Here we consider the verification and semantic integration for the set of first-order time ontologies by Allen-Hayes, Ladkin, and van Benthem that axiomatize time as points, intervals, or a combination of both within an ontology repository environment. Semantic integration of the set of time ontologies is explored via the notion of theory interpretations using an automated reasoner as part of the methodology. We use the notion of representation theorems for verification by characterizing the models of the ontology up to isomorphism and proving that they are equivalent to the intended structures for the ontology. Provided is a complete account of the meta-theoretic relationships between ontologies along with corrections to their axioms, translation definitions, proof of representation theorems, and a discussion of various issues such as class-quantified interpretations, the impact of namespacing support for Common Logic, and ontology repository support for semantic integration as related to the time ontologies examined.

Cheap electronic storage and Internet bandwidth has increased the amount of online data. Large quantities of metadata are created to manage this wealth of information. Methods to organize and structure metadata has led to the development of ontologies - data that is organized to describe the relation between elements. The creation of large ontologies has brought forth the need for ontology management strategies. Ontology alignment and merging techniques are standard operations for ontology management. Accurate ontology alignment methods are typically semi-automatic, meaning they require periodic user input. This becomes infeasible on large ontologies and the accuracy and efficiency drops significantly when these algorithms are forced to align without human interaction. Bioinformatics, for example, has seen the influx of large ontologies, such as signal pathway sets with thousands of elements or protein-protein interaction (PPI) databases with hundreds of thousands of elements. This drives the need for a reliable method of large-scale ontology alignment. Many bioinformatics ontologies contain references to domain ontologies - manually curated ontologies describing additional, general information about the terms in the ontologies. For example, more than 2/3 of proteins in PPI data sets contain at least one annotation to the domain ontology the Gene Ontology. We use the domain ontology references as features to compute similarity between elements. However, there are few efficient ways to compute similarity from structured features. We present a novel, automatic method for aligning ontologies based on such domain ontology features. Specifically, we use simulated annealing to reduce the complexity of the domain ontologys structure by finding approximate relevant clusters of elements. An intermediate step performs hierarchical clustering based on the similarity between elements of the ontology. Then the mapping between clusters across aligning ontologies is built. The final step builds an alignment between matched clusters. To evaluate our methods, we perform an alignment between Human (Homo Sapiens) and Yeast (Saccharomyces cerevisiae) signal pathways provided by the Reactome database. The results were compared against reliable homology studies of proteins. The final mapping produces alignments that are significantly more accurate than the traditional ontology alignment methods, without any human involvement.

Thesis (M.S.)--California Polytechnic State University, 2009. / Title from PDF title page; viewed on Apr. 21, 2009. "March, 2009." "In partial fulfillment of the requirements for the degree [of] Master of Science in Computer Science." "Presented to the faculty of California Polytechnic State University, San Luis Obispo." Major professor: Franz Kurfess, Ph. D. Includes bibliographical references (p. 40-42). Also available on microfiche.

Thesis (Ph. D.)--University of Florida, 2005. / Title from title page of source document. Document formatted into pages; contains 126 pages. Includes vita. Includes bibliographical references.

