Exploring instances for matching heterogeneous database schemas utilizing Google similarity and regular expression

Instance based schema matching aims to identify correspondences between different schema attributes. Several approaches have been proposed to discover these correspondences in which instances including those with numeric values are treated as strings. This prevents discovering common patterns or performing statistical computation between numeric instances. Consequently, this causes unidentified matches for numeric instances which further effect the results. In this paper, we propose an approach for addressing the problem of finding matches between schemas of semantically and syntactically related attributes. Since we only fully exploit the instances of the schemas, we rely on strategies that combine the strength of Google as a web semantic and regular expression as pattern recognition. To demonstrate the accuracy of our approach, we have conducted an experimental evaluation using real world datasets. The results show that our approach is able to find 1-1 matches with high accuracy in the range of 93% - 99%. Furthermore, our proposed approach outperformed the previous approaches using a sample of instances

BIOZON: a system for unification, management and analysis of heterogeneous biological data

BACKGROUND: Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION: Here we present a system (Biozon) that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways). It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. CONCLUSION: The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at

Web Data Integration for Non-Expert Users

oday, there is an abundance of structured data available on the web in the form of RDF graphs and relational (i.e., tabular) data. This data comes from heterogeneous sources, and realizing its full value requires integrating these sources so that they can be queried together. Due to the scale and heterogeneity of the data sources on the web, integrating them is typically an automatic process. However, automatic data integration approaches are not completely accurate since they infer semantics from syntax in data sources with a high degree of heterogeneity. Therefore, these automatic approaches can be considered as a first step to quickly get reasonable quality data integration output that can be used in issuing queries over the data sources. A second step is refining this output over time while it is being used. Interacting with the data sources through the output of the data integration system and refining this output requires expertise in data management, which limits the scope of this activity to power users and consequently limits the usability of data integration systems. This thesis focuses on helping non-expert users to access heterogeneous data sources through data integration systems, without requiring the users to have prior knowledge of the queried data sources or exposing them to the details of the output of the data integration system. In addition, the users can provide feedback over the answers to their queries, which can then be used to refine and improve the quality of the data integration output. The thesis studies both RDF and relational data. For RDF data, the thesis focuses on helping non-expert users to query heterogeneous RDF data sources, and utilizing their feedback over query answers to improve the quality of the interlinking between these data sources. For relational data, the thesis focuses on improving the quality of the mediated schema for a set of relational data sources and the semantic mappings between these sources based on user feedback over query answers

Semantics-based approach for generating partial views from linked life-cycle highway project data

The purpose of this dissertation is to develop methods that can assist data integration and extraction from heterogeneous sources generated throughout the life-cycle of a highway project. In the era of computerized technologies, project data is largely available in digital format. Due to the fragmented nature of the civil infrastructure sector, digital data are created and managed separately by different project actors in proprietary data warehouses. The differences in the data structure and semantics greatly hinder the exchange and fully reuse of digital project data. In order to address those issues, this dissertation carries out the following three individual studies. The first study aims to develop a framework for interconnecting heterogeneous life cycle project data into an unified and linked data space. This is an ontology-based framework that consists of two phases: (1) translating proprietary datasets into homogeneous RDF data graphs; and (2) connecting separate data networks to each other. Three domain ontologies for design, construction, and asset condition survey phases are developed to support data transformation. A merged ontology that integrates the domain ontologies is constructed to provide guidance on how to connect data nodes from domain graphs. The second study is to deal with the terminology inconsistency between data sources. An automated method is developed that employs Natural Language Processing (NLP) and machine learning techniques to support constructing a domain specific lexicon from design manuals. The method utilizes pattern rules to extract technical terms from texts and learns their representation vectors using a neural network based word embedding approach. The study also includes the development of an integrated method of minimal-supervised machine learning, clustering analysis, and word vectors, for computing the term semantics and classifying the relations between terms in the target lexicon. In the last study, a data retrieval technique for extracting subsets of an XML civil data schema is designed and tested. The algorithm takes a keyword input of the end user and returns a ranked list of the most relevant XML branches. This study utilizes a lexicon of the highway domain generated from the second study to analyze the semantics of the end user keywords. A context-based similarity measure is introduced to evaluate the relevance between a certain branch in the source schema and the user query. The methods and algorithms resulting from this research were tested using case studies and empirical experiments. The results indicate that the study successfully address the heterogeneity in the structure and terminology of data and enable a fast extraction of sub-models of data. The study is expected to enhance the efficiency in reusing digital data generated throughout the project life-cycle, and contribute to the success in transitioning from paper-based to digital project delivery for civil infrastructure projects

From Text to Knowledge with Graphs: modelling, querying and exploiting textual content

This paper highlights the challenges, current trends, and open issues related to the representation, querying and analytics of content extracted from texts. The internet contains vast text-based information on various subjects, including commercial documents, medical records, scientific experiments, engineering tests, and events that impact urban and natural environments. Extracting knowledge from this text involves understanding the nuances of natural language and accurately representing the content without losing information. This allows knowledge to be accessed, inferred, or discovered. To achieve this, combining results from various fields, such as linguistics, natural language processing, knowledge representation, data storage, querying, and analytics, is necessary. The vision in this paper is that graphs can be a well-suited text content representation once annotated and the right querying and analytics techniques are applied. This paper discusses this hypothesis from the perspective of linguistics, natural language processing, graph models and databases and artificial intelligence provided by the panellists of the DOING session in the MADICS Symposium 2022

