An Ontology Engineering textbook

My first textbook “An Introduction to Ontology Engineering” (pdf) is just released as an open textbook. I have revised, updated, and extended my earlier lecture notes on ontology engineering, amounting to about 1/3 more new content cf. its predecessor. Its main aim is to provide an introductory overview of ontology engineering and its secondary aim is to provide hands-on experience in ontology development that illustrate the theory.

The contents and narrative is aimed at advanced undergraduate and postgraduate level in computing (e.g., as a semester-long course), and the book is structured accordingly. After an introductory chapter, there are three blocks:

• Logic foundations for ontologies: languages (FOL, DLs, OWL species) and automated reasoning (principles and the basics of tableau);
• Developing good ontologies with methods and methodologies, the top-down approach with foundational ontologies, and the bottom-up approach to extract as much useful content as possible from legacy material;
• Advanced topics that has a selection of sub-topics: Ontology-Based Data Access, interactions between ontologies and natural languages, and advanced modelling with additional language features (fuzzy and temporal).

Each chapter has several review questions and exercises to explore one or more aspects of the theory, as well as descriptions of two assignments that require using several sub-topics at once. More information is available on the textbook’s page [also here] (including the links to the ontologies used in the exercises), or you can click here for the pdf (7MB).

Feedback is welcome, of course. Also, if you happen to use it in whole or in part for your course, I’d be grateful if you would let me know. Finally, if this textbook will be used half (or even a quarter) as much as the 2009/2010 blogposts have been visited (around 10K unique visitors since posting them), that would mean there are a lot of people learning about ontology engineering and then I’ll have achieved more than I hoped for.

UPDATE: meanwhile, it has been added to several open (text)book repositories, such as OpenUCT and the Open Textbook Archive, and it has been featured on unglue.it in the week of 13-8 (out of its 14K free ebooks).

Orchestrating 28 logical theories of mereo(topo)logy

Parts and wholes, again. This time it’s about the logic-aspects of theories of parthood (cf. aligning different hierarchies of (part-whole) relations and make them compatible with foundational ontologies). I intended to write this post before the Ninth Conference on Knowledge Capture (K-CAP 2017), where the paper describing the new material would be presented by my co-author, Oliver Kutz. Now, afterwards, I can add that “Orchestrating a Network of Mereo(topo) logical Theories” [1] even won the Best Paper Award. The novelties, in broad strokes, are that we figured out and structured some hitherto messy and confusing state of affairs, showed that one can do more than generally assumed especially with a new logics orchestration framework, and we proposed first steps toward conflict resolution to sort out expressivity and logic limitations trade-offs. Constructing a tweet-size “tl;dr” version of the contents is not easy, and as I have as much space here on my blog as I like, it ended up to be three paragraphs here: scene-setting, solution, and a few examples to illustrate some of it.

Problems

As ontologists know, parthood is used widely in ontologies across most subject domains, such as biomedicine, geographic information systems, architecture, and so on. Ontology (the philosophers) offer a parthood relation that has a bunch of computationally unpleasant properties that are structured in a plethora of mereologicial and meretopological theories such that it has become hard to see the forest for the trees. This is then complicated in practice because there are multiple logics of varying expressivity (support more or less language features), with the result that only certain fragments of the mereo(topo)logical theories can be represented. However, it’s mostly not clear what can be used when, during the ontology authoring stage one may want to have all those features so as to check correctness, and it’s not easy to predict what will happen when one aligns ontologies with different fragments of mereo(topo)logy.

Solution

We solved these problems by specifying a structured network of theories formulated in multiple logics that are glued together by the various linking constructs of the Distributed Ontology, Model, and Specification Language (DOL). The ‘structured network of theories’-part concerns all the maximal expressible fragments of the KGEMT mereotopological theory and five of its most well-recognised sub-theories (like GEM and MT) in the seven Description Logics-based OWL species, first-order logic, and higher order logic. The ‘glued together’-part refers to relating the resultant 28 theories within DOL (in Ontohub), which is a non-trivial (understatement, unfortunately) metalanguage that has the constructors for the glue, such as enabling one to declare to merge two theories/modules represented in different logics, extending a theory (ontology) with axioms that go beyond that language without messing up the original (expressivity-restricted) ontology, and more. Further, because the annoying thing of merging two ontologies/modules can be that the merged ontology may be in a different language than the two original ones, which is very hard to predict, we have a cute proof-of-concept tool so that it assists with steps toward resolution of language feature conflicts by pinpointing profile violations.