Στην παρούσα διπλωματική εργασία μελετώνται και συγκρίνονται μεταξύ τους μερικές από τις κυριότερες προγραμματιστικές διεπαφές (APIs) που έχουν αναπτυχθεί για τη διαχείριση οντολογικών εγγράφων του Σημαντικού Ιστού. Αυτές οι προγραμματιστικές διεπαφές είναι εκφρασμένες σε JAVA, και κάθε μία προσφέρει ιδιαίτερα χαρακτηριστικά για την διαχείριση οντολογιών. Οι προγραμματιστικές διεπαφές μελετήθηκαν και συγκρίθηκαν ως προς διάφορα χαρακτηριστικά. Σ’ αυτά περιλαμβάνονται οι οντολογικές γλώσσες τις οποίες υποστηρίζουν, ποια ιδιαίτερα υποσύνολα («διαλέκτους») γλωσσών με συγκεκριμένα χαρακτηριστικά υποστηρίζουν, αλλά και οι δυνατότητες ανακάλυψης γνώσης που παρέχουν, με την υποστήριξη κάποιας γλώσσας συγγραφής επερωτήσεων ή όχι. Επίσης μελετήσαμε τους στόχους κάθε διεπαφής και τα πεδία εφαρμογής της με τα συγκριτικά πλεονεκτήματα και τους περιορισμούς τους οποίους εισάγει. Τέλος, προτείνεται ένας μηχανισμός ανακάλυψης γνώσης από οντολογικά έγγραφα, και περιγράφεται η ανάπτυξή του. Ο μηχανισμός που αναπτύχθηκε είναι ένας μηχανισμός υποβολής ευφυών επερωτήσεων προς OWL οντολογίες, με ευρύτερες εκφραστικές δυνατότητες από τις υπάρχουσες προτάσεις, που συνήθως προσανατολίζονται σε RDF έγγραφα ή θέτουν διάφορους περιορισμούς ως προς τη φύση των επερωτήσεων. Για το σκοπό χρησιμοποιήθηκε μια νέα πρόταση στις γλώσσες επερωτήσεων, η SPARQL-DL. Επίσης, στόχοι κατά την ανάπτυξη του μηχανισμού ήταν η λειτουργικότητα και η επεκτασιμότητα της συνολικής εφαρμογής. Στο πρώτο κεφάλαιο, αρχικά γίνεται μια εισαγωγή στο Σημαντικό Ιστό, με την περιγραφή των γενικών χαρακτηριστικών του, της αναγκαιότητας των υπηρεσιών του και των διαφόρων προσεγγίσεων υλοποίησής του. Περιγράφονται τα συγκεκριμένα χαρακτηριστικά των γλωσσών που συμμετέχουν αυτή τη στιγμή ή προορίζονται για να συμμετάσχουν στη δόμησή του, με ιδιαίτερη έμφαση στη γλώσσα που συστήνει το World Wide Web Consortium, την OWL. Στο δεύτερο κεφάλαιο περιγράφονται οι γλώσσες συγγραφής επερωτήσεων που υπάρχουν αυτή τη στιγμή για την ανακάλυψη γνώσης από οντολογίες, τα συγκεκριμένα χαρακτηριστικά και οι αδυναμίες της κάθε μιας. Και πάλι δίνουμε ιδιαίτερη έμφαση στο πρότυπο του W3C, τη γλώσσα SPARQL, και στην προτεινόμενη εξέλιξή της, τη SPARQL-DL. Στο τρίτο κεφάλαιο περιγράφονται οι πιο κοινές προγραμματιστικές διεπαφές, τα χαρακτηριστικά που παρέχουν και οι αδυναμίες τους. Περιγράφονται ως προς τις οντολογικές γλώσσες που υποστηρίζουν, τις γλώσσες και γενικότερα τις μεθόδους επερωτήσεων που υποστηρίζουν και τα πεδία εφαρμογών στα οποία χρησιμοποιούνται. Περιγράφονται επίσης οι τρόποι διασύνδεσης των διάφορων διεπαφών μεταξύ τους ή με άλλα τμήματα λογισμικού, όπως μηχανισμούς συλλογισμού (reasoners). Στο τέταρτο και τελευταίο κεφάλαιο περιγράφεται ένας μηχανισμός υποβολής ευφυών επερωτήσεων και παρουσιάζεται η ανάπτυξή του. Περιγράφονται οι επιλογές των εργαλείων που χρησιμοποιήθηκαν και οι γενικότερες σχεδιαστικές επιλογές. Εκτελούνται πειράματα ώστε να αξιολογηθεί αυτός ο μηχανισμός υποβολής επερωτήσεων και να διερευνηθούν οι περιορισμοί τους οποίους εισάγουν τα συγκεκριμένα εργαλεία που χρησιμοποιήσαμε αλλά και οι δυνατότητες που προκύπτουν από αυτά. Παρουσιάζονται οι πιθανές επεκτάσεις της εφαρμογής που αναπτύχθηκε, με επιπλέον χαρακτηριστικά, ώστε για παράδειγμα να γίνει προσβάσιμη από απομακρυσμένες εφαρμογές. Τέλος, παρουσιάζεται ένα πιθανό σενάριο χρήσης της εφαρμογής σε πραγματικό περιβάλλον, ώστε να γίνουν περισσότερο εμφανή τα πλεονεκτήματα και η χρησιμότητα ενός τέτοιου μηχανισμού ανακάλυψης γνώσης. / We study and compare the main Application Programming Interfaces (APIs) that have been developed for manipulating ontologies of the Semantic Web. These APIs are expressed in JAVA, and each one offers specific characteristics for managing ontologies. The APIs were studied and compared towards different aspects of functionality. These include the ontology languages each one supports, which specific idioms of those languages they support, and also the capabilities for retrieving knowledge that they provide, via supporting some query language or not. Furthermore, we studied the specific goals of each API and its application fields, with the respective advantages and the limitations it imports. Finally we suggest a mechanism for knowledge retrieval and describe its development. The mechanism we develop implements query answering for queries asked against OWL ontologies, with expanded capabilities compared to the existing query mechanisms, which are mostly oriented to RDF graphs or pose various restrictions regarding the queries. For this purpose we utilize the recently proposed SPARQL-DL query language. Additional goals during the development of this mechanism are ease of use and extensibility of the overall application.

