Fuzzy concept analysis for semantic knowledge extraction

2010 - 2011Availability of controlled vocabularies, ontologies, and so on is enabling feature to provide some added values in terms of knowledge management. Nevertheless, the design, maintenance and construction of domain ontologies are a human intensive and time consuming task. The Knowledge Extraction consists of automatic techniques aimed to identify and to define relevant concepts and relations of the domain of interest by analyzing structured (relational databases, XML) and unstructured (text, documents, images) sources. Specifically, methodology for knowledge extraction defined in this research work is aimed at enabling automatic ontology/taxonomy construction from existing resources in order to obtain useful information. For instance, the experimental results take into account data produced with Web 2.0 tools (e.g., RSS-Feed, Enterprise Wiki, Corporate Blog, etc.), text documents, and so on. Final results of Knowledge Extraction methodology are taxonomies or ontologies represented in a machine oriented manner by means of semantic web technologies, such as: RDFS, OWL and SKOS. The resulting knowledge models have been applied to different goals. On the one hand, the methodology has been applied in order to extract ontologies and taxonomies and to semantically annotate text. On the other hand, the resulting ontologies and taxonomies are exploited in order to enhance information retrieval performance and to categorize incoming data and to provide an easy way to find interesting resources (such as faceted browsing). Specifically, following objectives have been addressed in this research work: Ontology/Taxonomy Extraction: that concerns to automatic extraction of hierarchical conceptualizations (i.e., taxonomies) and relations expressed by means typical description logic constructs (i.e., ontologies). Information Retrieval: definition of a technique to perform concept-based the retrieval of information according to the user queries. Faceted Browsing: in order to automatically provide faceted browsing capabilities according to the categorization of the extracted contents. Semantic Annotation: definition of a text analysis process, aimed to automatically annotate subjects and predicates identified. The experimental results have been obtained in some application domains: e-learning, enterprise human resource management, clinical decision support system. Future challenges go in the following directions: investigate approaches to support ontology alignment and merging applied to knowledge management.X n.s

Knowledge Components and Methods for Policy Propagation in Data Flows

Data-oriented systems and applications are at the centre of current developments of the World Wide Web (WWW). On the Web of Data (WoD), information sources can be accessed and processed for many purposes. Users need to be aware of any licences or terms of use, which are associated with the data sources they want to use. Conversely, publishers need support in assigning the appropriate policies alongside the data they distribute. In this work, we tackle the problem of policy propagation in data flows - an expression that refers to the way data is consumed, manipulated and produced within processes. We pose the question of what kind of components are required, and how they can be acquired, managed, and deployed, to support users on deciding what policies propagate to the output of a data-intensive system from the ones associated with its input. We observe three scenarios: applications of the Semantic Web, workflow reuse in Open Science, and the exploitation of urban data in City Data Hubs. Starting from the analysis of Semantic Web applications, we propose a data-centric approach to semantically describe processes as data flows: the Datanode ontology, which comprises a hierarchy of the possible relations between data objects. By means of Policy Propagation Rules, it is possible to link data flow steps and policies derivable from semantic descriptions of data licences. We show how these components can be designed, how they can be effectively managed, and how to reason efficiently with them. In a second phase, the developed components are verified using a Smart City Data Hub as a case study, where we developed an end-to-end solution for policy propagation. Finally, we evaluate our approach and report on a user study aimed at assessing both the quality and the value of the proposed solution

A model for information retrieval driven by conceptual spaces

A retrieval model describes the transformation of a query into a set of documents. The question is: what drives this transformation? For semantic information retrieval type of models this transformation is driven by the content and structure of the semantic models. In this case, Knowledge Organization Systems (KOSs) are the semantic models that encode the meaning employed for monolingual and cross-language retrieval. The focus of this research is the relationship between these meanings’ representations and their role and potential in augmenting existing retrieval models effectiveness. The proposed approach is unique in explicitly interpreting a semantic reference as a pointer to a concept in the semantic model that activates all its linked neighboring concepts. It is in fact the formalization of the information retrieval model and the integration of knowledge resources from the Linguistic Linked Open Data cloud that is distinctive from other approaches. The preprocessing of the semantic model using Formal Concept Analysis enables the extraction of conceptual spaces (formal contexts)that are based on sub-graphs from the original structure of the semantic model. The types of conceptual spaces built in this case are limited by the KOSs structural relations relevant to retrieval: exact match, broader, narrower, and related. They capture the definitional and relational aspects of the concepts in the semantic model. Also, each formal context is assigned an operational role in the flow of processes of the retrieval system enabling a clear path towards the implementations of monolingual and cross-lingual systems. By following this model’s theoretical description in constructing a retrieval system, evaluation results have shown statistically significant results in both monolingual and bilingual settings when no methods for query expansion were used. The test suite was run on the Cross-Language Evaluation Forum Domain Specific 2004-2006 collection with additional extensions to match the specifics of this model

