Butterfly: A Model of Provenance

Semantically rich metadata is foreseen to be pervasive in tomorrow\u27s cyber world. People are more willing to store metadata in the hope that such extra information will enable a wide range of novel business intelligent applications. Provenance is metadata which describes the derivation history of data. It is considered to have great potential for helping the reasoning, analyzing, validating, monitoring, integrating and reusing of data. Although there are a few application-specific systems equipped with some degree of provenance tracking functionality, few formal models of provenance are present. A general purpose, formal model of provenance is desirable not only to widely promote the storage and inventive usage of provenance, but also to prepare for the emergence of so called provenance management system. In this thesis, I propose Butterfly, a general purpose provenance model, which offers the capability to model, store, and query provenance. It consists of a semantic model for describing provenance, and an extensible algebraic query model for querying provenance. An initial implementation of the provenance model is also briefly discussed

A generic persistence model for CLP systems (and two useful implementations)

This paper describes a model of persistence in (C)LP languages and two different and practically very useful ways to implement this model in current systems. The fundamental idea is that persistence is a characteristic of certain dynamic predicates (Le., those which encapsulate state). The main effect of declaring a predicate persistent is that the dynamic changes made to such predicates persist from one execution to the next one. After proposing a syntax for declaring persistent predicates, a simple, file-based implementation of the concept is presented and some examples shown. An additional implementation is presented which stores persistent predicates in an external datábase. The abstraction of the concept of persistence from its implementation allows developing applications which can store their persistent predicates alternatively in files or databases with only a few simple changes to a declaration stating the location and modality used for persistent storage. The paper presents the model, the implementation approach in both the cases of using files and relational databases, a number of optimizations of the process (using information obtained from static global analysis and goal clustering), and performance results from an implementation of these ideas

Application of Definability to Query Answering over Knowledge Bases

Answering object queries (i.e. instance retrieval) is a central task in ontology based data access (OBDA). Performing this task involves reasoning with respect to a knowledge base K (i.e. ontology) over some description logic (DL) dialect L. As the expressive power of L grows, so does the complexity of reasoning with respect to K. Therefore, eliminating the need to reason with respect to a knowledge base K is desirable. In this work, we propose an optimization to improve performance of answering object queries by eliminating the need to reason with respect to the knowledge base and, instead, utilizing cached query results when possible. In particular given a DL dialect L, an object query C over some knowledge base K and a set of cached query results S={S1, ..., Sn} obtained from evaluating past queries, we rewrite C into an equivalent query D, that can be evaluated with respect to an empty knowledge base, using cached query results S' = {Si1, ..., Sim}, where S' is a subset of S. The new query D is an interpolant for the original query C with respect to K and S. To find D, we leverage a tool for enumerating interpolants of a given sentence with respect to some theory. We describe a procedure that maps a knowledge base K, expressed in terms of a description logic dialect of first order logic, and object query C into an equivalent theory and query that are input into the interpolant enumerating tool, and resulting interpolants into an object query D that can be evaluated over an empty knowledge base. We show the efficacy of our approach through experimental evaluation on a Lehigh University Benchmark (LUBM) data set, as well as on a synthetic data set, LUBMMOD, that we created by augmenting an LUBM ontology with additional axioms

Answering Object Queries over Knowledge Bases with Expressive Underlying Description Logics

Many information sources can be viewed as collections of objects and descriptions about objects. The relationship between objects is often characterized by a set of constraints that semantically encode background knowledge of some domain. The most straightforward and fundamental way to access information in these repositories is to search for objects that satisfy certain selection criteria. This work considers a description logics (DL) based representation of such information sources and object queries, which allows for automated reasoning over the constraints accompanying objects. Formally, a knowledge base K=(T, A) captures constraints in the terminology (a TBox) T, and objects with their descriptions in the assertions (an ABox) A, using some DL dialect L. In such a setting, object descriptions are L-concepts and object identifiers correspond to individual names occurring in K. Correspondingly, object queries are the well known problem of instance retrieval in the underlying DL knowledge base K, which returns the identifiers of qualifying objects. This work generalizes instance retrieval over knowledge bases to provide users with answers in which both identifiers and descriptions of qualifying objects are given. The proposed query paradigm, called assertion retrieval, is favoured over instance retrieval since it provides more informative answers to users. A more compelling reason is related to performance: assertion retrieval enables a transfer of basic relational database techniques, such as caching and query rewriting, in the context of an assertion retrieval algebra. The main contributions of this work are two-fold: one concerns optimizing the fundamental reasoning task that underlies assertion retrieval, namely, instance checking, and the other establishes a query compilation framework based on the assertion retrieval algebra. The former is necessary because an assertion retrieval query can entail a large volume of instance checking requests in the form of K|= a:C, where "a" is an individual name and "C" is a L-concept. This work thus proposes a novel absorption technique, ABox absorption, to improve instance checking. ABox absorption handles knowledge bases that have an expressive underlying dialect L, for instance, that requires disjunctive knowledge. It works particularly well when knowledge bases contain a large number of concrete domain concepts for object descriptions. This work further presents a query compilation framework based on the assertion retrieval algebra to make assertion retrieval more practical. In the framework, a suite of rewriting rules is provided to generate a variety of query plans, with a focus on plans that avoid reasoning w.r.t. the background knowledge bases when sufficient cached results of earlier requests exist. ABox absorption and the query compilation framework have been implemented in a prototypical system, dubbed CARE Assertion Retrieval Engine (CARE). CARE also defines a simple yet effective cost model to search for the best plan generated by query rewriting. Empirical studies of CARE have shown that the proposed techniques in this work make assertion retrieval a practical application over a variety of domains