Τα τελευταία χρόνια γίνονται επιταχυνόμενες προσπάθειες για να ενσωματωθούν αποτελεσματικά οι ψηφιακές τεχνολογίες στην εκπαίδευση. Στόχος είναι να προσθέσει η ενσωμάτωση αυτή πραγματική και μετρίσιμη αξία στην εκπαιδευτική διαδικασία. Σκοπός αυτής της εργασίας είναι να παρουσιάσουμε τους τρόπους που η καθιερωμένη markup γλώσσα για τα μαθηματικά, η MathML, μπορεί να βοηθήσει την εκπαίδευση στον τομέα των μαθηματικών. Εξετάζουμε την MathML σαν ένα από τα εργαλεία που προσφέρει η ταχεία ανάπτυξη του Σημασιολογικού Ιστού (Semantic Web). Ειδικότερα παρουσιάζονται οι markup γλώσσες XML, HTML5, MathML και κάποια εργαλεία που βοηθούν στην ενσωμάτωση τέτοιων τεχνολογιών. Για την MathML, δημιουργήθηκε ένας οδηγός χρήσης, προσιτός σε κάθε χρήστη. Στον τομέα της εκπαίδευσης, θα δούμε με ποιους τρόπους ο Σ.Ι. και η MathML προσθέτουν άξια στην εκπαιδευτική διαδικασία. Δημιουργήθηκε σε MathML ένα σενάριο διδασκαλίας στην Τριγωνομετρίας. Μέσω του Θεμελιώδους θεωρήματος Λογισμού, θα δούμε πως μπορεί η MathML να χρησιμοποιηθεί σε συνδυασμό με μια μελλοντική οντολογία αυτόνομων ενοτήτων στα Μαθηματικά όπου η κάθε ενότητα μπορεί να αποτελεί βάση αυτομάθησης/αυτοαξιολόγησης. Τέλος, θα αναφερθούμε στις προοπτικές που υπάρχουν στο άμεσο μέλλον. / In latest years, people making efforts to integrate digital technology effectively in education. The aim of this Postgraduate Work is to give real and measurable value in educational process. The goal is to present some ways that the usual markup language, MathML may help in mathematical education. We investigate MathML, as one of the tools, which are offered by the development of Semantic Web. More specifically, we present XML, HTML5 and MathML markup languages, and some tools which are helpful in integration of these technologies. We create a more approachable guide for helping anyone to understand MathML. In education, we will investigate how Semantic Web and MathML can give extra value in education process. Also we created a teaching scenario using MathML, in Trigonometry. Through the Fundamental Calculus Theorem, we will see a usage of MathML combing it in a future ontology of autonomous units in Mathematics, where each unit can be a base in autoeducate/autoevaluate. In the end, we will refer in future perspectives.

