Access restrictions are essential in standard information systems and became an issue for ontologies in the following two aspects. Ontologies can represent explicit and implicit knowledge about an access policy. For this aspect we provided a methodology to represent and systematically complete role-based access control policies. Orthogonally, an ontology might be available for limited reading access. Independently of a specific ontology language or reasoner, we provided a lattice-based framework to assign labels to an ontology’s axioms and consequences. We looked at the problems to compute and repair one or multiple consequence labels and to assign a query-based access restriction. An empirical evaluation has shown that the algorithms perform well in practical scenarios with large-scale ontologies.

Semantika informacinių technologijų kontekste yra duomenų apdorojimas pagal prasmę ir kontekstą. Tam įgyvendinti yra taikomas natūralios kalbos apdorojimas, pritaikytas informacijos paieškai, išrinkimui, analizavimui.Taikant semantines technologijas, kūrėjams dažnai kyla klausimas, kaip sukurti semantinės paieškos sąsają, kad ji būtų patogi ir duotų kuo tikslesnius atsakymus į vartotojų užklausas. Šiame darbe aprašomas sukurtas metodas, kuris padeda vartotojui palaipsniui formuoti SPARQL užklausą iš atskirų elementų, dinamiškai keičiant vartotojo sąsają. / Increasing popularity of Semantic Web raises a question how we could make a simple user interface for building semantic queries while keeping high precision of results returned. This thesis presents a method that helps users to create SPARQL queries by allowing to dynamically add components to user interface. The goal of the work is to improve of user interface model for semantic queries by allowing users to construct and change it dynamically till obtaining the desirable answer results. That model was created on the base of analysis of Semantic Web languages, tools and existing portals, their functions and user interfaces. Algorithms for dynamic user interface generation based on user actions were developed that allow creating queries of various complexities with minimal amount of user interface components. Implementation and testing the prototype of the system using movie and wine ontologies has shown that dynamic construction and generation of query interface has desirable functionality and is easily applicable to various ontologies. Experimental comparison with existing semantic search portals has shown that the proposed dynamic user interface generation method could improve precision and recall of semantic queries and may be applied in semantic search portal applications.

Semantinis tinklas – tai duomenų tinklas, leidžiantis apjungti informaciją esančią įvairiuose šaltiniuose ir pavaizduoti visą surinktą informaciją kaip vientisą turinį. Semantiniame tinkle duomenys susieti ir prieinami per bendrąją tinko architektūrą, panaudojant URI adresus. Didžioji dalis duomenų yra neapjungti ir prienami atskiroms taikomosioms programoms. Apjungus šiuos įvairiuose šaltiniuose laikomus duomenis būtų sukurtas semantinis duomenų tinklas. Duomenims panaudoti, aprašyti bei susieti kuriami įvairūs karkasai, leidžiantys pakartotinai dalintis duomenimis visose taikymo srityse, įmonėse bei bendrijose. Struktūrizuota semantinė informacija naudojama automatiškai arba rankiniu būdu ir apdorojama kompiuterių. Semantinio tinklo metodai ir technologijos leidžia kompiuteriams suprasti pasauliniame tinkle (angl.World Wide Web) laikomos informacijos reikšmę arba kitaip semantiką. Semantinio tinklo technologijos panaudojamos: 1) duomenų integracijai, duomenų laikomų skirtingose vietose ir saugomų skirtingais formatais susiejimui; 2) resursų aptikimui ir klasifikacijai, sukuriant geresnį informacijos paieškos variklį; 3) tinklapių, svetainių ar skaitmeninių bibliotekų katalogavimui aprašant turinį, turinio ryšius; 4) sumaniųjų programinės įrangos agentų žinių mainams palengvinti; 5) turinio reitingavimui; 6) aprašant intelektualinės nuosavybės teises (tinklapiuose); Semantiniotinklų taikymas bei technologijos technologijos yra dar labai naujos, neištirtos, neišbandytos... [toliau žr. visą tekstą] / Semantic Network - is a data network of the information to combined from various sources and displayed as onesolid content. Data, in the Semantic networks is accessed using URIs, via a common network architecture. Semantic networks and technologies are still very new, unexplored, not tested inpractice and lacking of reference material. It isnecesery to analyzehow the technology is advanced and what technology and tools are used for semantic web application development. Objectives of this work: 1) To analyze how HTML data can be published; 2) To analyze the development of semantic web technologies; 3) To create an application automatically scanning the data from the HTML files; 4) To create an application that generates the OWL ontology of the relational database; 5) Apply semantic publishing for data; 6) To analize experimentaly HTML data colleting application and OWL generator.

