C. Maria Keet
Book chapters - Journal Publications - Conferences and Workshops - Other and technical reports - Editing - PhD Thesis
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Keet, C.M. and Franconi, E. (eds.). CSBio reader: extended abstracts of the 'CS&IT with/for biology' Seminar Series. Free University of Bozen-Bolzano, 2005.
Keet, C.M. A Formal Theory of Granularity. PhD Thesis, KRDB Research Centre, Faculty of Computer Science, Free University of Bozen-Bolzano, Italy. 2008.
Marijke Keet."Europeanization of education". International Workshop on the Impact of EU Education Policy and Educational System Reforms on Youth and Society, 29/30 March 2006, Brussels, Belgium.
Marijke Keet."Book review 'La personalità nonviolenta' [the non-violent personality]". Irish Peace Society, 2004.
Marijke Keet."Causes of terrorism". Everything2.com, 2003.
Marijke Keet."Interview with the Hizbollah webmaster". Sesame, 2003, 217:22.
Marijke Keet."The role of Pakistan in deterring terrorism". An Focal, 2003, 13,11:24.
Marijke Keet."Agriculture and (under)development". The Conflict Resolution Information Source, Conflict Research Consortium, University of Colorado. 2002. (here too)
Marijke Keet."Women's rights in Islamic marriage". Irish Peace Society, 2002.
Several Required OWL Features for Indigenous Knowledge Management Systems.
Alberts, R., Fogwill, T., Keet, C.M. 7th Workshop on OWL: Experiences and Directions (OWLED'12)
This paper describes the features required of OWL to realise and enhance Indigenous Knowledge (IK) digital repositories. Several needs for Indigenous Knowledge management systems (IKMSs) are articulated, based on extensive stakeholder input, and analysed on the suitability of semantic web technologies in addressing them. Based on their potential for impact and maturity, several possible applications are recommended for further investigation and inclusion into current or new IKMSs, including: ontology based querying and browsing; a natural language independent ontology for multilingual data access; support for collaborative knowledge generation; and the formalisation of IK for scientific discovery. For each of these possible applications, the required OWL features are discussed, which include representation of vagueness, mereotopology, modularisation, and extended support for internationalisation and annotation. back - article
Representing mereotopological relations in OWL ontologies with OntoPartS.
Keet, C.M., Fernández-Reyes, F.C., Morales-González, A. 9th Extended Semantic Web Conference (ESWC'12)
Representing and reasoning over mereotopological relations (parthood and location) in an ontology is a well-known challenge, because there are many relations to choose from and OWL has limited expressiveness in this regard. To address these issues, we structure mereotopological relations based on the KGEMT mereotopological theory. A correctly chosen relation counterbalances some weaknesses in OWL's representation and reasoning services. To achieve effortless selection of the appropriate relation, we hide the complexities of the underlying theory through automation of modelling guidelines in the new tool OntoPartS. It uses, mainly, the categories from DOLCE, which avoids lengthy question sessions, and it includes examples and verbalizations. OntoPartS was experimentally evaluated, which demonstrated that selecting and representing the desired relation was done efficiently and more accurately with OntoPartS. back - article
Transforming semi-structured life science diagrams into meaningful domain ontologies with DiDOn.
Keet, C.M. Journal of Biomedical Informatics
Bio-ontology development is a resource-consuming task despite the many open source ontologies available for reuse. Various strategies and tools for bottom-up ontology development have been proposed from a computing angle, yet the most obvious one from a domain expert perspective is unexplored: the abundant diagrams in the sciences. To speed up and simplify bio-ontology development, we propose a detailed, micro-level, procedure, DiDOn, to formalise such semi-structured biological diagrams availing also of a foundational ontology for more precise and interoperable subject domain semantics. The approach is illustrated using Pathway Studio as case study. back - article
Enhancing Identification Mechanisms in UML Class Diagrams with Meaningful Keys (extended version).
Keet, C.M. Technical Report SoCS11-1
The task of declaring good keys is more relevant for ER and ORM than UML, because the former two require a modeller to do so in the methodology or CASE tool, whereas UML uses internal, system-generated, identifiers, with a little-known underspecified option for user-defined identifiers. This raises questions, such as which semantic identification mechanisms should be included and how to incorporate it in UML to foster consistent usage. The distinct implicit assumptions and explicit formalisations of extant identification schemes are elucidated by considering both ontology and (E)ER and ORM. Whereas ontology seeks identity, conceptual data modelling uses strong or weak identification of entities. To increase the ontological foundations of UML, the more detailed insights lead to a proposal for two language enhancements for UML, being formally defined simple and compound identifiers and the notion of defined class, which also have a corresponding extension of UML's metamodel. back - article
Enhancing Identification Mechanisms in UML Class Diagrams with Meaningful Keys.
Keet, C.M. SAICSIT Annual Research Conference 2011 (SAICSIT'11)
Unlike identification with keys and reference schemes in ER and ORM, UML uses internal, system-generated, identifiers, with a little-known underspecified option for user-defined identifiers. To increase the ontological foundations of UML, we propose two language enhancements for UML, being formally defined simple and compound identifiers and the notion of defined class, which also have a corresponding extension of UML's metamodel. back - article
Rough Subsumption Reasoning with rOWL.