Complex systems models are designed in heterogeneous domains and this heterogeneity is rarely considered explicitly when describing and validating processes. Moreover, these systems usually involve several domain experts and several design models corresponding to different analyses (views) of the same system. However, no explicit information regarding the characteristics neither of the domain nor of the performed system analyses is given. In our thesis, we propose a general framework offering first, the formalization of domain knowledge using ontologies and second, the capability to strengthen design models by making explicit references to the domain knowledgeformalized in these ontology. This framework also provides resources for making explicit the features of an analysis by formalizing them within models qualified as ‘’points of view ‘’. We have set up two deployments of our approach: a Model Driven Engineering (MDE) based deployment and a formal methods one based on proof and refinement. This general framework has been validated on several no trivial case studies issued from system engineering.

The thesis discusses bird depictions in the Aegean Bronze Age. The iconographical study is based on a catalogue of almost 2000 objects showing bird images from Crete, the Cyclades, the Greek Mainland and the Dodecanese dating to EB I - LB IIIC. Three research aims are addressed. The first aim is the reliable and accurate identification of the depicted bird species by finding a middle ground between the two approaches that have prevailed in past scholarship, which either consisted of overambitious attempts at species identification or resorted to overgeneralised accounts of bird imagery. A systematic identification methodology, based on a combination of techniques from iconography, ornithology and in particular anthropological studies of folk taxonomies, is developed. The second aim is the interpretation of any specific symbolic functions and ideological roles of birds in different regions and periods. This analysis rests on the combined study of media and find contexts as well as the chosen bird species and iconographical associations. The third aim is the reconstruction of types of ontologies prevalent in different regions. Based on a structuralist model of ontologies developed by the anthropologist Descola, the bird depictions are studied by looking for features that are typical of analogical, naturalist, totemic or animist art. Each research aim has yielded numerous results, which deepen our understanding of biological knowledge and cultural diversity in the Aegean Bronze Age. First, the vast majority of bird depictions can be identified as belonging to one of the following folk-taxonomical groups: columbids (doves), birds of prey/corvids, waterbirds, wading birds, owls, hoopoes, galliformes, swallows and seabirds. Second, the existence of a multitude of particular functions and roles of birds is revealed. These vary significantly according to time and regions, mirroring historical developments and the presence of different cultural attitudes towards birds. Third, marked regional differences are detectable with regard to ontologies. Cretan and Cycladic bird art is consistent with animist iconography discernible because of a pronounced artistic naturalism, an emphasis on movement and agency, and the presence of shamanic imagery. The images from the Greek Mainland can be characterised as being consistent with an ontology termed analogical by Descola because of a preference of stylised and modular depictions and the persistence of symbolic functions through time. This work lays a foundation opening up a new perspective on interpreting iconography of the Aegean Bronze Age.

