documents). If we put the object property at the top level (or, as in Protégé 4.1, as immediate subproperty of topObjectProperty), then we obtain the behaviour as if the property were intransitive (and therefore Giraffe is not classified as a subclass of Herbivore). However, the direct-part property is really nontransitive in the ontology. When direct-part is put as subproperty of is-part-of, then it inherits the transitivity characteristic from is-part-of and therefore Giraffe is classified as a Herbivore (because now leaf and Twig are part of plant thanks to the transitivity).

Obviously, it holds for any OWL/OWL2 object property that one cannot assert intransitivity explicitly, that an object property’s characteristics are inherited to its subproperties, and this kind of behaviour of nontransitive object properties depends on where you place it in the RBox—whether you like it or not.

How to go forward?

Direct parthood is called isComponentOf in the componency ontology design pattern and is a subproperty of isPartOf. Its inverse is called haspart_directly in the W3C best practices document on Simple Part-Whole relations [1], and is a subproperty of the transitive haspart. The componency.owl notes that isComponentOf is “hasPart relation without transitivity”, the ODP page’s “intent” of the pattern is that it is intended to “represent (non-transitively) that objects either are proper parts of other objects, or have proper parts”, and the W3C best Practices note that, unlike mereological parthood, it is “not transitive”. Hence, if you include either one in your OWL ontology, you will not obtain the intended behaviour. Therefore, I do not recommend using either suggestion.

Setting aside the W3C’s best practices motivation for inclusion of haspart_directly—easier querying for immediate parts, but for the ontology purist this ought not to be the motivation for its inclusion—it is worth digging a little deeper into the semantics of the direct parthood. Maybe a modeller actually wants to represent collections with their members, like each Fleet has as direct parts more than one Ship, or constitution of objects, like clay is directly part of some vase? In both cases, however, we deal with meronymic part-whole relations, not mereological ones (see [2] and references therein); hence, they should not be subsumed by the mereological part-of relation anyway. They can be modelled as sister properties of the part-of relation and have the intended nontransitive behaviour as in, e.g., the pwrelations.owl ontology with a taxonomy of part-whole relations (that can be imported into the wildlife ontology).

Alternatively, there is always the option to choose a sufficiently expressive non-OWL language to represent the direct parthood and the rest of the subject domain and use one of the many first/second order theorem provers.

References

[1] Alan Rector and Chris Welty. Simple Part-Whole relations in OWL ontologies. W3C Editor’s draft, 11 August 2005.

[2] C. Maria Keet and Alessandro Artale. Representing and Reasoning over a Taxonomy of Part-Whole Relations. Applied Ontology, 2008, 3(1-2): 91-110.

African Wildlife Ontology tutorial ontologies

(update 30-9-2019: there are newer versions that can be used with or without the OE book)

Following the invitation by Deshen Moodley from the University of KwaZulu-Natal to give a guest lecture for his Ontology and Knowledge Based Systems fourth year (honours) course, I looked up the African Wildlife Ontology he intended to use and that was introduced in the A Semantic Web Primer book by Grigoris Antoniou and Frank van Harmelen [1]. Given the state of that tutorial ontology, I could not resist fiddling with it to make the tutorial ontology a little more comprehensive.

Googling for an existing version in OWL on the Web, I came across Guy Lapalme’s version that, however, gave me an error loading it in Protégé 4.1-beta due to the use of collection in the definition of Herbivore. Having removed that and renamed the .xml extension into .owl, this version is renamed AfricanWildlifeOntology0.owl. The ontology has 10 classes and 3 object properties concerning animals such as Lion, Giraffe, Plant, eats, and is-part-of. Note the annotations in the ontology that give an idea of what should be modelled (else: see 4.3.1 pages 119-133 in [1]). Upon running the reasoner, it will classify, among others, that Carnivore is a subclass of Animal.

All this is not really exciting though, and the tutorial ontology is not of a particularly good quality. First, I added knowledge: I played with proper parthood and added a few more plant parts and animals, such as Impala, Warthog, and RockDassie, and also refined knowledge such that giraffes eat not only leaves but also twigs and there are omnivores, too. This version of the African Wildlife Ontology is named AfricanWildlifeOntology1.owl. With this additional knowledge, warthogs are classified as omnivores, lions as carnivores, giraffes as herbivores, and so on. We still miss out on having impalas classified as herbivores; what can—or should—you add to the ontology to achieve that?

