PURO: Capturing the Background of OWL Ontologies

Tracking #: 2112-3325

Vojtěch Svátek
Martin Homola
Ján Kluka
Marek Dudas
Miroslav Vacura

Responsible editor: 
Aldo Gangemi

Submission type: 
Full Paper
Many modeling decisions in OWL ontologies are enforced by formal constraints of the language or by pragmatic application concerns, and thus deviate from faithful modeling of reality in terms of the Universal/Particular and Relationship/Object distinctions. The proposed PURO language aims to complement OWL in this respect via providing a conceptual layer relaxing some of the OWL constraints, while it remains simple in terms of its basic repertory of constructs. We formulate the notion of ontological background model (OBM) and demonstrate how models expressed in PURO can serve as OBMs for OWL ontologies. We also provide a full first-order axiomatization of the stable core of PURO, interrelate and exemplify its primitives, and enumerate their typical OWL manifestations. Further, we analyze a number of PURO use cases in various stage of maturity, and elaborate on several evaluation experiments corroborating the usability of the PURO language. Connections to related research such as OntoClean or OntoUML are also established.
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Review #1
By Enrico Daga submitted on 01/Apr/2019
Major Revision
Review Comment:

This manuscript was submitted as 'full paper' and should be reviewed along the usual dimensions for research contributions which include
(1) originality: the article touches interesting modelling problems related mainly to N-Ary relations and meta-classes
(2) significance of the results: results are not demonstrated to be particularly significant
(3) quality of writing: the article is clear and well written
The article is an overview of the authors' research on a language to represent the "background knowledge" of OWL ontologies. Distinctive features of PURO are the support for meta-classes and N-Ary relations. As such, it's objective is to be a tool for high-level modelling operations for drafting, interpreting, transforming, and align OWL ontologies. The article gives a detailed overview of the language, highlights its potential with relation to key use cases, reports on two user based studies and gives a broad discussion of the work in related areas. I find the concept of ontological background appealing and useful and sympathise with the authors' claim on the impact that low-level language features/limitations impact bad practices in ontology engineering. However, the article in the present form has some major drawbacks, mainly related to the unbalance between the broadness of the problems discussed (the potential of the approach) and the actual, measured efficacy of the contribution. Also, the article length and heterogeneity of content made it difficult to review.
1 - Introduction
Motivation for the work is the limits of OWL in representing n-ary relations and meta classes and this is illustrated with two applications of the Music Ontology (MO) and Good Relations. The proposed PURO language is meant to provide "1) better human interaction with semantic web ontologies, and 2) automatic checking of certain aspects of conceptualisation coherence." However, I struggled to relate the two user studies reported in the Evaluation section to these goals.
Objective of the article is to produce a coherent union of the core aspects of the language, considering past publications only focused on partial elements.
2 - Ontological background models
This section gives a definition of ontological background models (OBM). OBMs are conceived in relation to foreground models (OFM) as the latter are encoded in another language (here OWL) and have the objective of being operational, while the former has mainly the role of capturing the state of affairs of reality at a more intuitive level. The relation between OFM and OBM is named B-modeling. However, this definition seems to imply that foreground models generally pre-exist background models, which is not true even in many use cases presented in the article. Clearly it is not the case, but then why defining it from the FM? An easier way to think about it is to assume that any model has a background model that better captures reality while being less constrained (and this would apply to any PURO model as well, right?)
The definition: 1) BM is less biased than FM and closer to reality; 2) BM is partially aligned with FM; and 3) BM is in a different representational space.
Also, the biases are not meant to be deterministic (!), BM should not introduce additional biases (but they are not deterministic, so how to check what they could be...), and BM does not need to preserve all the information of FM. Also, we should assume that "closer to reality" implies that BM has some additional semantics that is somehow lost in FM. Also Definition 2 is not very useful, it just says that you can have an BM without a FM as soon as it is "possible" - clearly it always is.
I have the impression that the definition given is too vague and that any two models in different formalisms having some domain overlap could be OBM of each other! I guess "closer to reality" is the key element here, but I struggle to see this claim as something clear enough to be useful, especially in pragmatic contexts. I think that a clear characterisation of the concepts of "bias" and "closer to reality" is needed.
Also, there is no discussion on the ontological paradigm of OBMs and OFMs- open world, close world, not relevant, why?
Ultimately, Ontology engineering has developed a significant literature on methodologies but there is no discussion about the role of OBMs in that sense. For example, the formalisation of Competency Questions (CQ) [1] has a strong overlap with the ontology drafting use case discussed here.
3 - The language of PURO
This section presents PURO as a theory in first-order logic. The section is very clear and highlights the basic differences with RDF and OWL, primarily the capacity of representing N-Ary relations (with Roles) and meta-modelling features such as multi-level typing and what has been called "heterogenous types" - covering meta-concepts such as "Deprecated Type". However, I would like to see a discussion of these in the light of OWL2 Annotation properties. Considering that PURO is not proposed for its inferencing capabilities one could just develop a hierarchy of OWL2 AnnotationProperty to support multi-level typing and annotations, right?
An interesting element of the approach of PURO to N-Ary relations is the support for directionality in participating roles. For example, an N-Ary relation may include participants A,B,C, and D, in different roles, but some of them are origin and others target in the relationship. This feature support several combination of directional relationships. I am intrigued by this feature and expected more use cases and discussion about the impact in modelling pragmatic (user studies). A similar observation can be made for the MISO patterns for multi-object placeholder, referring to the interesting problem of referring to multiplicity ("Amazon sells books", many unspecified individuals not certainly the class Book). All this is really interesting.