Keet, C.M. SAICSIT Annual Research Conference 2011 (SAICSIT'11)
There are various recent efforts to broaden applications of ontologies with vague knowledge, motivated in particular by applications of bio(medical)-ontologies, as well as to enhance rough set information systems with a knowledge representation layer by giving more attention to the intension of a rough set. This requires not only representation of vague knowledge but, moreover, reasoning over it to make it interesting for both ontology engineering and rough set information systems. We propose a minor extension to OWL 2 DL, called rOWL, and define the novel notions of rough subsumption reasoning and classification for rough concepts and their approximations. back - article
Bottom-up ontology development reusing semi-structured life sciences diagrams.
Keet, C.M. AFRICON'11 -- Special Session on Robotics and Artificial Intelligence in Africa
Bio-ontology development is a resource-consuming task despite the many open source ontologies available for reuse. Various strategies and tools for bottom-up ontology development have been proposed from a computing angle, yet the most obvious one from a domain expert perspective is unexplored: the abundant diagrams. To speed up and simplify bio-ontology development, we propose guidelines to formalise such diagrams in several logic languages availing also of a foundational ontology to achieve a more precise representation of the subject domain semantics and increase interoperability. The guidelines are demonstrated with a transformation of the Pathway Studio diagrams into an OWLized bio-ontology with BFO and RO. back - article
The use of foundational ontologies in ontology development: an empirical assessment.
Keet, C.M. 8th Extended Semantic Web Conference (ESWC'11)
There is an assumption that ontology developers will use a top-down approach by using a foundational ontology, because it purportedly speeds up ontology development and improves quality and interoperability of the domain ontology. Informal assessment of these assumptions reveals ambiguous results that are not only open to different interpretations but also such that foundational ontology usage is not foreseen in most methodologies. Therefore, we investigated these assumptions in a controlled experiment. After a lecture about DOLCE, BFO, and part-whole relations, one-third chose to start domain ontology development with an OWLized foundational ontology. On average, those who commenced with a foundational ontology added more new classes and class axioms, and significantly less object properties than those who started from scratch. No ontology contained errors regarding part-of vs. is-a. The comprehensive results show that the 'cost' incurred spending time getting acquainted with a foundational ontology compared to starting from scratch was more than made up for in size, understandability, and interoperability already within the limited time frame of the experiment. back - article
An empirical assessment of the use of foundational ontologies in ontology development.
Keet, C.M. KRDB Research Centre Technical Report KRDB10-6, Faculty of Computer Science, Free University of Bozen-Bolzano, Italy. 19p
There is an assumption that ontology developers will use a top-down approach by using a foundational ontology, because it purportedly speeds up ontology development and improves quality and interoperability of the domain ontology. Informal assessment of these assumptions reveals ambiguous results that are not only open to different interpretations but also such that foundational ontology usage is not foreseen in most methodologies. Therefore, we investigated these assumptions in a controlled experiment. After a lecture about DOLCE, BFO, and part-whole relations, one-third chose to start domain ontology development with an OWLized foundational ontology (6 out of 18 ontologies developed by 52 participants). On average, those who commenced with a foundational ontology added more new classes and class axioms, and significantly less object properties than those who started from scratch. The comprehensive results show that the `cost' incurred in spending time getting acquainted with a foundational ontology---in casu, DOLCE and a taxonomy of part-whole relations---compared to starting from scratch was more than made up for in size, understandability, and interoperability already within the limited time frame of the experiment. back - article
A basic characterization of relation migration.
Keet, C.M. and Artale, A. International Workshop on Fact-Oriented Modeling (ORM'10)
Representing and reasoning over evolving objects has been investigated widely. Less attention has been devoted to the similar notion of relation migration, i.e., how tuples of a relation (ORM facts) can evolve along time. We identify different ways how a relation can change over time and give a logic-based semantics to the notion of relation migration to capture its behaviour. We also introduce the notion of lifespan of a relation and clarify the interactions between object migration and relation migration. Its use in graphical conceptual data modelling is illustrated with a minor extension to ORM2 so as to more easily communicate such constraints with domain experts. back - article
A top-level categorization of types of granularity
Keet, C.M.. In: Novel Developments in Granular Computing: Applications for Advanced Human Reasoning and Soft Computation. IGI Global. 2010.
Multiple different understandings and uses exist of what granularity is and how to implement it, where the former influences success of the latter with regards to storing granular data and using granularity for automated reasoning over the data or information, such as granular querying for information retrieval. We propose a taxonomy of types of granularity and discuss for each leaf type how the entities or instances relate within its granular level and between levels. Such distinctions give guidelines to a modeler to better distinguish between the types of granularity in the design phase and the software developer to improve on implementations of granularity. Moreover, these foundational semantics of granularity provide a basis from which to develop a comprehensive theory of granularity. back - preprint
Ontology engineering with rough concepts and instances.