However, adding classes and object properties to an ontology does not necessarily make a better quality ontology. One aspect that does with respect to the subject domain, is to refine the represented knowledge so as to limit the possible models, such as giraffes eating both leaves and twigs and adding more characteristics to the object properties, like that the is-part-of is not only transitive, but also reflexive, and is-proper-part-of is transitive and irreflexive or asymmetric (the latter we can add thanks to the increased expressiveness of OWL 2 DL compared to OWL-DL). Another aspect is purely engineering: if you intend to put your ontology online, you should name the ontology (in Protégé select “refactor” and “change ontology URI”) so that its contents can be identified appropriately on the Semantic Web. Third, we can improve the ontology’s quality by using a foundational ontology.

Foundational ontologies provide principal categories of kinds of entities and relations to give a basic structure to a reference or domain ontology. With it, you can avoid reinventing the wheel during ontology development by availing of outcomes from research into the foundations of ontologies and it can guide you to make the modelling process easier to carry out successfully. In addition, it facilitates linking your ontology with other ontologies that also adhere to a foundational ontology. Foundational ontologies contain basic categories such as IndependentContinuant/Endurant (roughly: to represent objects) and Occurent/Perdurant (informally: processes), and Quality for representing attributes, and then their respective sub-categories, such as AmountOfMatter, Feature, PhysicalObject, Achievement, Function, and SpatialRegion; see, e.g., DOLCE, BFO, GFO, GUM, and SUMO.

For the sake of example, let us take DOLCE [2] to enrich the African Wildlife Ontology. To do this, we need to import into our wildlife ontology an OWLized version of DOLCE; in this case, we import DOLCE-lite.owl. Then, consider first the taxonomic component of DOLCE (see Wonderweb deliverable D18 Fig 2 p14 and Table 1 p15 or explore the imported ontology with its annotations). Where does Plant fit in in the DOLCE categorisation? Giraffes drink water: where should we put Water? Impalas run (fast); where should we put Running? Lions eat impalas, and in the process, the impalas die; where should we put Death? The answers can be found in AfricanWildlifeOntology2.owl. DOLCE is more than a taxonomy, and we can also inspect in more detail its object properties and reuse the already defined properties instead of re-inventing them. First, the African Wildlife Ontology’s is-part-of is the same as DOLCE’s part, and likewise for their respective inverses. Concerning the subject domain, here are a few modelling questions. The elephant’s Tusks (ivory) are made of Apatite (calcium phosphate, an amount of matter); which DOLCE relation can be reused? Giraffes eat leaves and twigs; how do Plant and Twig relate? How would you represent the Size (Height, Weight, etc.) of an average adult elephant; with DOLCE’s Quality or an OWL data property? Answers to the former two questions are included in AfricanWildlifeOntology2.owl.

How does it work out when we import BFO into AfricanWildlifeOntology1.owl? Aside from minor differences (e.g., Death is not a type of Achievement as in DOLCE, but a ProcessBoundary instead, and animals and plants are subtypes of Object), there is a major difference with respect to the object properties (BFO has none). A possible outcome of linking the wildlife ontology to BFO is included in AfricanWildlifeOntology3.owl. To do these last two exercises with DOLCE and BFO in a transparent and reusable way, however, we need a mapping between the two foundational ontologies. Even more so: if there was a proper mapping, only one of the two exercises would have sufficed and the software would have taken care of the mappings between the two. But, alas, such a mapping and implementation is yet to be done.

One could take the development a step further by adding types of part-whole relations [3] so as to be more precise than only a generic part-of relation (e.g., Root is a structural part of some Plant and NatureReserve is located-in some Country) and/or consider a Content Ontology Design Pattern [4], such as being more finicky about names for plants and animals with, perhaps, the Linnaean Taxonomy content pattern or adding some information on the Climatic Zone where the plants and animals live, and so on. (But note that regarding content, one also can take a bottom-up approach to ontology development with resources such as the Environment Ontology or pick and choose from ‘semantified’ Biodiversity Information Standards etc.)

References

[1] Antoniou, G, van Harmelen, F. A Semantic Web Primer. MIT Press, 2003.

[2] Masolo, C., Borgo, S., Gangemi, A., Guarino, N., Oltramari, A. WonderWeb Deliverable D18–Ontology library. WonderWeb. 2003.

[3] Keet, C.M. and Artale, A. Representing and Reasoning over a Taxonomy of Part-Whole Relations. Applied Ontology, IOS Press, 2008, 3(1-2): 91-110.

[4] Presutti, V., Gangemi, A., David, S., de Cea, G. A., Surez-Figueroa, M. C., Montiel-Ponsoda, E., Poveda, M. A library of ontology design patterns: reusable solutions for collaborative design of networked ontologies. NeOn deliverable D2.5.1, Institute of Cognitive Sciences and Technologies (CNR). 2008.