Datalog± Ontology Consolidation

Knowledge bases in the form of ontologies are receiving increasing attention as they allow to clearly represent both the available knowledge, which includes the knowledge in itself and the constraints imposed to it by the domain or the users. In particular, Datalog ± ontologies are attractive because of their property of decidability and the possibility of dealing with the massive amounts of data in real world environments; however, as it is the case with many other ontological languages, their application in collaborative environments often lead to inconsistency related issues. In this paper we introduce the notion of incoherence regarding Datalog± ontologies, in terms of satisfiability of sets of constraints, and show how under specific conditions incoherence leads to inconsistent Datalog ± ontologies. The main contribution of this work is a novel approach to restore both consistency and coherence in Datalog± ontologies. The proposed approach is based on kernel contraction and restoration is performed by the application of incision functions that select formulas to delete. Nevertheless, instead of working over minimal incoherent/inconsistent sets encountered in the ontologies, our operators produce incisions over non-minimal structures called clusters. We present a construction for consolidation operators, along with the properties expected to be satisfied by them. Finally, we establish the relation between the construction and the properties by means of a representation theorem. Although this proposal is presented for Datalog± ontologies consolidation, these operators can be applied to other types of ontological languages, such as Description Logics, making them apt to be used in collaborative environments like the Semantic Web.Fil: Deagustini, Cristhian Ariel David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Martinez, Maria Vanina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Falappa, Marcelo Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Simari, Guillermo Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación. Instituto de Ciencias e Ingeniería de la Computación; Argentin

Quality measures for ETL processes: from goals to implementation

Extraction transformation loading (ETL) processes play an increasingly important role for the support of modern business operations. These business processes are centred around artifacts with high variability and diverse lifecycles, which correspond to key business entities. The apparent complexity of these activities has been examined through the prism of business process management, mainly focusing on functional requirements and performance optimization. However, the quality dimension has not yet been thoroughly investigated, and there is a need for a more human-centric approach to bring them closer to business-users requirements. In this paper, we take a first step towards this direction by defining a sound model for ETL process quality characteristics and quantitative measures for each characteristic, based on existing literature. Our model shows dependencies among quality characteristics and can provide the basis for subsequent analysis using goal modeling techniques. We showcase the use of goal modeling for ETL process design through a use case, where we employ the use of a goal model that includes quantitative components (i.e., indicators) for evaluation and analysis of alternative design decisions.Peer ReviewedPostprint (author's final draft

Gerando redes de conhecimento a partir de descrições de fenótipos

Orientadores: André Santanchè, Júlio César dos ReisDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Diversos sistemas computacionais usam informações sobre seres vivos, tais como chaves de identificação ¿ artefatos criados por biólogos para identificar espécimes de seres vivos seguindo uma cadeia de questões acerca das suas características observáveis (fenótipos). Tais questões estão em formato de texto livre, por exemplo, "Possui olhos grandes e pre- tos". Contudo, texto livre dificulta a interpretação de informação por máquinas, limitando sua capacidade de realização de tarefas de busca, integração e comparação de termos. Esta dissertação propõe um método para extrair informação a respeito de fenótipos a partir de textos escritos em linguagem natural, colocando-os no formato de Entidade-Qualidade ¿ um formato de dados biológicos para representar estruturas anatômicas (Entidade) e o seu modificador (Qualidade). A proposta permite que Entidades e Qualidades, reconhecidas automaticamente a partir de informação do nível textual, sejam relacionadas com con- ceitos presentes em ontologias de domínio. Ela adota ferramentas de Processamento de Linguagem Natural existentes, bem como contribui com novas técnicas que exploram as características de escrita e estruturação implícitas em textos presentes nas chaves de iden- tificação. A abordagem foi validada utilizando os dados da base FishBase, sobre a qual foram conduzidos experimentos explorando um conjunto de testes anotado manualmente para avaliar a precisão e aplicabilidade do método de extração proposto. Os resultados obtidos mostram os benefícios da técnica e possibilidades de estudos científicos utilizando a rede de conhecimento extraídaAbstract: Several computing systems rely on information about living beings, such as identification keys ¿ artifacts created by biologists to identify specimens following a flow of questions about their observable characters (phenotype). These questions are described in a free- text format, e.g., "big and black eye". Free-texts hamper the automatic information interpretation by machines, limiting their ability to perform search and comparison of terms, as well as integration tasks. This thesis proposes a method to extract phenotypic information from natural language texts from biology legacy information systems, trans- forming them in an Entity-Quality formalism ¿ a format to represent each phenotype character (Entity) and its state (Quality). Our approach aligns automatically recognized Entities and Qualities with domain concepts described in ontologies. It adopts existing Natural Language Processing techniques, adding an extra original step, which exploits intrinsic characteristics of phenotypic descriptions and of the organizational structure of identification keys. The approach was validated over the FishBase data. We conducted extensive experiments based on a manually annotated Gold Standard set to assess the precision and applicability of the proposed extraction method. The obtained results re- veal the feasibility of our technique, its benefits and possibilities of scientific studies using the extracted knowledge networkMestradoCiência da ComputaçãoMestre em Ciência da Computação1406900CAPE

Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows

To be easily constructed, shared and maintained, complex in silico bioinformatics analysis are structured as workflows. Furthermore, the growth of computational power and storage demand from this domain, requires workflows to be efficiently executed. However, workflow performances usually rely on the ability of the designer to extract potential parallelism. But atomic bioinformatics tasks do not often exhibit direct parallelism which may appears later in the workflow design process. In this paper, we propose a Model-Driven Architecture approach for capturing the complete design process of bioinformatics workflows. More precisely, two workflow models are specified: the first one, called design model, graphically captures a low throughput prototype. The second one, called execution model, specifies multiple levels of coarse grained parallelism. The execution model is automatically generated from the design model using annotation derived from the EDAM ontology. These annotations describe the data types connecting differents elementary tasks. The execution model can then be interpreted by a workflow engine and executed on hardware having intensive computation facility

Building Data Warehouses with Semantic Web Data

The Semantic Web (SW) deployment is now a realization and the amount of semantic annotations is ever increasing thanks to several initiatives that promote a change in the current Web towards the Web of Data, where the semantics of data become explicit through data representation formats and standards such as RDF/(S) and OWL. However, such initiatives have not yet been accompanied by e cient intelligent applications that can exploit the implicit semantics and thus, provide more insightful analysis. In this paper, we provide the means for e ciently analyzing and exploring large amounts of semantic data by combining the inference power from the annotation semantics with the analysis capabilities provided by OLAP-style aggregations, navigation, and reporting. We formally present how semantic data should be organized in a well-de ned conceptual MD schema, so that sophisticated queries can be expressed and evaluated. Our proposal has been evaluated over a real biomedical scenario, which demonstrates the scalability and applicability of the proposed approach

TiFi: Taxonomy Induction for Fictional Domains [Extended version]

Taxonomies are important building blocks of structured knowledge bases, and their construction from text sources and Wikipedia has received much attention. In this paper we focus on the construction of taxonomies for fictional domains, using noisy category systems from fan wikis or text extraction as input. Such fictional domains are archetypes of entity universes that are poorly covered by Wikipedia, such as also enterprise-specific knowledge bases or highly specialized verticals. Our fiction-targeted approach, called TiFi, consists of three phases: (i) category cleaning, by identifying candidate categories that truly represent classes in the domain of interest, (ii) edge cleaning, by selecting subcategory relationships that correspond to class subsumption, and (iii) top-level construction, by mapping classes onto a subset of high-level WordNet categories. A comprehensive evaluation shows that TiFi is able to construct taxonomies for a diverse range of fictional domains such as Lord of the Rings, The Simpsons or Greek Mythology with very high precision and that it outperforms state-of-the-art baselines for taxonomy induction by a substantial margin