Keet, C.M. 17th International Conference on Knowledge Engineering and Knowledge Management (EKAW'10)
A scenario in ontology development and its use is hypothesis testing, such as finding new subconcepts based on the data linked to the ontology. During such experimentation, knowledge tends to be vague and the associated data is often incomplete, which OWL ontologies normally do not consider explicitly. To fill this gap, we use OWL 2 and their application infrastructures together with rough sets. Although OWL 2 QL is insufficient to represent most of rough set's semantics, the mapping layer of its Ontology-Based Data Access framework that links concepts in the ontology to queries over the data source suffice to ascertain if a concept is rough, which subsequently can be modelled more precisely in an OWL 2 DL ontology. We summarise the trade-offs and validate it with the HGT ontology and its 17GB genomics database and with sepsis, which demonstrates it is an encouraging step toward comprehensive and usable rough ontologies. back - article
Dependencies between Ontology Design Parameters.
Keet, C.M. International Journal of Metadata, Semantics and Ontologies
Development and use of ontologies is increasing, but hampered by new challenges, such as determining which ontologies to reuse and which language to use. Ontology development methodologies provide scenarios, but they do not address the dependencies between the permutations at the different stages in the development process. To improve the efficiency and effectiveness of this endeavour, we group inputs into parameters and examine the dependencies between them. The parameters considered are: nine main purpose(s) of the ontology, reuse of the three main types of ontologies, eight different ways for bottom-up ontology development, eight ontology languages, and four types of reasoning services. All dependencies between these parameters have been assessed and useful combinations are motivated. The dependencies are due to, primarily, computational challenges and types of subject domain of the ontologies. This analysis is assessed against a set of ontologies and a survey among ontology developers, whose results concur with the theoretical assessment. back - article
On the feasibility of Description Logic knowledge bases with rough concepts and vague instances
Keet, C.M. 23rd International Workshop on Description Logics (DL'10)
A usage scenario of bio-ontologies is hypothesis testing, such as finding relationships or new subconcepts in the data linked to the ontology. Whilst validating the hypothesis, such knowledge is uncertain or vague and the data is often incomplete, which DL knowledge bases do not take into account. In addition, it requires scalability with large amounts of data. To address these requirements, we take the SROIQ(D) and DL-Lite family of languages and their application infrastructures augmented with notions of rough sets. Although one can represent only little of rough concepts in DL-Lite, useful aspects can be dealt with in the mapping layer that links the concepts in the ontology to queries over the data source. We discuss the trade-offs and demonstrate validation of the theoretical assessment with the HGT application ontology about horizontal gene transfer and its 17GB database by taking advantage of the Ontology-Based Data Access framework. However, the prospects for comprehensive and usable rough DL knowledge bases are not good, and may require both sophisticated modularization and scientific workflows to achieve systematic use of rough ontologies. back - article - supplementary material
Granular perspective as semantically enriched granulation hierarchy
C.M. Keet, IJGCRSIS
One can granulate data and information in multiple ways to generate granulation hierarchies. What the characteristics of such hierarchies are and what consequences they have on levels of granularity is, however, left implicit. We propose an explicit representation of such additional information of granulation hierarchies and transform them to granular perspectives that can be uniquely identified, hence, distinguished, by means of formally representing their semantics using a criterion and type of granularity used for granulation. The granular perspectives, in turn, are equipped with both a simple relation and with mereological relations to consistently relate them, thereby facilitating cross-granular querying. Given the premises, definitions, and proven properties, consequences for characterising levels of granularity within such perspectives are demonstrated. back - article
Web-based Graphical Querying of Databases through an Ontology: the WONDER System.
Calvanese, D., Keet, C.M., Nutt, W., Rodriguez-Muro, M., Stefanoni, G. ACM Symposium on Applied Computing (ACM SAC 2010)
Biological scientists have made large amounts of data available on the Web, which can be accessed by canned or precomputed queries presented via web forms. To satisfy further information needs, users currently have to have a good understanding of SQL and how the data is stored in the database. While accessing information at the ontological layer seems more appropriate, this poses two challenges: (1) to query data in databases and triple stores through an ontology with little performance overhead, and (2) to provide an intuitive web-based access to users that are not IT experts. To address these issues, we draw upon the theory and technology developed for Ontology-Based Data Access for DL-Lite. With an OWL ontology and the DIG-QuOnto reasoner as building blocks, we have developed an application that allows for graphical ontology browsing, query formulation, and answer retrieval via a Web browser. We have evaluated our system for Web-ONtology baseD Extraction of Relational data (WONDER) with an existing large genomics database about horizontal gene transfer and found that it meets both the scalability and the usability requirements. back - article
Positionalism of relations and its consequences for fact-oriented modelling.
Keet, C.M. International Workshop on Fact-Oriented Modeling (ORM'09)
Natural language-based conceptual modelling as well as the use of diagrams have been essential components of fact-oriented modelling from its inception. However, transforming natural language to its corresponding object-role modelling diagram, and vv., is not trivial. This is due to the more fundamental problem of the different underlying ontological commitments concerning positionalism of the fact types. The natural language-based approach adheres to the standard view whereas the diagram-based approach has a positionalist commitment, which is, from an ontological perspective, incompatible with the former. This hinders seamless transition between the two approaches and affects interoperability with other conceptual modelling languages. One can adopt either the limited standard view or the positionalist commitment with fact types that may not be easily verbalisable but which facilitates data integration and reusability of conceptual models with ontological foundations. back - article
Functional dependencies in OWL ABox.