Šiuo metu yra plačiai naudojamos ontologijos įvairiems uždaviniams spręsti. Dažnai susiduriama su problema kuriant naujas ontologijas, tai užima daug laiko. Darbo tikslas sukurti metodika, kuri nusakytų principus ontologijų jungimui bei moduliniam kūrimui. Analizuojant mokslinę literatūrą buvo nustatyti esami ontologijų jungimo bei kūrimo procesai. Tačiau, šie procesai neužtikrina korektiško ontologijų jungimo bei kūrimo. Todėl buvo detalizuoti konkretesni procesai, kuriais buvo parengta metodika. Siekiant praktiškai pritaikyti ir palyginti metodiką su kitomis analizės metu nagrinėtomis metodikomis, buvo sukurtas prototipas, kurio veikimas grįstas parengta metodika. Eksperimento metu buvo jungiamos bei kuriamos naujos ontologijos. Įvertinus gautus rezultatus buvo pastebėta jog, parengta ontologijų modulinio kūrimo ir jungimo metodika leidžia patogiau kurti bei jungti ontologijas naudojanti kitas ontologijas ar jų dalis. / At present, ontologies are widely used for various tasks. The main problem is that takes a lot of time of creating new ontologies. There are no methodologies which allow to merge ontologies or reuse various parts of ontology. The aim of research is to create the methodology of modular development and linking OWL 2 ontologies. This work covers analysis how to create and link the ontologies. During the research, a process was specified for creating and linking ontologies. This process allows creating modular ontologies for better maintenance and reuse. The experiment was accomplished in order to compare the new methodology whit existing one by creating a prototypical tool for merging ontologies. Three ontologies were created and merged using the prototype tool and Protégé. A comparison of results has shown the advantages of the created prototypical tool and methodology behind it against existing ones. The new methodology allows easily merging ontologies and creating new ontologies by reusing various parts of existing ontologies.

Per pastaruosius metus ontologijų kūrimas- tikslių formalių specifikacijos terminų ir specifikacijų sąryšių dalykinėje srityje, pradėjo plėstis nuo dirbtinio intelekto srities laboratorijų iki dalykinių sričių ekspertų darbalaukių. Ontologijos tapo dažnos pasauliniame žinių tinkle. Ontologijos naudojamos internete nuo didelių sistematikos klasifikavimo puslapių iki tokių kaip „Yahoo“ ,iki internetinių prekių klasifikavimo ir jų savybių klasifikavimo pardavimui tinklapių, tokių kaip „Amazon.com“. Jeigu informacija yra vienodos struktūros, t.y. visi terminai naudojami tie patys, automatinės paieškos sistemos gali sujungti informacija iš skirtingų šaltinių ir pateikti vartotojui kaip visumą. Ontologija apibrėžia dažnai naudojamą žodyną tyrinėtojams, kuriems reikia dalintis informacija dalykinėje srityje. Į tai įeina dalykinėje srityje kompiuterių interpretuojami apibrėžimai apie pagrindines sąvokas, sąryšius tarp jų. Informacija, žodynai tyrinėtojams, kompiuterių interpretuojami apibrėžimai ir kitą yra saugomi reliacinėse duomenų bazėse. Darbo tikslas: padidinti ontologijų išgavimo iš reliacinių duomenų bazių galimybes sukuriant ir realizuojant tam skirtą algoritmą, leidžiantį atstatyti ontologiją iš duomenų bazės be informacinių nuostolių. / In recent years the development of ontologines- formal specifications of the terms in the domain and relations among them has been expanding from the Artificial-Intelligence laboratories to the desktops of domain experts. Ontologies have become common on the World-Wide Web. The ontologies on the Web range from large taxonomies categorizing Web sites such as on „Yahoo“ to categorizations of products for sale and their features such as on „Amazon.com“. It is a language for encoding knowledge on Web pages to make it understandable to electronic agents searching for information. An ontology defines a common vocabulary for researchers who need to share information in a domain. It includes machine interpretable definitions of basic concepts in the domain and relations among them. Encoded information, vocabulary for researchers, formal specifications of the terms and other are saved in relational databases. The aim of this research is to improve possibilities of querying ontologies when these are kept in relational databases by creating and realizating the algorithm, which allows to transform ontology from relational databases. Experiments have shown that the method works for relation databases which were created by OWL2toRDB algorithm.