A Framework for Top-K Queries over Weighted RDF Graphs

abstract: The Resource Description Framework (RDF) is a specification that aims to support the conceptual modeling of metadata or information about resources in the form of a directed graph composed of triples of knowledge (facts). RDF also provides mechanisms to encode meta-information (such as source, trust, and certainty) about facts already existing in a knowledge base through a process called reification. In this thesis, an extension to the current RDF specification is proposed in order to enhance RDF triples with an application specific weight (cost). Unlike reification, this extension treats these additional weights as first class knowledge attributes in the RDF model, which can be leveraged by the underlying query engine. Additionally, current RDF query languages, such as SPARQL, have a limited expressive power which limits the capabilities of applications that use them. Plus, even in the presence of language extensions, current RDF stores could not provide methods and tools to process extended queries in an efficient and effective way. To overcome these limitations, a set of novel primitives for the SPARQL language is proposed to express Top-k queries using traditional query patterns as well as novel predicates inspired by those from the XPath language. Plus, an extended query processor engine is developed to support efficient ranked path search, join, and indexing. In addition, several query optimization strategies are proposed, which employ heuristics, advanced indexing tools, and two graph metrics: proximity and sub-result inter-arrival time. These strategies aim to find join orders that reduce the total query execution time while avoiding worst-case pattern combinations. Finally, extensive experimental evaluation shows that using these two metrics in query optimization has a significant impact on the performance and efficiency of Top-k queries. Further experiments also show that proximity and inter-arrival have an even greater, although sometimes undesirable, impact when combined through aggregation functions. Based on these results, a hybrid algorithm is proposed which acknowledges that proximity is more important than inter-arrival time, due to its more complete nature, and performs a fine-grained combination of both metrics by analyzing the differences between their individual scores and performing the aggregation only if these differences are negligible.Dissertation/ThesisM.S. Computer Science 201

Protein Structure Data Management System

With advancement in the development of the new laboratory instruments and experimental techniques, the protein data has an explosive increasing rate. Therefore how to efficiently store, retrieve and modify protein data is becoming a challenging issue that most biological scientists have to face and solve. Traditional data models such as relational database lack of support for complex data types, which is a big issue for protein data application. Hence many scientists switch to the object-oriented databases since object-oriented nature of life science data perfectly matches the architecture of object-oriented databases, but there are still a lot of problems that need to be solved in order to apply OODB methodologies to manage protein data. One major problem is that the general-purpose OODBs do not have any built-in data types for biological research and built-in biological domain-specific functional operations. In this dissertation, we present an application system with built-in data types and built-in biological domain-specific functional operations that extends the Object-Oriented Database (OODB) system by adding domain-specific additional layers Protein-QL, Protein Algebra Architecture and Protein-OODB above OODB to manage protein structure data. This system is composed of three parts: 1) Client API to provide easy usage for different users. 2) Middleware including Protein-QL, Protein Algebra Architecture and Protein-OODB is designed to implement protein domain specific query language and optimize the complex queries, also it capsulates the details of the implementation such that users can easily understand and master Protein-QL. 3) Data Storage is used to store our protein data. This system is for protein domain, but it can be easily extended into other biological domains to build a bio-OODBMS. In this system, protein, primary, secondary, and tertiary structures are defined as internal data types to simplify the queries in Protein-QL such that the domain scientists can easily master the query language and formulate data requests, and EyeDB is used as the underlying OODB to communicate with Protein-OODB. In addition, protein data is usually stored as PDB format and PDB format is old, ambiguous, and inadequate, therefore, PDB data curation will be discussed in detail in the dissertation

The Bag Semantics of Ontology-Based Data Access

Ontology-based data access (OBDA) is a popular approach for integrating and querying multiple data sources by means of a shared ontology. The ontology is linked to the sources using mappings, which assign views over the data to ontology predicates. Motivated by the need for OBDA systems supporting database-style aggregate queries, we propose a bag semantics for OBDA, where duplicate tuples in the views defined by the mappings are retained, as is the case in standard databases. We show that bag semantics makes conjunctive query answering in OBDA coNP-hard in data complexity. To regain tractability, we consider a rather general class of queries and show its rewritability to a generalisation of the relational calculus to bags