Calbimonte, J.-P., Porto, F., and Keet, C.M. XXIV Brazilian Symposium on Databases (SBBD'09)
Functional Dependency has been extensively studied in database theory. Most recently, there have been some works investigating the implications of extending Description Logics with functional dependencies. As it turns out, more complex functional dependencies at the type-level can lead to undecidability, which thus restricts its usage in the TBox. This paper therefore focuses on enhancing its applicability to instances in the ABox. We specify 'FD' as a new constructor, realized as an OWL concept. FD instances are mapped to Horn clauses and evaluated against the ABox according to user's desired behavior. The latter allows users to determine whether FDs should be interpreted as constraints, assertions or views in the knowledge base. Our approach thereby gives ontology users data guarantees and features usually found only in databases. back - article
Constraints for representing transforming entities in bio-ontologies.
Keet, C.M. 11th Congress of the Italian Association for Artificial Intelligence (AI*IA 2009)
Things change---develop, mature morph---but not everything in the same way. Representing this knowledge in ontologies faces issues on three fronts: what the category of the participating objects are, which type of relations they involve, and where constraints should be added. More precise distinctions can be made by using OntoClean's properties and a novel status property that is generalised from formal temporal conceptual data modeling. Criteria are identified, formulated in 17 additional constraints, and assessed on applicability for representing transformations more accurately. This enables developers of (bio-)ontologies to represent and relate entities more precisely, such as monocyte & macrophage and healthy & unhealthy organs. back - article
From granulation hierarchy to granular perspective.
Keet, C.M. IEEE International Conference on Granular Computing (GrC'09)
It is well-known that one can granulate data and information in multiple ways to generate a plethora of granulation hierarchies each with their levels of granularity. It is left implicit what the characteristics of such hierarchies are, and what consequences they have on levels of granularity. We propose a way to represent such additional information of granulation hierarchies by upgrading them to full granular perspectives and to provide a consistent way to uniquely identify, hence, distinguish, such perspectives based on their semantics by using a criterion and type of granularity used for granulation. In addition, with the chosen premises, definitions, and proven properties, we demonstrate some consequences for characterising levels of granularity within such granular perspectives. back - article
Ontology design parameters for aligning agri-informatics with the Semantic Web.
Keet, C.M. 3rd International Conference on Metadata and Semantics (MTSR'09) -- Special Track on Agriculture, Food & Environment
In recent years there have been many efforts in the development of bio-ontologies, where the applied life sciences can see the benefits reaped from, and hurdles observed with, such early-adopter efforts. With the plethora of resources, where should one start developing one's own domain ontology, what resources are available for reuse to speed up its development, for which purposes can the ontology be developed? We group inputs that determine effectiveness of ontology development and use into four types of parameters: purpose, ontology reuse, ways of ontology learning, and the language and reasoning services. We illustrate this for the agriculture domain by building upon experiences gained in previous and current projects. back - article
Structuring GIS information with types of granularity: a case study
Estructuración de información SIG con tipos de granularidad: un estudio de caso
Keet, C.M. VI International Conference on Geomatics
Dealing with granularity in the GIS domain is a well-known issue, and multiple data-centric engineering solutions have been developed to deal with finer- and coarser-grained data and information within one information system. These are, however, difficult to maintain and cumbersome for interoperability. To address these issues, we propose eight types of granularity and a facilitating basic theory of granularity to structure granulation hierarchies in the GIS domain. Several common hierarchies will be re-assessed and refined. It illustrates a methodology of first representing what one desires to consider for a GIS application, i.e., at the semantic layer, so as to enable reaping benefits of flexibility, reusability, transparency, and interoperability at the implementation layer. back - article
La granularidad en el dominio de SIG es un tema conocido, y múltiples soluciones centradas en datos e implementaciónes se han desarrollado para manejar datos e informaciónes más finas y más gruesas dentro un sistema de información. Éstos son, sin embargo, difíciles de mantener y engorrosos para la interoperabilidad. Para abordar estos problemas, proponemos ocho tipos de granularidad y una teoría de granularidad básica para facilitar la estructuración de granulación en las jerarquías en el dominio SIG. Varios jerarquías comunes serán re-evaluadas y perfeccionadas. Se ilustra una metodología para representar lo que uno desea considerar para un aplicación SIG, es decir, a la capa semántica, a fin de que puedan cosechar los beneficios de la flexibilidad, reutilización, la transparencia y la interoperabilidad en la capa de aplicación. back - article
Enhancing web portals with Ontology-Based Data Access: the case study of South Africa's Accessibility Portal for people with disabilities
Keet, C.M., Alberts, R., Gerber, A., Chimamiwa, G.