L'inclusion de requête est un problème bien étudié sur plusieurs décennies de recherche. En règle générale, il est défini comme le problème de déterminer si le résultat d'une requête est inclus dans le résultat d'une autre requête pour tout ensemble de données. Elle a des applications importantes dans l'optimisation des requêtes et la vérification de bases de connaissances. L'objectif principal de cette thèse est de fournir des procédures solides et com- plètes pour déterminer l'inclusion des requêtes SPARQL en vertu d'exprimés en axiomes logiques de description. De plus, nous mettons en œuvre ces procédures à l'appui des résultats théoriques par l'expérimentation. À ce jour, test d'inclusion de requête a été effectuée à l'aide de différentes techniques: homomorphisme de graphes, bases de données canoniques, les tech- niques de la théorie des automates et par une réduction au problème de la va- lidité de la logique. Dans cette thèse, nous utilisons la derniere technique pour tester l'inclusion des requêtes SPARQL utilisant une logique expressive appelée μ-calcul. Pour ce faire, les graphes RDF sont codés comme des systèmes de transitions, et les requêtes et les axiomes du schéma sont codés comme des formules de μ-calcul. Ainsi, l'inclusion de requêtes peut être réduit á test de validité de formule logique. L'objectif de cette thèse est d'identifier les divers fragments de SPARQL (et PSPARQL) et les langages de description logique de schéma pour lequelle l'inculsion est décidable. En outre, afin de fournir théoriquement et expériment- alement éprouvées procédures de vérifier l'inclusion de ces fragments décid- ables. Pas durer au moins mais, cette thèse propose un point de repère pour les solveurs d'inclusion. Ce benchmark est utilisé pour tester et comparer l'état actuel des solveurs d'inclusion. / Query containment is a well-studied problem spanning over several decades of research. Generally, it is defined as the problem of determining if the result of one query is included in the result of another query for any given dataset. It has major applications in query optimization and knowledge base verification. The main objective of this thesis is to provide sound and complete procedures to determine containment of SPARQL queries under expressive description logic axioms. Further, to support theoretical results by experimentation. To date query containment has been done using different techniques: containment mapping, canonical databases, automata theory techniques and through a reduction to the validity problem in logic. In this thesis, we use the later technique to address containment using an expressive logic called mu-calculus. In doing so, RDF graphs are encoded as transitions systems, and queries and schema axioms are encoded as mu-calculus formulae. Thereby, query containment can be reduced to validity test in the logic. The focus of this thesis is to identify various fragments of SPARQL (and PSPARQL) and description logic schema languages for which containment is decidable. Additionally, to provide theoretically and experimentally proven procedures to check containment of those decidable fragments. Last not but least, this thesis proposes a benchmark for containment solvers. This benchmark is used to test and compare the current state-of-the-art containment solvers.