Examples

The paper describes nine mechanisms with DOL and the mereotopological theories. Here I’ll start with a simple one: we have Minimal Topology (MT) partially represented in OWL 2 EL/QL in “theory8” where the connection relation (C) is just reflexive (among other axioms; see table in the paper for details). Now what if we add connection’s symmetry, which results in “theory4”? First, we do this by not harming theory8, in DOL syntax (see also the ESSLI’16 tutorial):

logic OWL2.QL
ontology theory4 =
theory8
then
ObjectProperty: C Characteristics: Symmetric %(t7)

What is the logic of theory4? Still in OWL, and if so, which species? The Owl classifier shows the result:

Another case is that OWL does not let one define an object property; at best, one can add domain and range axioms and the occasional ‘characteristic’ (like aforementioned symmetry), for allowing arbitrary full definitions pushes it out of the decidable fragment. One can add them, though, in a system that can handle first order logic, such as the Heterogeneous toolset (Hets); for instance, where in OWL one can add only “overlap” as a primitive relation (vocabulary element without definition), we can take such a theory and declare that definition:

logic CASL.FOL
ontology theory20 =
theory6_plus_antisym_and_WS
then %wdef
. forall x,y:Thing . O(x,y) <=> exists z:Thing (P(z,x) /\ P(z,y)) %(t21)
. forall x,y:Thing . EQ(x,y) <=> P(x,y) /\ P(y,x) %(t22)

As last example, let me illustrate the notion of the conflict resolution. Consider theory19—ground mereology, partially—that is within OWL 2 EL expressivity and theory18—also ground mereology, partially—that is within OWL 2 DL expressivity. So, they can’t be the same; the difference is that theory18 has parthood reflexive and transitive and proper parthood asymmetric and irreflexive, whereas theory19 has both parthood and proper parthood transitive. What happens if one aligns the ontologies that contain these theories, say, O1 (with theory18) and O2 (with theory19)? The Owl classifier provides easy pinpointing and tells you the profile: OWL 2 full (or: first order logic, or: beyond OWL 2 DL—top row) and why (bottom section):

Now, what can one do? The conflict resolution cannot be fully automated, because it depends on what the modeller wants or needs, but there’s enough data generated already and there are known trade-offs so that it is possible to describe the consequences:

• Choose the O1 axioms (with irreflexivity and asymmetry on proper part of), which will make the ontology interoperable with other ontologies in OWL 2 DL, FOL or HOL.
• Choose O2’s axioms (with transitivity on part of and proper part of), which will facilitate linking to ontologies in OWL 2 RL, 2 EL, 2 DL, FOL, and HOL.
• Choose to keep both sets will result in an OWL 2 Full ontology that is undecidable, and it is then compatible only with FOL and HOL ontologies.

As serious final note: there’s still fun to be had on the logic side of things with countermodels and sub-networks and such, and with refining the conflict resolution to assist ontology engineers better. (or: TBC)

As less serious final note: the working title of early drafts of the paper was “DOLifying mereo(topo)logy”, but at some point we chickened out and let go of that frivolity.

References

[1] Keet, C.M., Kutz, O. Orchestrating a Network of Mereo(topo)logical Theories. Ninth International Conference on Knowledge Capture (K-CAP’17), Austin, Texas, USA, December 4-6, 2017. ACM Proceedings.

Part-whole relations and foundational ontologies

Part-whole relations seem like a never-ending story—and it still doesn’t bore me. In this case, the ingredients were the taxonomy of part-whole relations [1] and a couple of foundational ontologies and the aim was to link the former to the latter. But what started off with the intention to write just a short workshop note, for seemingly clear and just in need of actually doing it, turned out to be not so straightforward after all. The selected foundational ontologies were not as compatible as assumed, and creating the corresponding orchestration of OWL files was a ‘non-trivial exercise’.

What were (some of) the issues? On the one hand, there are multiple part-whole relations, which are typically named differently when they have a specific domain or range. For instance, to relate a process to a sub-process (e.g., eating involves chewing), to relate a region to a region it contains, relating portions of stuff, and so on. Those relations are fairly well established in the literature. What they do demand for, however, is clarity as to what those categories really are. For instance, with the process example, is that to be understood as Process as meant in the DOLCE ontology, or, say, Process in BFO? What if a foundational ontology does not have a category needed for a commonly used part-whole relation?

The first step to answer such questions was to assess several foundational ontologies on 1) which of the part-whole relations they have now, and which categories are present that are needed for the domain and range declarations for those common part-whole relations. I assessed that for DOLCE, BFO, GFO, SUMO, GIST, and YAMATO. This foundational ontology comparison is summarised in tables 1 and 2 in the paper that emanated from the assessment [2], entitled “A note on the compatibility of part-whole relations with foundational ontologies” that I recently presented at FOUST-II: 2nd Workshop on Foundational Ontology, Joint Ontology Workshops 2017 in Bolzano, Italy. In short: none fits perfectly for various reasons, but there are more and less suitable ontologies for a possible alignment. DOLCE and SUMO were evaluated to have the best approximations. It appeared at the workshops presentation’s Q&A session, where two of the DOLCE developers were present, that the missing Collective was an oversight, or: the ontology is incomplete and it was not an explicit design choice to exclude it. This, then, would make DOLCE the best/easiest fit.