Individualmente, as linhas de pesquisa da Inteligência Artificial têm proposto abordagens para a resolução de inúmeros problemas complexos do mundo real. O paradigma orientado a agentes provê os agentes autônomos, capazes de perceber os seus ambientes, reagir de acordo com diferentes circunstâncias e estabelecer interações sociais com outros agentes de software ou humanos. As redes Bayesianas fornecem uma maneira de representar graficamente as distribuições de probabilidades condicionais e permitem a realização de raciocínios probabilísticos baseados em evidências. As ontologias são especificações explícitas e formais de conceituações, que são usadas em uma variedade de áreas de pesquisa, incluindo os Sistemas Multiagentes. Contudo, existem aplicações cujos requisitos não podem ser atendidos por uma única tecnologia. Circunstâncias como estas exigem a integração de tecnologias desenvolvidas por distintas áreas da Ciência da Computação. Esta dissertação trata a integração do modelo de agentes BDI (Belief-Desire-Intention) e das redes Bayesianas. Além disso, é adotada uma abordagem baseada em ontologias para representar o conhecimento incerto dos agentes. O primeiro passo em direção a integração foi o desenvolvimento de uma ontologia para representar a estrutura das redes Bayesinas. Esta ontologia tem como principal objetivo permitir a interoperabilidade agentes compatíveis com a arquitetura proposta. No entanto, a ontologia também facilita o entendimento necessário para abstrair os estados mentais e processos cognitivos dos agentes através de elementos das redes Bayesianas. Uma vez construída a ontologia, a mesma foi integrada com a arquitetura BDI. Através da integração do modelo BDI com as redes Bayesianas foi obtida uma arquitetura cognitiva de agentes capaz de deliberar sob incerteza. O processo de integração foi composto de duas etapas: abstração dos estados mentais através de elementos das redes Bayesianas e especificação do processo deliberativo. Finalmente, foi desenvolvido um estudo de caso, que consistiu na aplicação da arquitetura proposta no Agente Social, um componente de um portal educacional multiagente (PortEdu). / Individually, Artificial Intelligence research areas have proposed approaches to solve several complex real-world problems. The agent-based paradigm provided autonomous agents, capable of perceiving their environment, reacting in accordance with different situations, and establishing social interactions with other software agents and humans. Bayesian networks provided a way to represent graphically the conditional probability distributions and an evidence-based probabilistic reasoning. Ontologies are an effort to develop formal and explicit specifications of concepts, which have been used by a wide range of research areas, including Multiagent Systems. However, there are applications whose requirements can not be addressed by a single technology. Circumstances like these demand the integration of technologies developed by distinct areas of Computer Science. This work is particularly concerned with the integration of Belief-Desire-Intention (BDI) agent architecture and Bayesian networks. Moreover, it is adopted an ontology-based approach to represent the agent’s uncertain knowledge. To bring together those technologies, it was developed an ontology to represent the structure of Bayesian networks knowledge representation. This ontology supports the interoperability among agents that comply with the proposed architecture, and it also facilitates the understanding necessary to abstract the agents’ mental states and cognitive processes through elements of Bayesian networks. Once specified the ontology, it was integrated with the BDI agent architecture. By integrating BDI architecture and Bayesian networks, it was obtained a cognitive agent architecture capable of reasoning under uncertainty. It was performed in two stages: abstraction of mental states through Bayesian networks and specification of the deliberative process. Finally, it was developed a case study, which consists in applying the probabilistic BDI architecture in the Social Agent, a component of a multiagent educational portal (PortEdu).

We describe an online clinical decision support (CDS) system, Lung Cancer Assistant (LCA), which we have developed to aid the clinicians in arriving at informed treatment decisions for lung cancer patients at multidisciplinary team (MDT) meetings. LCA integrates rule-based and probabilistic decision support within a single platform. To our knowledge, this is the first time this has been achieved in the context of CDS in cancer care. Rule-based decision support is achieved by an original ontological guideline rule inference framework that operates on a domain-specific module of Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT), containing clinical concepts and guideline rule knowledge elicited from the major national and international guideline publishers. It adopts a conventional argumentation-based decision model, whereby the decision options are listed along with arguments derived by matching the patient records to the guideline rule base. As an additional feature of this framework, when a new patient is entered, LCA displays the most similar patients to the one being viewed. Probabilistic inference is provided by a Bayesian Network (BN) whose structure and parameters have been learned based on the English Lung Cancer Database (LUCADA). This allows LCA to predict the probability of patient survival and lay out how the selection of different treatment plans would affect it. Based on a retrospective patient subset from LUCADA, we present empirical results on the treatment recommendations provided by both functionalities of LCA and discuss their strengths and weaknesses. Finally, we present preliminary work, which may allow utilising the BN to calculate survival odd ratios that could be translated into quantitative degrees of support for the guideline rule-based arguments. An online version of LCA is accessible on http://lca.eng.ox.ac.uk.