4 - Gluing PURO with OWL: transformations and alignments
This section presents PURO as a language complementary to OWL and discusses how to transform and align both formalism. In Definition 5 the terms source and target are used, although these do not imply directionality. I would suggest to not use them and replace them with "PURO model" and "OWL model", to avoid confusion. Several operations are discussed for mapping and linking PURO terms with OWL structures, discussed as different processes such as "PURO model operationalisation in OWL", "PURO model reengineering" (from OWL to PURO), "PURO model coverage alignment" (only specifying a whole OWL ontology that cover the PURO model), and "OWL ontology annotation with PURO". I feel this section as redundant with Section 5. Since the theory presented here about these operations is purposely "weak" (meaning non prescriptive, flexible) the conclusions do not seem insightful.
5 - PURO use cases
This section presents a number of use cases partly derived from existing publications, and developed ad different stages of maturity. The objective of the section is to demonstrate the "versatility" of the language and not to "bring convincing evidence on the superiority of PURO to alternate approaches in handling each particular problem". I may be wrong but this sentence seems counterproductive. I am convinced that PURO could be better than OWL in its capacity to support users in conceptualising certain aspects of a domain (e.g. N-Ary relations). I may be wrong but it should be objective of this section to show that PURO is better than OWL at something, and of the Evaluation section to demonstrate that.
I appreciate your task is not an easy one. Generally, it is difficult for users to deal with one formal language (e.g. Warren [2]). How to obtain evidence that using two languages would benefit users?
I think the ontology drafting is a strong use case particularly on developing specific aspects. The ontology design pattern analysis and education use case is interesting, although difficult to judge (in comparison to what? I can imagine that using conceptual maps or UML diagrams but is this being evaluated?)
Overall, use cases seem to refer to different things related to PURO: the DL Formalism, its Graphic Language, and a set of tools (the ecosystem). Sometimes is not clear whether use cases refer to PURO as DL formalism, a graphical language or as a tool to support B-operations. All these are different things. Generally, the majority of presented use cases have not being properly evaluated, many are at a "Proof of concept" maturity level, and one is purely hypothetical! This is a bit underwhelming considering the article aims at providing a general overview of PURO. I would recommend to focus on few core properties of PURO, the ones that have been better studies/demonstrated, and leave the rest as for a future work section.
6 - PURO evaluations
This section extensively presents two user study, one conducted with the authors and another with students. Evaluating, for example, whether PURO adds anything to OWL or not is a good question (Q1). However, of the various questions posed here, none of them directly address the primary claim of the article, stated in the introduction (and reported above). Again, I think the problem is that authors should be clear on what it is that PURO should be better at doing and focus on evaluating that thing(s).
However, the conclusions are not particularly strong in any direction, nor statistically relevant, therefore, it is hard to judge whether the questions have been answered or not (probably not).
Experiment 1 has been conducted with the two authors of the paper. I think it should be conducted by at least three experts, not including authors/inventors of PURO, and results measured with Inter-Rated agreement, in order to be able to decide whether: 1) PURO is coherent; 2) it's expected mapping to OWL consistent; etc... you cannot do that by yourself! The second study is described in rich detail but its results not statistically relevant. Why even reporting it? Would it be possible to organise a study whose results would be then statistically relevant? This section is also very long compared to the actual content, and very difficult to review.
7 - Discussion
I disagree that there is a thing called 'ontoligistic' thinking and that some people may be better at doing it than others. I also thought that the objective of PURO was to support people with less expertise in OWL modelling, so justifying the results saying that some users are less good at the job does not seem to be fair. Also, it has been demonstrated that even simple operations like deciding between instance-of and subClassOf is not a trivial thing (see Warren [2]).
8 - Related research
This section is good except it misses a discussion of PURO use cases in the context of ontology engineering methodologies.
9 - Conclusions and future work
I like the definition of PURO as "a language allowing to graphically draft ontology skeletons" but the article tries to put together too many things, in my opinion. It is clear that there is a lot of work behind this submission but there is as much work to be done if the authors want to support all those claims about it's validity and utility. One option would be to narrow down the scope of the contribution and focus only on the use cases that have proven to be valid, such as the ontology drafting use case, eventually comparing with alternative approaches such as using protege to draft class and property hierarchies.