I’ll save you the trials and tribulations creating the orchestrated OWL files. The part-whole relations, their inverses, and their proper parthood versions were manually linked to modules of DOLCE and SUMO, and automatically linked to BFO and GFO. That was an addition of 49 relations (OWL object properties) and 121 logical axioms, which were then extended further with another 11 mereotopological relations and its 16 logical axioms. These files are accessible online directly here and also listed with brief descriptions.

While there is something usable now and, by design at least, these files are reusable as well, what it also highlighted is that there are still some outstanding questions, as there already were for the top-level categories of previously aligned foundational ontologies [3]. For instance, some categories seem the same, but they’re in ‘incompatible’ parts of the taxonomy (located in disjoint branches), so then either not the same after all, or this happened unintentionally. Only GIST has been updated recently, and it may be useful if the others foundational ontologies were to be as well, so as to obtain clarity on these issues. The full interaction of part-whole relations with classical mereology is not quite clear either: there are various extensions and deviations, such as specifically for portions [4,5], but one for processes may be interesting as well. Not that such prospective theories would be usable as-is in OWL ontology development, but there are more expressive languages that start having tooling support where it could be an interesting avenue for future work. I’ll write more about the latter in an upcoming post (covering the K-CAP 2017 paper that was recently accepted).

On a last note: the Joint Ontology Workshops (JOWO 2017) was a great event. Some 100 ontologists from all over the world attended. There were good presentations, lively conversations, and it was great to meet up again with researchers I had not seen for years, finally meet people I knew only via email, and make new connections. It will not be an easy task to surpass this event next year at FOIS 2018 in Cape Town.

References

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

[2] Keet, C.M. A note on the compatibility of part-whole relations with foundational ontologies. FOUST-II: 2nd Workshop on Foundational Ontology, Joint Ontology Workshops 2017, 21-23 September 2017, Bolzano, Italy. CEUR-WS Vol. (in print)

[3] Khan, Z.C., Keet, C.M. Foundational ontology mediation in ROMULUS. Knowledge Discovery, Knowledge Engineering and Knowledge Management: IC3K 2013 Selected Papers. A. Fred et al. (Eds.). Springer CCIS vol. 454, pp. 132-152, 2015. preprint

[4] Donnelly, M., Bittner, T. Summation relations and portions of stuff. Philosophical Studies, 2009, 143, 167-185.

[5] Keet, C.M. Relating some stuff to other stuff. 20th International Conference on Knowledge Engineering and Knowledge Management (EKAW’16). Blomqvist, E., Ciancarini, P., Poggi, F., Vitali, F. (Eds.). Springer LNAI vol. 10024, 368-383. 19-23 November 2016, Bologna, Italy.

Aligning different relations: the case of part-whole relations—LDK2017

Despite the best intentions, I did not get around to writing a post on the paper that I presented last week at the First International Conference on Language, Data and Knowledge 2017, 19-20 June, Galway, Ireland, and now Paul Groth also ‘beat’ me to it writing a nice conference report of it. On the bright side, it is an opportunity to say upfront I really enjoyed the conference and look forward to the next edition in 2019. The ESWC’17 organisers might be slightly disappointed that there was no special track on the multilingual semantic web after all, but I did get the distinct impression that the LDK17 authors might just all have gambled on LDK17—an opportunity to binge two days on all things natural language & Semantic Web—rather than on one track at an overpriced conference (despite the allure of it being A-rated).

So, what was my paper about that could have been submitted to either? I ended up struggling—and solving—an issue with aligning OWL object properties that were not simple 1:1 mappings, in a similar scope as our ESWC17 paper (introduced here) [4], but then with too many complications. Complications were due to the different conceptualisations of part-whole relations and that one of the requirements was to solve what to do with an object property (relation, relationship) that does not have a neat, single, label, and therewith neither fitting with the common OWL modelling paradigm nor with the recently agreed-upon ontolex-lemon model for linguistic annotations.

The start of all this sounded nice and doable: we need to generate natural language for healthcare, using, e.g., SNOMED CT, in local languages in South Africa, focussing on the largest one, being isiZulu. Medical terminologies are riddled with part-whole relations, so we sought to address that one (simple existentials already having been solved), availing of a standard list of part-whole relations (e.g. [1]). That turned out to be a non-trivial exercise, but doable eventually [2]. What wasn’t addressed in [2] was that some ‘common’ part-whole relations, such as membership and containment, weren’t like that in isiZulu, at all. Moreover, it wasn’t just a language issue, but ontological as well. The LDK17 paper “Representing and aligning similar relations: parts and wholes in isiZulu vs English” [3] describes this in some detail.