Knowledge management and Discovery for advanced Enterprise Knowledge Engineering

2012 - 2013The research work addresses mainly issues related to the adoption of models, methodologies and knowledge management tools that implement a pervasive use of the latest technologies in the area of Semantic Web for the improvement of business processes and Enterprise 2.0 applications. The first phase of the research has focused on the study and analysis of the state of the art and the problems of Knowledge Discovery database, paying more attention to the data mining systems. The most innovative approaches which were investigated for the "Enterprise Knowledge Engineering" are listed below. In detail, the problems analyzed are those relating to architectural aspects and the integration of Legacy Systems (or not). The contribution of research that is intended to give, consists in the identification and definition of a uniform and general model, a "Knowledge Enterprise Model", the original model with respect to the canonical approaches of enterprise architecture (for example with respect to the Object Management - OMG - standard). The introduction of the tools and principles of Enterprise 2.0 in the company have been investigated and, simultaneously, Semantic Enterprise based appropriate solutions have been defined to the problem of fragmentation of information and improvement of the process of knowledge discovery and functional knowledge sharing. All studies and analysis are finalized and validated by defining a methodology and related software tools to support, for the improvement of processes related to the life cycles of best practices across the enterprise. Collaborative tools, knowledge modeling, algorithms, knowledge discovery and extraction are applied synergistically to support these processes. [edited by author]XII n.s

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

Knowledge Patterns for the Web: extraction, tranformation and reuse

This thesis aims at investigating methods and software architectures for discovering what are the typical and frequently occurring structures used for organizing knowledge in the Web. We identify these structures as Knowledge Patterns (KPs). KP discovery needs to address two main research problems: the heterogeneity of sources, formats and semantics in the Web (i.e., the knowledge soup problem) and the difficulty to draw relevant boundary around data that allows to capture the meaningful knowledge with respect to a certain context (i.e., the knowledge boundary problem). Hence, we introduce two methods that provide different solutions to these two problems by tackling KP discovery from two different perspectives: (i) the transformation of KP-like artifacts to KPs formalized as OWL2 ontologies; (ii) the bottom-up extraction of KPs by analyzing how data are organized in Linked Data. The two methods address the knowledge soup and boundary problems in different ways. The first method provides a solution to the two aforementioned problems that is based on a purely syntactic transformation step of the original source to RDF followed by a refactoring step whose aim is to add semantics to RDF by select meaningful RDF triples. The second method allows to draw boundaries around RDF in Linked Data by analyzing type paths. A type path is a possible route through an RDF that takes into account the types associated to the nodes of a path. Then we present K~ore, a software architecture conceived to be the basis for developing KP discovery systems and designed according to two software architectural styles, i.e, the Component-based and REST. Finally we provide an example of reuse of KP based on Aemoo, an exploratory search tool which exploits KPs for performing entity summarization

Creation and extension of ontologies for describing communications in the context of organizations

Thesis submitted to Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa, in partial fulfillment of the requirements for the degree of Master in Computer ScienceThe use of ontologies is nowadays a sufficiently mature and solid field of work to be considered an efficient alternative in knowledge representation. With the crescent growth of the Semantic Web, it is expectable that this alternative tends to emerge even more in the near future. In the context of a collaboration established between FCT-UNL and the R&D department of a national software company, a new solution entitled ECC – Enterprise Communications Center was developed. This application provides a solution to manage the communications that enter, leave or are made within an organization, and includes intelligent classification of communications and conceptual search techniques in a communications repository. As specificity may be the key to obtain acceptable results with these processes, the use of ontologies becomes crucial to represent the existing knowledge about the specific domain of an organization. This work allowed us to guarantee a core set of ontologies that have the power of expressing the general context of the communications made in an organization, and of a methodology based upon a series of concrete steps that provides an effective capability of extending the ontologies to any business domain. By applying these steps, the minimization of the conceptualization and setup effort in new organizations and business domains is guaranteed. The adequacy of the core set of ontologies chosen and of the methodology specified is demonstrated in this thesis by its effective application to a real case-study, which allowed us to work with the different types of sources considered in the methodology and the activities that support its construction and evolution