Web portal software is relatively easy to set up and populate from the perspective of the end-user, but it leaves the back-end database devoid of subject domain semantics due to the requirement for a generic implementation. This approach seriously hampers effective search capabilities to retrieve relevant information. Ontology-based data access (OBDA) could, in theory, solve this problem through adding a semantic `layer' over such web portal implementations. To this end, we provide and demonstrate the proof-of-concept methodology by enhancing the operational National Accessibility Portal of South Africa. We developed the ADOLENA ontology, which is based on both the semantics in the database and augmented with notions from foundational and related domain ontologies. ADOLENA was then made compliant with the OWL2 profile DL-LiteA and mapped to the relational database using the OBDA Plugin for Protege. Experimentation with OBDA queries unequivocally demonstrates its advantages compared to the portal's keyword-based search. back - article
Essential, mandatory, and shared parts in conceptual data models
Artale, A. and Keet, C.M. In: Innovations in Information Systems modeling: Methods and Best Practices. IGI Global, Advances in Database Research Series, Halpin, T.A., Proper, H.A., Krogstie, J. (Eds.).
This chapter focuses on formally representing life cycle semantics of part-whole relations in conceptual data models by utilizing the temporal modality. We approach this by resorting to the temporal conceptual data modelling language ERvt and extend it with the novel notion of status relations. This enables a precise axiomatization of the constraints for essential parts and wholes compared to mandatory parts and wholes, as well as introduction of temporally suspended partwhole relations. To facilitate usage in the conceptual stage of information systems development, a set of closed questions and decision diagram are proposed. The long-term objectives are to ascertain which type of shareability and which lifetime aspects are possible for part-whole relations, investigate the formal semantics for sharability, and how to model these kind of differences in conceptual data models. back - preprint
Formalising temporal constraints on part-whole relations
Artale, A., Guarino, N., and Keet, C.M. 11th International Conference on Principles of Knowledge Representation and Reasoning (KR'08)
Representing part-whole relations and effectively using them in domain ontologies and conceptual data models poses multiple challenges. In this paper we face the issue of representing the notions of essential and immutable parts and wholes in addition to the usual mandatory participation of the part or whole in the partwhole relation. Our approach is based on i) an explicit temporalization of the part-whole relation, which allows us to introduce a novel notion of status for part-whole relationships; ii) an explicit account of the ontological nature of the classes involved in a part-whole relationships, which distinguishes between rigid and antirigid classes. The main novelty in this paper is to resort to a temporal logic approach to capture the above mentioned notions. The formalization proposed here is grounded on the temporal description logic DLRUS and is based on previous successful efforts to formalize temporal conceptual models. back - article
Toward cross-granular querying over modularized ontologies
Keet, C.M. International Workshop on Ontologies: Reasoning and Modularity (WORM'08)
To address the problems of both structured coordination of linked and modularised ontologies and to query a large dynamic ontology system, we propose a basic granularity framework and a set of functions to query such a granulated system. The granularity framework enforces a constrained and structured modularization. This facilitates automation of both dividing a large body of represented information as well as re-linking the pieces. The functions enable basic cross-granular querying in a transparent and scalable way, as they rely on the unambiguous management layer provided by the granularity framework, and are reusable for ontologies represented and stored in different formats. back - article
A formal comparison of conceptual data modeling languages
Keet, C.M. 13th International Workshop on Exploring Modeling Methods in Systems Analysis and Design (EMMSAD'08)
An essential aspect of conceptual data modeling methodologies is the language's expressiveness so as to represent the subject domain as precise as possible to obtain good quality models and, consequently, software. To gain better insight in the characteristics of the main conceptual modeling languages, we conducted a comparison between ORM, ORM2, UML, ER, and EER with the aid of Description Logic languages of the DLR family and the new formally defined generic conceptual data modeling language CMcom that is based on DLRifd. ORM, ER, EER, and UML class diagrams are proper fragments of ORM2 and CMcom has the most expressive common denominator with these languages. CMcom simplifies prospects for automated, online, interoperability among the considered languages so that modelers not only can continue using their preferred modeling language yet be compatible with the other ones, but also have a common ground that eases database and software integration based on commonly used conceptual data models. back - article
Essential and mandatory part-whole relations in conceptual data models
Artale, A., Keet, C.M. 21st International Workshop on Description Logics (DL'08)
A recurring problem in conceptual modelling and ontology development is the representation of part-whole relations, with a requirement to be able to distinguish between essential and mandatory parts. To solve this problem, we formally characterize the semantics of these shareability notions by resorting to the temporal conceptual model ERvt and its formalization in the description logic DLRus. back - article
Unifying industry-grade class-based conceptual data modeling languages with CMcom
Keet, C.M. 21st International Workshop on Description Logics (DL'08)
From the side of modelers and early-adopter industry, interest in reasoning over conceptual models and other online usage of conceptual models is growing. To obtain a more precise insight in the characteristics of the main conceptual modeling languages, we define the (semi-)standardized ORM, ORM2, UML, ER, and EER diagram languages in terms of the new generic conceptual data modeling language CMcom that is based on the DL language DLRifd. CMcom has the most expressive common denominator with these languages. CMcom advances prospects for automated, online, interoperability among diverse conceptual data models and ensures compatibility with and between industry-grade conceptual data modeling languages. back - article
A Meta-Model for Ontologies with ORM2
Tziviskou, C., Keet, C.M. Third International Workshop on Object-Role Modelling (ORM'07)
Development of ontology development tools and ontology-enhanced software applications requires thorough understanding of ontology languages in order to implement them according to their specification. We present a formal specification of the ontologies part of the Web Services Modeling Language WSML documentation as a conceptual model in ORM2. Such an approach abstracts the semantics about ontological constructs, axioms, and properties from their implementation in arbitrary formats, thereby making the model easily understandable and reusable. This formal model in ORM2, which is understandable by both logician and software developer, can be used as any other conceptual model to develop applications, thereby ensuring smooth transition from theory to implementations that are faithful to the theory. back - article
Granulation with indistinguishability, equivalence or similarity
Keet, C.M. IEEE International Conference on Granular Computing (GrC2007)
One of the relations used with granularity is indistinguishability, where distinguishable entities in a finer-grained granule are indistinguishable in a coarser-grained granule. This relation is a subtype of equivalence relation, which is used in the other direction to create finer-grained granules. Together with the notion of similarity, we formally prove some intuitive properties of the indistinguishability relation for both qualitative and quantitative granularity, that with a given granulation there must be at least two granules (levels of granularity) for it to be granular, and derive a strict order between finer and coarser granules. Based on these results, granulation hierarchy is defined as extra assisting structure to augment implementations. back - article
Representing and Reasoning over a Taxonomy of Part-Whole Relations
Keet, C.M., Artale, A. Applied Ontology, 2008, 3(1-2): 91-110.