Here’s a (simplified) list of (assumed to be) common part-whole relations, which takes into account both transitivity differences and domain and range:

Now here’s the one based on the isiZulu language and some ontological analysis of that:

That is: there are both generalisations—some distinctions are not being made—and specialisations—some distinctions are made here but not elsewhere. For instance, ‘musician is part of some orchestra’ and ‘heart is part of some human’ (or vv.) is all done and described in the same way (ingxenye ‘part of’ and SC+CONJ for ‘has part’ [more about that below]). Yet, there is a difference between an individual (e.g., a voter) participating in some process and a collective (e.g., the electorate) participating in a process, or vv. The paper describes this more precisely, going into some detail regarding the differences in categories of domain and range and into the consequences on transitivity of mereological parthood.

The other ‘odd thing’—cf. current multilingual Semantic Web assumptions and technologies, that is—is that while the conceptualisation of ‘has part’ exists, it does not have a single label as in English (or in several other languages, such as heeft as deel), but it is dependent on the noun class of the noun of the class that play the part and play the whole in the relation. It combines the subject concord (~conjugation) of the noun class of the noun that plays the whole with a conjunction that is phonologically conditioned based on the first letter of the noun that plays the part; with verbalisation in the plural and three phonological cases, there are 18 possible strings all denoting ‘has part’. This still could be sorted with a language with inverses, provided the part-of direction has a name, like the ingxenye. This is not the case for containment, however. Instead of the relation (object property) having a name—be this a verb like ‘contained in’ or some noun phrase—it is the noun that plays the whole (the container, if you will) that gets modified. For instance, imvilophu ‘envelope’ and emvilophini denoting ‘contained in the envelope’, or, for individuals and locations, the city iTheku ‘Durban’ and eThekwini meaning ‘located in Durban’ (no typo—there’s some phonological conditioning I’m brushing over). While I have gotten used to such constructions, it generated some surprise among several attendees that one can have notions, concepts, views on or interpretations or descriptions of reality, that exist but do not have even one single string of text throughout to refer to regardless the context it is used.

The naming issue was solved by adding some arbitrary string as ‘name’ of the object property, and relating that to the function that verbalises that specific part-whole relation. The former issue, i.e., not all the same part-whole relations, required a bit more work, using ontology pattern alignments, by extending one correspondence pattern from the ODP catalogue and introducing a new one (see paper for the formal details), using the same broad framework of formalisation as proposed in [4].

All this was then implemented and aligned, and verified to not result in some unsatisfiable classes, object properties, or inconsistency (files). This also works in the isiZulu verbalisation tool we demo-ed at ESWC17 (described in the previous post) [5], all as part of the NRF-funded GeNI project.

Now, ideally, I already would have had the time to read the papers I flagged in my LDK17 conference notes with “check paper”. I haven’t yet due to end-of-semester tasks. So, on the basis of just a positive-seeming presentation, here are a few that are on the top of my list to check out first, for quite different reasons:

• Interaction between natural language reading capabilities and math education, focusing on language production (i.e., ‘can you talk about it?’) [6], mainly because math education in South Africa faces a lot of problems. It also generated a lively discussion in the Q&A session.
• The OnLiT ontology for linguistic [7] and LLODifying linguistic glosses [8] terminology (also: one of the two also won the best paper award).
• Deep text generation, for it was looking at trying to address skewed or limited data to learn from [9], which is an issue we face when trying to do some NLP with most South African languages.

References

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

[2] Keet, C.M., Khumalo, L. On the verbalization patterns of part-whole relations in isiZulu. 9th International Natural Language Generation conference (INLG’16), September 5-8, 2016, Edinburgh, UK. ACL.

[3] Keet, C.M. Representing and aligning similar relations: parts and wholes in isiZulu vs English. In: Gracia J., Bond F., McCrae J., Buitelaar P., Chiarcos C., Hellmann S. (eds) Language, Data, and Knowledge LDK 2017. Springer LNAI vol 10318, 58-73.

[4] Fillottrani, P.R., Keet, C.M. Patterns for Heterogeneous TBox Mappings to Bridge Different Modelling Decisions. 14th Extended Semantic Web Conference (ESWC’17). Springer LNCS. Portoroz, Slovenia, May 28 – June 2, 2017.

[5] Keet, C.M. Xakaza, M., Khumalo, L. Verbalising OWL ontologies in isiZulu with Python. 14th Extended Semantic Web Conference (ESWC’17). Springer LNCS. Portoroz, Slovenia, May 28 – June 2, 2017. (demo paper)

[6] Crossley, S., Kostyuk, V. Letting the genie out of the lamp: using natural language processing tools to predict math performance. In: Gracia J., Bond F., McCrae J., Buitelaar P., Chiarcos C., Hellmann S. (eds) Language, Data, and Knowledge LDK 2017. Springer LNAI vol 10318, 330-342.