Ontology reuse and synthesis for modelling and simulation

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonThe proliferation and ubiquity of SemanticWeb technologies have transformed the way computer society reshapes its technology through knowledge integration, knowledge reuse and knowledge sharing. Ontology, one of the Semantic Web components, is a way to represent domain knowledge into a human-understandable and machine-readable format. Ontology in simulation has been seen as a conceptual model of a system in an explicit and unambiguous manner, where it can be applied to better capture the modeler’s perspective of the domain. Regarding an ontology for simulation modeling, by reusing ontologies, it helps to reduce time and effort in attaining the domain knowledge, and at the same time assist in domain understanding. For a semantically-richer simulation ontology, it is useful to engage with real data and existing ontologies. This research contributes a rigorous method that extracts domain knowledge, synthesizes processes performed within the domain, and builds a minimal and viable ontology for simulation modeling, knownas aMinimal Viable Simulation Ontology (MVSimO). The research method initially applies ontology selection techniques in Ontology Reuse Framework (ORF) to obtain suitable existing ontologies for reuse. ORF incorporates a module extraction technique during the domain conceptualization phase, where the modules will represent domain knowledge as sub-ontologies. Formal Concept Analysis is later applied to the real-world data to reveal the process details of the domain. Finally, the development of MVSimO is completed by the derivation of event semantic of the processes. The effectiveness of ontology selection and synthesizing methods, is reviewed by evaluating the selected ontology knowledge extracted, and the detailed ontological model of MVSimO. The evaluation of,MVSimO is performed to determine its agreement to the established simulation model of the domain. The evaluation results are encouraging, providing concrete outcomes of the new technique of ontology reuse and new development to the research area

Verification of knowledge shared across design and manufacture using a foundation ontology

Seamless computer-based knowledge sharing between departments of a manufacturing enterprise is useful in preventing unnecessary design revisions. A lack of interoperability between independently developed knowledge bases, however, is a major impediment in the development of a seamless knowledge sharing system. Interoperability, being an ability to overcome semantic and syntactic differences during computer-based knowledge sharing can be enhanced through the use of ontologies. Ontologies in computer science terms are hierarchical structures of knowledge stored in a computer-based knowledge base. Ontologies have been accepted by all as an interoperable medium to provide a non-subjective way of storing and sharing knowledge across diverse domains. Some semantic and syntactic differences, however, still crop up when these ontological knowledge bases are developed independently. A case study in an aerospace components manufacturing company suggests that shape features of a component are perceived differently by the designing and manufacturing departments. These differences cause further misunderstanding and misinterpretation when computer-based knowledge sharing systems are used across the two domains. Foundation or core ontologies can be used to overcome these differences and to ensure a seamless sharing of knowledge. This is because these ontologies provide a common grounding for domain ontologies to be used by individual domains or department. This common grounding can be used by the mediation and knowledge verification systems to authenticate the meaning of knowledge understood across different domains. For this reason, this research proposes a knowledge verification framework for developing a system capable of verifying knowledge between those domain ontologies which are developed out of a common core or foundation ontology. This framework makes use of ontology logic to standardize the way concepts from a foundation and core-concepts ontology are used in domain ontologies and then by using the same principles the knowledge being shared is verified. The Knowledge Frame Language which is based on Common Logic is used for formalizing example ontologies. The ontology editor used for browsing and querying ontologies is the Integrated Ontology Development Environment (IODE) by Highfleet Inc. An ontological product modelling technique is also developed in this research, to test the proposed framework in the scenario of manufacturability analysis. The proposed framework is then validated through a Java API specially developed for this purpose. Real industrial examples experienced during the case study are used for validation