O cerrado é a maior, mais rica e provavelmente a mais ameaçada savana tropical do mundo. No entanto, grande parte de sua área foi ocupada por empreendimentos de agropecuária, nos quais não foram respeitados princípios básicos de conservação, sendo que cada grupo ou táxon reage de forma diferente a mudanças ambientais desse tipo. As aves de rapina, como os Falconiformes e os Strigiformes, são especialmente prejudicadas, pois são considerados predadores de topo de muitas teias alimentares. Porém, para saber como essas aves são afetadas pelas mudanças ambientais causadas pela ação do homem é necessário entender quais fatores são relevantes na \"escolha\" do ambiente de determinada espécie e assim compreender a razão de uma possível seletividade de hábitat. Sendo assim, o presente estudo observou características ecológicas de duas espécies de corujas comuns e bem distribuídas no Brasil, Megascops choliba e Athene cunicularia. Dentre os objetivos estão analisar a metodologia de estudo dessas aves de rapina, com possíveis efeitos na detecção de contatos e verificar o uso de hábitat, em diferentes fisionomias de cerrado, por parte das duas espécies de corujas. O estudo foi realizado na região da Estação Ecológica de Itirapina, no interior do estado de São Paulo. Para contatar as corujas foram realizados experimentos de playback em pontos de amostragem distribuídos em quatro fisionomias (neste estudo consideradas habitats) de cerrado. A atividade vocal de M. choliba variou conforme a temperatura e a umidade relativa. Esta espécie respondeu mais ao playback em condições de temperatura e umidade relativa altas. Athene cunicularia mostrou variar sua atividade vocal conforme a fase da lua e a intensidade do vento. Indivíduos desta espécie respondem mais intensamente ao playback em noites de lua cheia e menos em noites com ventos mais fortes. As duas espécies de corujas se distribuem diferentemente entre as fisionomias de cerrado. Athene cunicularia distribui-se distintamente entre fisionomias fechadas e abertas (Hk-w = 9,976; p = 0,0188), utilizando mais frequentemente as os campos limpo e sujo. Megascops choliba também se distribui diferentemente entre as fisionomias de cerrado (Hk-w = 10,88; p = 2 0,0137), utilizando preferencialmente o campo cerrado e o cerrado s.s.. Segundo os modelos tidos como os melhores, pela seleção de modelos feita através do AIC (Aikaike\'s Information Criterion), a variável com maior poder explicativo é o número de arbóreas para as duas espécies. Megascops choliba e A. cunicularia se segregam ecologicamente, havendo partição divergente de recursos espaciais, devido a seus requisitos para nidificação e forrageamento. Ocorre sobreposição intermediária no uso do habitat entre ambas espécies (O = 0,466). Já quanto a amplitude de nicho espacial (uso de habitat) M. choliba foi generalista (Bst = 0,753) e A. cunicularia intermediária (Bst = 0,453). Sendo assim, estas espécies divergem na seleção de habitat, se distribuindo diferentemente entre as fisionomias de cerrado de acordo com o número de arbóreas. Este estudo sugere, ainda, a importância de se levar em consideração as variáveis climáticas em estudos com o uso de vocalizações de aves de rapina noturnas, servindo também de subsídio para pesquisas futuras sobre censo dessas aves. / The Cerrado biome is the largest, richest and perhaps the most threatened tropical savannah of the world. However, most part of its natural areas has been transformed on agrosystems and pastures where basic principles of conservation weren\'t respected. Each biological group or taxa are affected on different ways by this change. Birds of prey are particularly affected because of its position in trophic webs, as they are top predators. To understand how these birds are affected by change caused by human land use, it is necessary to understand which factors are important for habitat selection, and then understand the species-habitat relationship. Thus, we observed ecological aspects of two widespread and common owls on Brazil: Tropical Screech-Owls (Megascops choliba) and Burrowing Owl (Athene cunicularia). The main objectives of this study included an analysis of methodological aspects of studying these owls species through playback and observe their habitat use. The study was conducted in the Estação Ecológica de Itirapina, State of São Paulo, Brazil. For doing it, we used playback experiments to detect these owls on four different cerrado physiognomies Vocal activities of Tropical Screech-owls were more detected in conditions of higher temperature and humidity. On the other hand, the Athene cunicularia answered more to playback in lower wind speed conditions and/or at full moon nights. The Burrowing Owl explored more frequently open physiognomies of cerrado, as campo limpo and campo sujo (Hk-w = 9.976; p = 0.0188). Conversely, Megascops choliba is more often found on campo cerrado, avoiding campo limpo (Hk-w = 10.88; p = 0.0137). According to Aikaike\'s Information Criterion (AIC) selection model, the most important variable to explain the distribution of both species in cerrado is the number of trees. There was ecological segregation between Megascops choliba and A. cunicularia. The spatial niche was intermediarily segregated (Pianka´s niche overlap measure O = 0.466), according their different needs for nesting and foraging. Additionally, these owls displayed broader (M. choliba Bst = 0.753) or intermediate (A. cunicularia Bst = 0.453) spatial niche breadths. On this sense, these owls have different needs on habitat selection, and their different distributions in cerrado were related more intrinsically to the number of trees present on each physiognomy, which is related to their nesting and foraging requirements. Aditionally, this study suggests, the importance to consider the influence of weather conditions on broadcast survey techniques for nocturnal raptors, which may be considered in further studies on census of these birds.