[7] Klimek, B., McCrae, J.P., Lehmann, C., Chiarcos, C., Hellmann, S. OnLiT: and ontology for linguistic terminology. In: Gracia J., Bond F., McCrae J., Buitelaar P., Chiarcos C., Hellmann S. (eds) Language, Data, and Knowledge LDK 2017. Springer LNAI vol 10318, 42-57.

[8] Chiarcos, C., Ionov, M. Rind-Pawlowski, M., Fäth, C., Wichers Schreur, J., Nevskaya. I. LLODifying linguistic glosses. In: Gracia J., Bond F., McCrae J., Buitelaar P., Chiarcos C., Hellmann S. (eds) Language, Data, and Knowledge LDK 2017. Springer LNAI vol 10318, 89-103.

[9] Dethlefs N., Turner A. Deep Text Generation — Using Hierarchical Decomposition to Mitigate the Effect of Rare Data Points. In: Gracia J., Bond F., McCrae J., Buitelaar P., Chiarcos C., Hellmann S. (eds) Language, Data, and Knowledge LDK 2017. Springer LNAI vol 10318, 290-298.

More stuff: relating stuffs and amounts of stuff to their parts and portions

With all the protests going on in South Africa, writing this post is going to be a moment of detachment of it (well, I’m trying), for it concerns foundational aspects of ontologies with respect to “stuff”. Stuff is the philosophers’ funny term for those kind of things that cannot be counted, or only counted in quantities, and are in natural language generally referred to by mass nouns. For instance, water, gold, mayonnaise, oil, and wine as kinds of things, yet one can talk of individual objects of them only in quantities, like a glass of wine, a spoonful of mayonnaise, and a litre of oil. It is one thing to be able to say which types of stuff there are [1], it is another matter how they relate to each other. The latter is described in the paper recently accepted at the 20th International Conference on Knowledge Engineering and Knowledge management (EKAW’16), entitled “Relating some stuff to other stuff” [2].

Is something like that even relevant, when students are protesting for free education, among other demands? Yes. At the end of the day, it is part and parcel of a healthy environment to live in. For instance, one should be able to realise traceability in food and medicine supply chains, to foster practices, and check compliance, of good production processes and supply chains, so that you will not buy food that makes you ill or take medicines that are fake [3,4]. Such production processes and product logistics deal with ‘stuffs’ and their portions and parts that get separated and put together to make the final product. Current implementations have only underspecified ‘links’ (if at all) that doesn’t let one infer automatically what (or who) the culprit is. Existing theoretical accounts from philosophy and in domain ontologies are incomplete, so they wouldn’t help you further either. The research described in the paper solves this issue.

Seven relations for portions and stuff-parts were identified, which have a temporal dimension where needed. For instance, the upper-half of the wine in your wine glass is a portion of the whole amount of wine in the glass, yet that amount of wine was a portion of the amount of wine in the bottle when you opened it, and yet it has as part some amount of alcohol. (Some reader may not find this example nice, for it being with alcohol, but Western Cape, where Cape Town is situated, is the wine region of the country.) The relations are structured in a little hierarchy, as informally depicted in the figure below.

Section of the basic taxonomy of part-whole relations of [5] (less and irrelevant sections in grey or suppressed), extended with the stuff relations and their position in the hierarchy.

Their formal definitions are included in the paper.

Another aspect of the solution is that it distinguishes between 1) the extensional and intensional level—like, between ‘an amount of wine’ and ‘wine’—because different constraints apply (following from that latter can be instantiated the former cannot), and 2) the amount of stuff and the (repeatable) quantity, as one can have 1kg of many things.

Just theory isn’t good enough, though, for one would want to use it in some way to indeed get those benefits of traceability in the supply chains. After considering the implementation options (see paper for details), I settled for an extension to the Stuff Ontology core ontology that now also imports a special purpose module OMmini of the Ontology of Units of Measure (see also the Stuff Ontology page). The latter sounds easier than that it worked in praxis, but that’s a topic of a different post. The module is there, and the links between the OMmin.owl and stuff.owl have been declared.

Although the implementation is atemporal in the end, it is still possible to do some automated reasoning for traceability. This is mainly thought availing of property chains to approximate the relevant temporal aspects. For instance, with $scatteredPortionOf \circ portionOf \sqsubseteq scatteredPortionOf$ then one can infer that a scattered portion in my glass of wine that was a portion of bottle #1234 of organic Pinotage wine of an amount of wine, contained in cask #3, with wine from wine farm X of Stellar Winery from the 2015 harvest is a scattered portion of that amount of matter (that cask). Or take the (high-level) pharmaceutical supply chain from [4]: a portion (that is on a ‘pallet’) of the quantity of medicine produced by the manufacturer goes to the warehouse, of which a portion (in a ‘case’) goes to the distribution centre. From there, a portion ends up on the dispensing shelf, and someone buys it. Then tracing any customer’s portion of medicine—i.e., regardless the actual instance—can be inferred with the following chain: $scatteredPortionOf \circ scatteredPortionOf \circ scatteredPortionOf \sqsubseteq scatteredPortionOf$

Sure, the research presented hasn’t solved everything yet, but at least software developers now have a (better) way to automate traceability in supply chains. It also allows one to be more fine-grained in the analysis where a culprit may be, so that there are fewer cases of needless scares. For instance, we know that when there’s an outbreak of Salmonella, then we only have to trace where the batch of egg yolk went (typically in the tiramisu served in homes for the elderly), where it came from (which farm), and got mixed with in the production process, while the amounts of egg white on your lemon merengue still would be safe to eat even when it came from the same batch that had at least one infected egg.