Many types of part-whole relations have been proposed in the literature to aid the conceptual modeller to choose the most appropriate type, but many of those relations lack a formal specification to give clear and unambiguous semantics to them. To remedy this, a formal taxonomy of types of mereological and meronymic part-whole relations is presented that distinguishes between transitive and intransitive relations and the kind of entity types that are related. The demand to use it effectively brings afore new requirements for automated reasoning over a hierarchy of relations. To ensure logically and ontologically correct inferencing over both the class and role hierarchy, the new reasoning service RBox compatibility for Description Logics reasoners is introduced. The proposed combination of formal semantics and the new reasoning service will improve the representation of the application domain when using part-whole relations in conceptual models and ontologies. back - article
Enhancing comprehension of ontologies and conceptual models through abstractions.
Keet, C.M. 10th Congress of the Italian Association for Artificial Intelligence (AI*IA 2007)
In addition to the Database Comprehension Problem, where diagrammatic conceptual data models are too large for a modeller or domain expert to comprehend or manage, an Ontology Comprehension Problem is emerging. The latter faces not only the same visualization issues, but also that the logical theories are less accessible to the domain expert. Formal ontologies are, however, more amenable to automated abstractions to improve understandability. Three ways of abstractions are introduced with corresponding abstraction functions that take into account foundational ontology categories. Usability of both the abstraction functions and the more and less detailed (views of) ontologies is enhanced by associating abstraction functions with a basic framework of levels, thereby facilitating querying and visualizing ontologies. back - article
Toward using biomedical ontologies: trade-offs between ontology languages
Keet, C.M., Rodriguez, M. AAAI 2007 Workshop on Semantic e-Science (SeS07)
Ontology representation languages for the Semantic Web have their strengths and weaknesses, in particular in the light of deploying them in information systems. We survey and compare the Description Logics-based OWL variants, and the DL-Lite and DLR families of languages. We demonstrate distinguishing features with examples from the biological and biomedical domains. Language choices that an ontology developer has to make are, among others, expressivity versus ontology usage for data-intensive tasks and having mereological parthood versus n-ary relations (where n > 2). Guidelines are suggested to facilitate choosing the language best fitted for a task. back - article - tech report
Prospects for and issues with mapping the Object-Role Modeling language into DLRifd
C Maria Keet. 20th International Workshop on Description Logics (DL'07)
Object-Role modellers miss the advantages of automated reasoning over their ORM conceptual models, which could be addressed by DL reasoners. DLs are not considered user-friendly and could benefit from the easy to use ORM diagrammatic and verbalization interfaces and modelling methodologies. Relating the two would greatly expand the scope for automated reasoning with additional scenarios to improve quality of software systems. Given that none of the extant DL languages are as expressive as ORM or its successor ORM2, the 'best-fit' DLRifd was chosen to map the formal conceptual modelling language ORM2. For the non-mappable constraints, pointers to other DL languages are provided, which could serve as impetus for research into DL language extensions or interoperability between existing DL languages. back - article
A survey of requirements for automated reasoning services for bio-ontologies in OWL
C Maria Keet, Marco Roos, and M. Scott Marshall. Third international Workshop OWL: Experiences and Directions (OWLED 2007)
There are few successful application of automated reasoning over OWL-formalised bio-ontologies, and requirements are often unclearly formulated. Of what is available, usage and prospective scenarios of automated reasoning is often different from the straightforward classification and satisfiability. We list nine types of scenarios and specify the requirements in more detail. Several of these requirements are already possible in practice or at least in theory, others are in need of further research, in particular regarding the linking of the OWL ontology to data, reasoning over roles, and dynamically linking modular ontologies. back - article
Part-whole relations in Object-Role Models
C Maria Keet. 2nd International Workshop on Object Role Modeling 2006 (ORM2006)
Representing parthood relations in ORM has received little attention, despite its added-value of the semantics at the conceptual level. We introduce a high-level taxonomy of types of meronymic and mereological relations, use it to construct a decision procedure to determine which type of part-whole role is applicable, and incrementally add mandatory and uniqueness constraints. This enables the conceptual modeller to develop models that are closer to the real-world subject domain semantics, hence improve quality of the software. back - article
Representations of the ecological niche
C Maria Keet. Third International Workshop on Philosophy and Informatics (WSPI2006)
A formal theory of the ecological niche is indispensable not only for semantic precision in philosophy to understand and compare it with other meanings of niche, but also when computer scientists and ecologists desire to create interoperable software where one can retrieve the niche of a species and compare their parameters. The proposed model is a more fine-grained description of the ecological niche, including the distinction between its complex concept, the abstract niche ('fundamental niche') with its hypervolume in multidimensional space, and its realisations ('realised niches'). The presented ecological niche may initiate new avenues for research in ecology, particularly concerning the conditions/categories of a hypervolume, as well as further philosophical inquiry and comparison with other niches. back - article - appendix