Informação sobre o estágio de câncer num paciente é fundamental quando médicos avaliam o progresso de seu tratamento. A determinação do estágio de câncer (cancer staging) é um processo que leva em consideração a descrição, localização, características e possíveis metástases dos tumores cancerosos de um paciente. Esse processo deve seguir um padrão de classificação como, por exemplo, o padrão TNM. Porém, na prática clínica, a execução desse processo pode ser tediosa, propensa a erros e gerar incertezas. Com o intuito de amenizar esses problemas, este trabalho tem como objetivo auxiliar radiologistas fornecendo uma segunda opinião na avaliação do estágio de câncer de um paciente. Para isso, tecnologias da Web Semântica, como ontologias e reasoning, foram usadas para classificar automaticamente estágios de câncer. Essa classificação usou anotações semânticas feitas por radiologistas, usando a ferramenta ePAD, e armazenadas no formato AIM. Um protótipo de classificador, baseado no padrão TNM, foi criado. Ele transforma anotações AIM em indivíduos da ontologia AIM4-O e, usando axiomas e regras (escritos na linguagens OWL-SWRL) representando o padrão TNM, ele automaticamente calcula o estágio de câncer de fígado de pacientes. A ontologia AIM4-O foi desenvolvida, como parte desse trabalho, para representar anotações AIM 4 em OWL. Esse classificador TNM foi avaliado, usando-se dados reais de relatórios radiológicos de pacientes do NCIs Genomic Data Commons (GDC), em termos de precisão e revocação, com resultados respectivos de 85,7% e 81,0% (quando comparado aos valores reais de estágio de câncer dos relatórios). Todo o processo foi validado com radiologistas do Radiology Dept. of the Stanford University. / Information about cancer staging in a patient is crucial when clinicians assess treatment progress. Determining cancer stage is a process that takes into account the description, location, characteristics and possible metastasis of cancerous tumors in a patient. It should follow classification standards, such as the TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious, error-prone and create uncertainty. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage in patients. For doing this, Semantic Web technologies, such as ontologies and reasoning, were used to automatically classify cancer stages. This classification used semantic annotations made by radiologists, using the ePAD tool, and stored using standard AIM format. A TNM based classifier prototype was created. It transforms AIM annotations in AIM4- O ontology individuals and, using axioms and rules (written in OWL-SWRL languages) representing the TNM standard, it automatically calculates patients liver cancer stage. The AIM4-O ontology was developed, as part of this work, to represent AIM 4 annotations in OWL. This TNM classifier was evaluated, using real patients radiology reports, from the NCIs Genomic Data Commons (GDC), in term of precision and recall, with 85.7% and 81.0% respective results (when compared to the actual cancer stages from the reports). The whole process was validated with radiologists from the Radiology Dept. of the Stanford University.

Access restrictions are essential in standard information systems and became an issue for ontologies in the following two aspects. Ontologies can represent explicit and implicit knowledge about an access policy. For this aspect we provided a methodology to represent and systematically complete role-based access control policies. Orthogonally, an ontology might be available for limited reading access. Independently of a specific ontology language or reasoner, we provided a lattice-based framework to assign labels to an ontology’s axioms and consequences. We looked at the problems to compute and repair one or multiple consequence labels and to assign a query-based access restriction. An empirical evaluation has shown that the algorithms perform well in practical scenarios with large-scale ontologies.

This master's thesis describes importing the ontology in language OWL 2 into the internal structures of 4A annotation server. It is concerned in anonymous nodes, for example in anonymous classes or anonymous properties. The solution was to use the library The OWL API for import ontology. The solution also allows automatic generation of names to anonymous classes and properties.