I’ll be presenting the paper at EKAW’16 in November in Bologna, Italy, and hope to see you there! It’s not a good time of the year w.r.t. weather, but that’s counterbalanced by the beauty of the buildings and art works, and the actual venue room is in one of the historical buildings of the oldest university of Europe.

References

[1] Keet, C.M. A core ontology of macroscopic stuff. 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW’14). K. Janowicz et al. (Eds.). 24-28 Nov, 2014, Linkoping, Sweden. Springer LNAI vol. 8876, 209-224.

[2] Keet, C.M. Relating some stuff to other stuff. 20th International Conference on Knowledge Engineering and Knowledge Management EKAW’16). Springer LNAI, 19-23 November 2016, Bologna, Italy. (accepted)

[3] Donnelly, K.A.M. A short communication – meta data and semantics the industry interface: what does the food industry think are necessary elements for exchange? In: Proc. of Metadata and Semantics Research (MTSR’10). Springer CCIS vol. 108, 131-136.

[4] Solanki, M., Brewster, C. OntoPedigree: Modelling pedigrees for traceability in supply chains. Semantic Web Journal, 2016, 7(5), 483-491.

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

On generating isiZulu sentences with part-whole relations

It all sounded so easy… We have a pretty good and stable idea about part-whole relations and their properties (see, e.g., [1]), we know how to ‘verbalise’/generate a natural language sentence from basic description logic axioms with object properties that use simple verbs [2], like $Professor \sqsubseteq \exists teaches.Course$ ‘each professor teaches at least one course’, and SNOMED CT is full of logically ‘simple’ axioms (it’s in OWL 2 EL, after all) and has lots of part-whole relations. So why not combine that? We did, but it took some more time than initially anticipated. The outcomes are described in the paper “On the verbalization patterns of part-whole relations in isiZulu”, which was recently accepted at the 9th International Natural Language Generation Conference (INLG’16) that will be held 6-8 September in Edinburgh, Scotland.

What it ended up to be, is that notions of ‘part’ in isiZulu are at times less precise and other times more precise compared to the taxonomy of part-whole relations. This interfered with devising the sentence generation patterns, it pushed the number of ‘elements’ to deal with in the language up to 13 constituents, and there was no way to avoid proper phonological conditioning. We already could handle quantitative, relative, and subject concords, the copulative, and conjunction, but what had to be added were, in particular, the possessive concord, locative affixes, a preposition (just the nga in this context), epenthetic, and the passive tense (with modified final vowel). As practically every element has to be ‘completed’ based on the context (notably the noun class), one can’t really speak of a template-based approach anymore, but a bunch of patterns and partial grammar engine instead. For instance, plain parthood, structural parthood, involvement, membership all have:

• (‘each whole has some part’) $QCall_{nc_{x,pl}}$ $W_{nc_{x,pl}}$ $SC_{nc_{x,pl}}-CONJ-P_{nc_y}$ $RC_{nc_y}-QC_{nc_y}-$dwa
• (‘each part is part of some whole’) $QCall_{nc_{x,pl}}$ $P_{nc_{x,pl}}$ $SC_{nc_{x,pl}}-COP-$ingxenye $PC_{\mbox{\em ingxenye}}-W_{nc_y}$ $RC_{nc_y}-QC _{nc_y}-$dwa

There are a couple of noteworthy things here. First, the whole-part relation does not have one single string, like a ‘has part’ in English, but it is composed of the subject concord (SC) for the noun class (nc) of the noun that play the role of the whole ( W ) together with the phonologically conditioned conjunction na- ‘and’ (the “SC-CONJ”, above) and glued onto the noun of the entity that play the role of the part (P). Thus, the surface realisation of what is conceptually ‘has part’ is dependent on both the noun class of the whole (as the SC is) and on the first letter of the name of the part (e.g., na-+i-=ne-). The ‘is part of’ reading direction is made up of ingxenye ‘part’, which is a noun that is preceded with the copula (COP) y– and together then amounts to ‘is part’. The ‘of’ of the ‘is part of’ is handled by the possessive concord (PC) of ingxenye, and with ingxenye being in noun class 9, the PC is ya-. This ya- is then made into one word together with the noun for the object that plays the role of the whole, taking into account vowel coalescence (e.g., ya-+u-=yo-). Let’s illustrate this with heart (inhliziyo, nc9) standing in a part-whole relation to human (umuntu, NC1), with the ‘has part’ and ‘is part of’ underlined:

• bonke abantu banenhliziyo eyodwa ‘All humans have as part at least one heart’
• The algorithm, in short, to get this sentence from, say $Human \sqsubseteq \exists hasPart.Heart$: 1) it looks up the noun class of umuntu (nc1); 2) it pluralises umuntu into abantu (nc2); 3) it looks up the quantitative concord for universal quantification (QCall) for nc2 (bonke); 4) it looks up the SC for nc2 (ba); 5) then it uses the phonological conditioning rules to add na- to the part inhliziyo, resulting in nenhliziyo and strings it together with the subject concord to banenhliziyo; 6) and finally it looks up the noun class of inhliziyo, which is nc9, and from that it looks up the relative concord (RC) for nc9 (e-) and the quantitative concord for existential quantification (QC) for nc9 (being yo-), and strings it together with –dwa to eyodwa.
• zonke izinhliziyo ziyingxenye yomuntu oyedwa ‘All hearts are part of at least one human’
• The algorithm, in short, to get this sentence from $Heart \sqsubseteq \exists isPartOf.Human$: 1) it looks up the noun class of inhliziyo (nc9); 2) it pluralises inhliziyo to izinhliziyo (nc10); 3) it looks up the QCall for nc10 (zonke); 4) it looks up the SC for nc10 (zi-), takes y- (the COP) and adds them to ingxenye to form ziyingxenye; 5) then it uses the phonological conditioning rules to add ya- to the whole umuntu, resulting in yomuntu; 6) and finally it looks up the noun class of umuntu, which is nc1, and from that the RC for nc10 (o-) and the QC for nc10 (being ye-), and strings it together with –dwa to oyedwa.

For subquantities, we end up with three variants: one for stuff-parts (as in ‘urine has part water’, still with ingxenye for ‘part’), one for portions of solid objects (as in ‘tissue sample is a subquantity of tissue’ or a slice of the cake) that uses umunxa instead of ingxenye, and one ‘spatial’ notion of portion, like that an operating theatre is a portion of a hospital, or the area of the kitchen where the kitchen utensils are is a portion of the kitchen, which uses isiqephu instead of ingxenye. Umunxa is in nc3, so the PC is wa- so that with, e.g., isbhedlela ‘hospital’ it becomes wesibhedlela ‘of the hospital’, and the COP is ng- instead of y-, because umunxa starts with an u. And yet again part-whole relations use locatives (like the containment type of part-whole relation). The paper has all those sentence generation patterns, examples for each, and explanations for them.

The meronymic part-whole relations participation and constitution have added aspects for the verb, such as generating the passive for ‘constituted of’: –akha is ‘to build’ for objects that are made/constituted of some matter in some structural sense, else –enza is used. They are both ‘irregular’ in the sense that it is uncommon that a verb stem starts with a vowel, so this means additional vowel processing (called hiatus resolution in this case) to put the SC together with the verb stem. Then, for instance za+akhiwe=zakhiwe but u+akhiwe=yakhiwe (see rules in paper).

Finally, this was not just a theoretical exercise, but it also has been implemented. I’ll readily admit that the Python code isn’t beautiful and can do with some refactoring, but it does the job. We gave it 42 test cases, of which 38 were answered correctly; the remaining errors were due to an ‘incomplete’ (and unresolvable case for any?) pluraliser and that we don’t know how to systematically encode when to pick akha and when enza, for that requires some more semantics of the nouns. Here is a screenshot with some examples:

The ‘wp’ ones are that a whole has some part, and the ‘pw’ ones that the part is part of the whole and, in terms of the type of axiom that each function verbalises, they are of the so-called ‘all some’ pattern.

The source code, additional files, and the (slightly annotated) test sentences are available from the GENI project’s website. If you want to test it with other nouns, please check whether the noun is already in nncPairs.txt; if not, you can add it, and then invoke the function again. (This remains this ‘clumsily’ until we make a softcopy of all isiZulu nouns with their noun classes. Without the noun class explicitly given, the automatic detection of the noun class is not, and cannot be, more than about 50%, but with noun class information, we can get it up to 90-100% correct in the pluralisation step of the sentence generation [4].)

References

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

[2] Keet, C.M., Khumalo, L. Basics for a grammar engine to verbalize logical theories in isiZulu. 8th International Web Rule Symposium (RuleML’14), A. Bikakis et al. (Eds.). Springer LNCS vol. 8620, 216-225. August 18-20, 2014, Prague, Czech Republic.