A taxonomy of types of granularity
C Maria Keet. IEEE International Conference on Granular Computing 2006 (GrC2006)
Multiple different understandings and uses exist of what granularity is and how to implement it, where the former influences success of the latter with regards to storing granular data and using granularity for reasoning over the data or information. We propose a taxonomy of types of granularity and discuss for each leaf type how the entities or instances relate within its granular level. Such unambiguous distinctions can guide a conceptual modeler to better distinguish between the types of granularity and the software developer to improve on implementations of granularity. back - article
Using abstractions to facilitate management of large ORM models and ontologies
C Maria Keet. International Workshop on Object Role Modeling 2005 (ORM2005)
Due to ever larger ORM models and ORM-represented ontologies, information management and its GUI representation is even more important. One useful mechanism is abstraction, which has received some attention in conceptual modelling and implementation, as well as its foundational characteristics. Extant heuristics for ORM abstractions are examined and enriched with several foundational aspects of abstraction. These improvements are applicable to a wider range of types of representations, including conceptual models and ontologies, thereby not only alleviating the Database Comprehension Problem, but also facilitate conceptual model and ontology browsing. back - article
Factors affecting ontology development in ecology
C Maria Keet. Data Integration in the Life Sciences 2005 (DILS2005)
Few ontologies in the ecological domain exist, but their development can take advantage of gained experience in other domains and from existing modeling practices in ecology. Taxonomies do not suffice because more expressive modeling techniques are already available in ecology, and the perspective of flow with its centrality of events and processes cannot be represented adequately in a taxonomy. Therefore, formal ontologies are required for sufficient expressivity and to be of benefit to ecologists, which also enables future reuse. We have created a formal mapping between the software-supported ecological modeling method and software tool STELLA and ontology elements, which simplifies bottom-up ontology development considerably and has excellent potential for semi-automated ontology development. However, the conducted experiments also revealed that ontology development for ecology is close to being part of ecological research that through the formalized representation of the knowledge more clearly points to lacunas and suggestions for further research in ecology. back - article - supplementary material
Applying partitions to infectious diseases
C Maria Keet and Anand Kumar. XIX International Congress of the European Federation for Medical Informatics (MIE2005)
Due to exponential growth in biological data, partitioning is a necessity to manage data and to use it for reasoning mechanisms to deduce and infer new information automatically. Starting from a categorisation of infectious diseases, we formalise the relations of relevant partitions, such as mode of transmission, pathological process, and infectious organism, with examples for pneumonia and cholera to illustrate usage of partitioning and the relations between the granular levels. back - article
Ontology integration for applied bioscience
C Maria Keet. Summer School & Workshop Semantic Interoperability and Data Mining in Biomedicine 2004
Ontology development in the subject domain of applied bioscience, such as biomedicine or food science, blend combinations of concepts of various core sciences, which are only valid for particular contexts within the chosen domain or sections thereof, which may imply reuse and integration of segments of various existing ontologies. This is illustrated with an example from the perspective of bottom- up ontology development for bacteriocin-related knowledge.
It is important first to determine what kind of integration is required for which type of goal, therefore a literature research was carried out resulting in a construction of a preliminary categorization of types of ontology integration together with a list of factors and properties that contribute to distinguishing the multiple methods of ÂintegrationÂ.
Some challenges are highlighted such as the potential for development of an ontology library that might facilitate reuse/integration, how to address context-dependent data where the same basic concepts reappear but with other constraints and options for modularization to abstract away details that may not be relevant in the particular situation to be ontologised. back - poster
Conceptual Modelling and Ontologies for Biology: experiences with the bacteriocin database
C Maria Keet. Agropecuaria Conference (Interjoven 2004)
This article outlines some characteristics of biological data, which affect its modelling as well as ontologies in the subject domain of biology (including ecology and agriculture), which in turn influence the quality of developed software and the reusability of the models. These aspects arose from a literature review and a case study of developing a bacteriocin database. Conflicting goals in software requirements and aspects for future research are highlighted. back - article - poster
Biological data and conceptual modelling methods
C Maria Keet. Journal of Conceptual Modeling, Issue 29, October 2003
The article highlights characteristics of biological data, and its effect on conceptual modelling. Regarding biological data and its semantics, there is no legacy to rely and build upon, there is an abundance of non-discrete data, uncertainties on relevant parameters and a general lack of standardization in nomenclatures and concepts. General features of ER, OO and ORM are discussed, emphasising differences in graphical representation, understandability from the customer's perspective and inclusiveness of types and attributes in the model. A second example, taxonomy, addresses (Extended-) OO, ad hoc solution POOM and the possibilities of FCA to formalize biological data and its concepts.