Ontology-based information extraction from learning management systems

In this work we present a system for information extraction from Learning Management Systems. This system is ontology-based. It retrieves information according to the structure of the ontology to populate the ontology. We graphically present statistics about the ontology data. These statistics present latent knowledge which is difficult to see in the traditional Learning Management System. To answer questions about the ontology, a question answering system was developed using Natural Language Processing in the conversion of the natural language question into an ontology query language; Sumário: Extração de Informação de Sistemas de Gestão para Educação Usando Ontologias Neste dissertação apresentamos um sistema de extracção de informação de sistemas de gestão para educação (Learning Management Systems). Este sistema é baseado em ontologias e extrai informação de acordo com a estrutura da ontologia para a popular. Também permite apresentar graficamente algumas estatísticas sobre os dados da ontologia. Estas estatísticas revelam o conhecimento latente que é difícil de ver num sistema tradicional de gestão para a educação. Para poder responder a perguntas sobre os dados da ontologia, um sistema de resposta automática a perguntas em língua natural foi desenvolvido usando Processamento de Língua Natural para converter as perguntas para linguagem de interrogação de ontologias

Multi modal multi-semantic image retrieval

PhDThe rapid growth in the volume of visual information, e.g. image, and video can overwhelm users’ ability to find and access the specific visual information of interest to them. In recent years, ontology knowledge-based (KB) image information retrieval techniques have been adopted into in order to attempt to extract knowledge from these images, enhancing the retrieval performance. A KB framework is presented to promote semi-automatic annotation and semantic image retrieval using multimodal cues (visual features and text captions). In addition, a hierarchical structure for the KB allows metadata to be shared that supports multi-semantics (polysemy) for concepts. The framework builds up an effective knowledge base pertaining to a domain specific image collection, e.g. sports, and is able to disambiguate and assign high level semantics to ‘unannotated’ images. Local feature analysis of visual content, namely using Scale Invariant Feature Transform (SIFT) descriptors, have been deployed in the ‘Bag of Visual Words’ model (BVW) as an effective method to represent visual content information and to enhance its classification and retrieval. Local features are more useful than global features, e.g. colour, shape or texture, as they are invariant to image scale, orientation and camera angle. An innovative approach is proposed for the representation, annotation and retrieval of visual content using a hybrid technique based upon the use of an unstructured visual word and upon a (structured) hierarchical ontology KB model. The structural model facilitates the disambiguation of unstructured visual words and a more effective classification of visual content, compared to a vector space model, through exploiting local conceptual structures and their relationships. The key contributions of this framework in using local features for image representation include: first, a method to generate visual words using the semantic local adaptive clustering (SLAC) algorithm which takes term weight and spatial locations of keypoints into account. Consequently, the semantic information is preserved. Second a technique is used to detect the domain specific ‘non-informative visual words’ which are ineffective at representing the content of visual data and degrade its categorisation ability. Third, a method to combine an ontology model with xi a visual word model to resolve synonym (visual heterogeneity) and polysemy problems, is proposed. The experimental results show that this approach can discover semantically meaningful visual content descriptions and recognise specific events, e.g., sports events, depicted in images efficiently. Since discovering the semantics of an image is an extremely challenging problem, one promising approach to enhance visual content interpretation is to use any associated textual information that accompanies an image, as a cue to predict the meaning of an image, by transforming this textual information into a structured annotation for an image e.g. using XML, RDF, OWL or MPEG-7. Although, text and image are distinct types of information representation and modality, there are some strong, invariant, implicit, connections between images and any accompanying text information. Semantic analysis of image captions can be used by image retrieval systems to retrieve selected images more precisely. To do this, a Natural Language Processing (NLP) is exploited firstly in order to extract concepts from image captions. Next, an ontology-based knowledge model is deployed in order to resolve natural language ambiguities. To deal with the accompanying text information, two methods to extract knowledge from textual information have been proposed. First, metadata can be extracted automatically from text captions and restructured with respect to a semantic model. Second, the use of LSI in relation to a domain-specific ontology-based knowledge model enables the combined framework to tolerate ambiguities and variations (incompleteness) of metadata. The use of the ontology-based knowledge model allows the system to find indirectly relevant concepts in image captions and thus leverage these to represent the semantics of images at a higher level. Experimental results show that the proposed framework significantly enhances image retrieval and leads to narrowing of the semantic gap between lower level machinederived and higher level human-understandable conceptualisation