Semantic Interaction in Web-based Retrieval Systems : Adopting Semantic Web Technologies and Social Networking Paradigms for Interacting with Semi-structured Web Data

Existing web retrieval models for exploration and interaction with web data do not take into account semantic information, nor do they allow for new forms of interaction by employing meaningful interaction and navigation metaphors in 2D/3D. This thesis researches means for introducing a semantic dimension into the search and exploration process of web content to enable a significantly positive user experience. Therefore, an inherently dynamic view beyond single concepts and models from semantic information processing, information extraction and human-machine interaction is adopted. Essential tasks for semantic interaction such as semantic annotation, semantic mediation and semantic human-computer interaction were identified and elaborated for two general application scenarios in web retrieval: Web-based Question Answering in a knowledge-based dialogue system and semantic exploration of information spaces in 2D/3D

Attribute lattice: a graph-based conceptual modeling grammar for heterogeneous data

One key characteristic of big data is variety. With massive and growing amounts of data existing in independent and heterogeneous (structured and unstructured) sources, assigning consistent and interoperable data semantics, which is essential for meaningful use of data, is an increasingly important challenge. I argue, conceptual models, in contrast to their traditional roles in the Information System development, can be used to represent data semantics as perceived by the user of data. In this thesis, I use principles from philosophical ontology, human cognition (i.e., classification theory), and graph theory to offer a theory-based conceptual modeling grammar for this purpose. This grammar reflects data from users of data perspective and independent from data source schema. I formally define the concept of attribute lattice as a graph-based, schema-free conceptual modeling grammar that represents attributes of instances in the domain of interest and precedence relations among them. Each node in an attribute lattice represents an attribute - a true statement (predicate) about some instances in the domain. Each directed arc represents a precedence relation indicating that possessing one attribute implies possessing another attribute. In this thesis, based on the premise that inherent classification is a barrier that hinders semantic interoperation of heterogeneous data sources, a human cognition based conceptual modeling grammar is introduced as an effective way to resolve semantic heterogeneity. This grammar represents the precedence relationship among attributes as perceived by human user and provides a mechanism to infer classes based on the pattern of precedences. Hence, a key contribution of attribute lattice is semantic relativism – that is, the classification in this grammar relies on the pattern of precedence relationship among attributes rather than fixed classes. This modeling grammar uses the immediate and semantic neighbourhoods of an attribute to designate an attribute as either a category, a class or a property and to specify the expansion of an attribute – attributes which are semantically equal to the given attribute. The introduced conceptual modeling grammar is implemented as an artifact to store and manage attribute lattices, to graphically represent them, and integrate lattices from various heterogeneous sources. With the ever-increasing amount of unstructured data (mostly text data) from various data sources such as social media, integrating text data with other data sources has gained considerable attention. This massive amount of data, however, makes finding the data relevant to a topic of interest a new challenge. I argue that the attribute lattice provides a robust semantic foundation to address this information retrieval challenge from unstructured data sources. Hence, a topic modeling approach based on the attribute lattice is proposed for Twitter. This topic model conceptualizes topic structure of tweets related to the domain of interest and enhances information retrieval by improving the semantic interpretability of hashtags

Extracting and Cleaning RDF Data

The RDF data model has become a prevalent format to represent heterogeneous data because of its versatility. The capability of dismantling information from its native formats and representing it in triple format offers a simple yet powerful way of modelling data that is obtained from multiple sources. In addition, the triple format and schema constraints of the RDF model make the RDF data easy to process as labeled, directed graphs. This graph representation of RDF data supports higher-level analytics by enabling querying using different techniques and querying languages, e.g., SPARQL. Anlaytics that require structured data are supported by transforming the graph data on-the-fly to populate the target schema that is needed for downstream analysis. These target schemas are defined by downstream applications according to their information need. The flexibility of RDF data brings two main challenges. First, the extraction of RDF data is a complex task that may involve domain expertise about the information required to be extracted for different applications. Another significant aspect of analyzing RDF data is its quality, which depends on multiple factors including the reliability of data sources and the accuracy of the extraction systems. The quality of the analysis depends mainly on the quality of the underlying data. Therefore, evaluating and improving the quality of RDF data has a direct effect on the correctness of downstream analytics. This work presents multiple approaches related to the extraction and quality evaluation of RDF data. To cope with the large amounts of data that needs to be extracted, we present DSTLR, a scalable framework to extract RDF triples from semi-structured and unstructured data sources. For rare entities that fall on the long tail of information, there may not be enough signals to support high-confidence extraction. Towards this problem, we present an approach to estimate property values for long tail entities. We also present multiple algorithms and approaches that focus on the quality of RDF data. These include discovering quality constraints from RDF data, and utilizing machine learning techniques to repair errors in RDF data