[1] Grüninger, Michael, and Mark S. Fox. "Methodology for the design and evaluation of ontologies." (1995).
[2] Warren, Paul, et al. "The usability of description logics." European Semantic Web Conference. Springer, Cham, 2014.

Review #2
Anonymous submitted on 17/Apr/2019
Review Comment:

This paper is about the PURO conceptual modelling language that would help users to design an ontology instead of directly using the OWL language.
This work is interesting but the paper suffers a major flaw: it is much too long.
Neither a reviewer nor a reader wants to examine or read 51 pages on the subject.
Would you submit a new version of the paper, it should not exceed 20 pages maximum and you should focus on the core language itself.

Review #3
Anonymous submitted on 16/Sep/2019
Major Revision
Review Comment:

The paper proposes PURO, a novel ontological background model (notion explained by the approach proposed in this paper), for ontologies in OWL.
Section 1 introduces the need for an ontological background model to motivate the modelling choices in OWL. Section 2 focuses on the notion of Ontological Background Model (OBM).
Section 3 introduces the PURO language as an OBM. Section 4 integrates PURO with OWL. Section n 5 illustrates PURO use cases. Section 6 provides an evaluation. Section 7 discusses the proposed modelling choices. Section 8 confronts related work. Section 9 concludes.

The paper is quite long and dense, although fairly well written in a number of parts.
I will focus my comments on Section 2 and 3 and on the presentation of the theory of PURO.

About Section 2:

In Section 2, the notion of Ontological Background Model is presented, although not very clearly to me. For instance, in Definition 1, is not very intelligible to me what is the “inherent state of affairs in the domani D”.

Since the definitions here are not really formalised, I fail to see the need of both terminology “being an OBM of “ and “B-models something”.

Note 6 apparently manifests a confusion between a KR language and an ontology. Do you take them to be the same? Many authors tend to view an ontology as a theory (with axioms or constraintes) rather than a language (e.g. DL per se are not ontologies, although you can write ontologies in DL.)

About Section 3 :

Firstly, I would not call PURO a language, the language is first-order logic, so PURO is a fist-order theory, right?

On page 3 PURO is claimed to be analogous to OWL “in its core triad” however as a fragment of first order logic, it appears to permit n-ary relations (e.g. hasParticipant) and complex logical formulas (e.g. non-restricted quantifications).

The presentation of the first-order theory of PURO is not very detailed.

As far as I understand from Section 3.1. the intended domains of PURO are sorted so partitioned into 4 classes: ontological entities, PURO terms, Quantitaive values, and Roles.

For instance, if “Entity” means (ontological entities), including objects and types, Axiom (3) appears not correct, as it permits “instance of” to hold between objects.
Am I missing something?

Also, using PURO terms as elements of the ontology left me asking what is the part where the PURO “terms” gets their meaning (semantics)?

A general worry here is that the crucial distinctions are in fact not formalised.
The distinction between particulars and universals, distinguished by the possibility of instantiation is not captured by an axiom of PURO (as far as I can see).

Also the “possibility of instantiation” seems to required a modal setting, whereas here no modal structure seems to be introduced.

To mention two quite related work, which in fact capture formally the distinction between instantiable and non-instantiable entities, I point at :

Giancarlo Guizzardi, Claudenir M. Fonseca, Alessander Botti Benevides, João Paulo A. Almeida, Daniele Porello, Tiago Prince Sales:
Endurant Types in Ontology-Driven Conceptual Modeling: Towards OntoUML 2.0. ER 2018: 136-150

And for relational types and relationships to:

C. M. Fonseca, D. Porello, G. Guizzardi, J.P. Almeida, N. Guarino
Relations in Ontology-Driven Conceptual Modelling. ER 2019 (To appear)

In general, it seems to me that UFO theory (its first order version) plays at least part of the role that PURO is intended to play, right? (Or even DOLCE)

I think that a comparison with the formalisation of UFO may be useful to develop a full first-order theory of PURO.

Finally, a methodological worry. In Section 8.2 the authors confront the methodology of PURO with respect to the methods of Foundational Ontologies (FO), e.g. DOLCE, UFO, or BFO.

They report “there is not yet a proper, fully documented, and philosophically anchored FO (foundational ontology) specifically developed with respect to PURO”.

I think this is somehow a reverse order of justification, e.g. wrt UFO and OntoUML.
The idea there is first you justify your ontological assumptions in a philosophically or cognitive grounded way, you formalise them to make them clear, accessible, and testable, then you get a modelling language (OntoUML).

In this way, you have a semantically rich theory that can in fact justify the modelling choices or aspects of a modelling languages .

It appears here that, you developed PURO, then you go looking for justifications for the assumptions therein.