From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of "pre-canned" queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the formulation of RDF triples-based queries. Both these approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledge-driven one. This provides us with a valuable opportunity to compare and qualitatively evaluate the two approaches. We describe several benefits of the knowledge-driven approach in comparison to the traditional way of accessing data, and highlight a few limitations as well. We believe that our analysis not only explicitly highlights the specific benefits and limitations of semantic Web technologies in our context but also contributes toward effective ways of translating a question in a researcher's mind into precise computational queries with the intent of obtaining effective answers from the data. While researchers often assume the benefits of semantic Web technologies, we explicitly illustrate these in practice

Secure Querying of Recursive XML Views: A Standard XPath-based Technique

Most state-of-the art approaches for securing XML documents allow users to access data only through authorized views defined by annotating an XML grammar (e.g. DTD) with a collection of XPath expressions. To prevent improper disclosure of confidential information, user queries posed on these views need to be rewritten into equivalent queries on the underlying documents. This rewriting enables us to avoid the overhead of view materialization and maintenance. A major concern here is that query rewriting for recursive XML views is still an open problem. To overcome this problem, some works have been proposed to translate XPath queries into non-standard ones, called Regular XPath queries. However, query rewriting under Regular XPath can be of exponential size as it relies on automaton model. Most importantly, Regular XPath remains a theoretical achievement. Indeed, it is not commonly used in practice as translation and evaluation tools are not available. In this paper, we show that query rewriting is always possible for recursive XML views using only the expressive power of the standard XPath. We investigate the extension of the downward class of XPath, composed only by child and descendant axes, with some axes and operators and we propose a general approach to rewrite queries under recursive XML views. Unlike Regular XPath-based works, we provide a rewriting algorithm which processes the query only over the annotated DTD grammar and which can run in linear time in the size of the query. An experimental evaluation demonstrates that our algorithm is efficient and scales well.Comment: (2011

An infrastructure for building semantic web portals

In this paper, we present our KMi semantic web portal infrastructure, which supports two important tasks of semantic web portals, namely metadata extraction and data querying. Central to our infrastructure are three components: i) an automated metadata extraction tool, ASDI, which supports the extraction of high quality metadata from heterogeneous sources, ii) an ontology-driven question answering tool, AquaLog, which makes use of the domain specific ontology and the semantic metadata extracted by ASDI to answers questions in natural language format, and iii) a semantic search engine, which enhances traditional text-based searching by making use of the underlying ontologies and the extracted metadata. A semantic web portal application has been built, which illustrates the usage of this infrastructure

RDF Querying

Reactive Web systems, Web services, and Web-based publish/ subscribe systems communicate events as XML messages, and in many cases require composite event detection: it is not sufficient to react to single event messages, but events have to be considered in relation to other events that are received over time. Emphasizing language design and formal semantics, we describe the rule-based query language XChangeEQ for detecting composite events. XChangeEQ is designed to completely cover and integrate the four complementary querying dimensions: event data, event composition, temporal relationships, and event accumulation. Semantics are provided as model and fixpoint theories; while this is an established approach for rule languages, it has not been applied for event queries before

How Many and What Types of SPARQL Queries can be Answered through Zero-Knowledge Link Traversal?

The current de-facto way to query the Web of Data is through the SPARQL protocol, where a client sends queries to a server through a SPARQL endpoint. Contrary to an HTTP server, providing and maintaining a robust and reliable endpoint requires a significant effort that not all publishers are willing or able to make. An alternative query evaluation method is through link traversal, where a query is answered by dereferencing online web resources (URIs) at real time. While several approaches for such a lookup-based query evaluation method have been proposed, there exists no analysis of the types (patterns) of queries that can be directly answered on the live Web, without accessing local or remote endpoints and without a-priori knowledge of available data sources. In this paper, we first provide a method for checking if a SPARQL query (to be evaluated on a SPARQL endpoint) can be answered through zero-knowledge link traversal (without accessing the endpoint), and analyse a large corpus of real SPARQL query logs for finding the frequency and distribution of answerable and non-answerable query patterns. Subsequently, we provide an algorithm for transforming answerable queries to SPARQL-LD queries that bypass the endpoints. We report experimental results about the efficiency of the transformed queries and discuss the benefits and the limitations of this query evaluation method.Comment: Preprint of paper accepted for publication in the 34th ACM/SIGAPP Symposium On Applied Computing (SAC 2019

Semantic Storage: Overview and Assessment

The Semantic Web has a great deal of momentum behind it. The promise of a ‘better web’, where information is given well defined meaning and computers are better able to work with it has captured the imagination of a significant number of people, particularly in academia. Language standards such as RDF and OWL have appeared with remarkable speed, and development continues apace. To back up this development, there is a requirement for ‘semantic databases’, where this data can be conveniently stored, operated upon, and retrieved. These already exist in the form of triple stores, but do not yet fulfil all the requirements that may be made of them, particularly in the area of performing inference using OWL. This paper analyses the current stores along with forthcoming technology, and finds that it is unlikely that a combination of speed, scalability, and complex inferencing will be practical in the immediate future. It concludes by suggesting alternative development routes