The more abstract conceptual modelling techniques ORM and FCA may be more promising in capturing the biological semantics as inclusive and formal as possible, in order to build-up an extensive repository and aid standardization, which in turn will improve the quality of developed software. back - article
Conceptual Modelling for Applied Bioscience: The Bacteriocin Database
C Maria Keet. CSPS/computational intelligence/0310001
Semantic aspects are discussed for constructing a conceptual model capturing data across biological disciplines (biochemistry, microbiology, genetics) and including applied sciences (food science), by taking the development of a relational database for bacteriocins as a test case.
Capturing the subject domain semantics of an applied bioscience faces different problems compared to conceptual modelling for the primary biological sciences, as the former requires an emphasis on practical solutions conceptually representing the integration of various disciplines, necessarily reducing representation of biological complexity, whereas the latter stresses conceptually and ontologically comprehensive models within their primary specialisations such as biochemistry and genetics. back - article
Applying audience costs to the terrorist theatre
C Maria Keet. Simulation & Gaming: an International Journal
The audience cost model, based on a War of Attrition, is generally applied to international politics. In this article the model is analyzed on its applicability to a terrorism framework, with regard to the terrorist theatre and democratic states desiring to 'combat' terrorism. In the non-negotiation phase, aggrieved groups exploit the audience cost model to their own benefit for instilling fear, alike a War of Nerves. Audience costs can be generated and identified in terrorist frameworks involving peace negotiations. However, modeling audience cost parameters, in particular the rate of deduction in crisis prolongation, depends on the situation being modeled and the preference, or moral bias, of the modeler and therefore is qualitative and not (yet) quantifiable. back
Experimental gaming: effects of negotiations between terrorists and the government
C Maria Keet. Online Journal of Peace and Conflict Resolution
An experimental game was designed and tested with volunteers and assessed several aspects of game theoretical models for political science, including the hypothesis that violence will increase when nearing a peace agreement between 'moderate' terrorists and the government, adverse effects of deadlines and coalition formation between actors involved in the peace negotiation process.
Although some behaviour of the players was in line with the expectations based on the game theory, a single regularity in either coalition-forming or bargaining behaviour in the three-player game government - terrorists negotiations could not be observed. However, the perceived relative importance and influence measurements obtained with the coalition calculator are a very promising approach to gain insight in the players' expectations and stability of a coalition. The set-up provides the outline for an adequate experimental game in a larger setting, i.e. a 'world' scenario, in addition to the single conflicts that were tested. back
Towards a resolution of terrorism using game theory - coalitions, negotiations and audience costs
C Maria Keet. Department of Politics and Public Admin Working Papers, University of Limerick. Number 1, December '03
Both terrorism and game theory are contested concepts within the social sciences, but in this paper, I will show that a rational approach (game theory) towards the emotion-laden idea and practice of terrorism does aid understanding of the "terrorist theatre".
First, an outline will be provided on the type of actors (game players) that are, or may be, involved to a more or lesser extend in (supporting) terrorism. Then several game models will be assessed on their applicability. This includes averting the joint bargaining paradox when asymmetric actors cooperate to achieve a joint goal, governments who may fare better from their point of view when dividing up refugees into geographically separate areas to decrease the possibility of cooperation between aggrieved groups and recognizing two-speed negotiations, which can have a (detrimental) effect on (deadline) negotiations. Further, an adaptation of the audience cost model explained the "war of nerves" of the terrorist theatre involving the generation of fear amongst its targets and the updating of information on moderate actors by action of extremists. Several mutations of the Prisoner's Dilemma were discussed as options to prevent mutual harm. back - preprint
Democracy in the European Union
C Maria Keet. UL Perspectives, Journal of Political Studies, 2, 71-80
There has been an increase in peacekeeping and an introduction in peacebuilding operations after the end of the Cold War, directed by the United Nations and actively supported by Western democracies, where one of the aims was to 'aid in establishing democracy' in a nation (e.g. UNTAC and ONUSAL) as a means for conflict resolution and prevention of recurrence of the conflict in the future, i.e. introducing democratic structures as a component for achieving positive peace. But what means democracy and what are democratic structures? And do 'we', citizens of the European Union, have the legitimate moral high ground to impose such a government system onto other peoples, in the light of the rising amount of criticism on the democratic deficit of the EU structures?
In this article I compare ideas about democracy as surfaced in the 18th century, when modern forms of democratic structures were, either by revolution or gradually, introduced in Western countries, with the EU and the nations that make up the EU, and the validity/sustainability of claims to introduce democracy as a means to achieve lasting peace in non-Western nations. back - Preprint: html pdf