[3] Keet, C.M., Khumalo, L. On the verbalization patterns of part-whole relations in isiZulu. 9th International Natural Language Generation conference (INLG’16), September 5-8, 2016, Edinburgh, UK. (in print)

[4] Byamugisha, J., Keet, C.M., Khumalo, L. Pluralising Nouns in isiZulu and Related Languages. 17th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing’16), Springer LNCS. April 3-9, 2016, Konya, Turkey. (in print)

Automatically finding the feasible object property

Late last month I wrote about the updated taxonomy of part-whole relations and claimed it wasn’t such a big deal during the modeling process to have that many relations to choose from. Here I’ll back up that claim. Primarily, it is thanks to the ‘Foundational Ontology and Reasoner enhanced axiomatiZAtion’ (FORZA) approach which includes the Guided ENtity reuse and class Expression geneRATOR (GENERATOR) method that was implemented in the OntoPartS-2 tool [1]. The general idea of the GENERATOR method is depicted in the figure below, which outlines two scenarios: one in which the experts perform the authoring of their domain ontology with the help of a foundational ontology, and the other one without a foundational ontology.

I think the pictures are clearer than the following text, but some prefer text, so here goes the explanation attempt. Let’s start with scenario A on the left-hand side of the figure: a modeller has a domain ontology and a foundational ontology and she wants to relate class two domain classes (indicated with C and D) and thus needs to select some object property. The first step is, indeed, selecting C and D (e.g., Human and Heart in an anatomy ontology); this is step (1) in the Figure.

Then (step 2) there are those long red arrows, which indicate that somehow there has to be a way to deal with the alignment of Human and of Heart to the relevant categories in the foundational ontology. This ‘somehow’ can be either of the following three options: (i) the domain ontology was already aligned to the foundational ontology, so that step (2) is executed automatically in the background and the modeler need not to worry, (ii) she manually carries out the alignment (assuming she knows the foundational ontology well enough), or, more likely, (iii) she chooses to be guided by a decision diagram that is specific to the selected foundational ontology. In case of option (ii) or (iii), she can choose to save it permanently or just use it for the duration of the application of the method. Step (3) is an automated process that moves up in the taxonomy to find the possible object properties. Here is where an automated reasoner comes into the equation, which can step-wise retrieve the parent class, en passant relying on taxonomic classification that offers the most up-to-date class hierarchy (i.e., including implicit subsumptions) and therewith avoiding spurious candidates. From a modeller’s viewpoint, one thus only has to select which classes to relate, and, optionally, align the ontology, so that the software will do the rest, as each time it finds a domain and range axiom of a relationship in which the parents of C and D participate, it is marked as a candidate property to be used in the class expression. Finally, the candidate object properties are returned to the user (step 4).

While the figure shows only one foundational ontology, one equally well can use a separate relation ontology, like PW or PWMT, which is just an implementation variant of scenario A: the relation ontology is also traversed upwards and on each iteration, the base ontology class is matched against relational ontology to find relations where the (parent of the) class is defined in a domain and range axiom, also until the top is reached before returning candidate relations.

The second scenario with a domain ontology only is a simplified version of option A, where the alignment step is omitted. In Figure-B above, GENERATOR would return object properties W and R as options to choose from, which, when used, would not generate an inconsistency (in this part of the ontology, at least). Without this guidance, a modeler could, erroneously, select, say, object property S, which, if the branches are disjoint, would result in an inconsistency, and if not declared disjoint, move class C from the left-hand branch to the one in the middle, which may be an undesirable deduction.

For the Heart and Human example, these entities are, in DOLCE terminology, physical objects, so that it will return structural parthood or plain parthood, if the PW ontology is used as well. If, on the other hand, say, Vase and Clay would have been the classes selected from the domain ontology, then a constitution relation would be proposed (be this with DOLCE, PW, or, say, GFO), for Vase is a physical object and Clay an amount of matter. Or with Limpopo and South Africa, a tangential proper parthood would be proposed, because they are both geographic entities.

The approach without the reasoner and without the foundational ontology decision diagram was tested with users, and showed that such a tool (OntoPartS) made the ontology authoring more efficient and accurate [2], and that aligning to DOLCE was the main hurdle for not seeing even more impressive differences. This is addressed with OntoPartS-2, so it ought to work better. What still remains to be done, admittedly, is that larger usability study with the updated version OntoPartS-2. In the meantime: if you use it, please let us know your opinion.

References

[1] Keet, C.M., Khan, M.T., Ghidini, C. Ontology Authoring with FORZA. 22nd ACM International Conference on Information and Knowledge Management (CIKM’13). ACM proceedings, pp569-578. Oct. 27 – Nov. 1, 2013, San Francisco, USA.

[2] Keet, C.M., Fernandez-Reyes, F.C., Morales-Gonzalez, A. Representing mereotopological relations in OWL ontologies with OntoPartS. 9th Extended Semantic Web Conference (ESWC’12), Simperl et al. (eds.), 27-31 May 2012, Heraklion, Crete, Greece. Springer, LNCS 7295, 240-254.