Luzzu - A Framework for Linked Data Quality Assessment

With the increasing adoption and growth of the Linked Open Data cloud [9], with RDFa, Microformats and other ways of embedding data into ordinary Web pages, and with initiatives such as schema.org, the Web is currently being complemented with a Web of Data. Thus, the Web of Data shares many characteristics with the original Web of Documents, which also varies in quality. This heterogeneity makes it challenging to determine the quality of the data published on the Web and to subsequently make this information explicit to data consumers. The main contribution of this article is LUZZU, a quality assessment framework for Linked Open Data. Apart from providing quality metadata and quality problem reports that can be used for data cleaning, LUZZU is extensible: third party metrics can be easily plugged-in the framework. The framework does not rely on SPARQL endpoints, and is thus free of all the problems that come with them, such as query timeouts. Another advantage over SPARQL based qual- ity assessment frameworks is that metrics implemented in LUZZU can have more complex functionality than triple matching. Using the framework, we performed a quality assessment of a number of statistical linked datasets that are available on the LOD cloud. For this evaluation, 25 metrics from ten different dimensions were implemented

Ranking Archived Documents for Structured Queries on Semantic Layers

Archived collections of documents (like newspaper and web archives) serve as important information sources in a variety of disciplines, including Digital Humanities, Historical Science, and Journalism. However, the absence of efficient and meaningful exploration methods still remains a major hurdle in the way of turning them into usable sources of information. A semantic layer is an RDF graph that describes metadata and semantic information about a collection of archived documents, which in turn can be queried through a semantic query language (SPARQL). This allows running advanced queries by combining metadata of the documents (like publication date) and content-based semantic information (like entities mentioned in the documents). However, the results returned by such structured queries can be numerous and moreover they all equally match the query. In this paper, we deal with this problem and formalize the task of "ranking archived documents for structured queries on semantic layers". Then, we propose two ranking models for the problem at hand which jointly consider: i) the relativeness of documents to entities, ii) the timeliness of documents, and iii) the temporal relations among the entities. The experimental results on a new evaluation dataset show the effectiveness of the proposed models and allow us to understand their limitation

Reasoning & Querying – State of the Art

Various query languages for Web and Semantic Web data, both for practical use and as an area of research in the scientific community, have emerged in recent years. At the same time, the broad adoption of the internet where keyword search is used in many applications, e.g. search engines, has familiarized casual users with using keyword queries to retrieve information on the internet. Unlike this easy-to-use querying, traditional query languages require knowledge of the language itself as well as of the data to be queried. Keyword-based query languages for XML and RDF bridge the gap between the two, aiming at enabling simple querying of semi-structured data, which is relevant e.g. in the context of the emerging Semantic Web. This article presents an overview of the field of keyword querying for XML and RDF

Systems approaches to drug repositioning

PhD ThesisDrug discovery has overall become less fruitful and more costly, despite vastly increased biomedical knowledge and evolving approaches to Research and Development (R&D). One complementary approach to drug discovery is that of drug repositioning which focusses on identifying novel uses for existing drugs. By focussing on existing drugs that have already reached the market, drug repositioning has the potential to both reduce the timeframe and cost of getting a disease treatment to those that need it. Many marketed examples of repositioned drugs have been found via serendipitous or rational observations, highlighting the need for more systematic methodologies. Systems approaches have the potential to enable the development of novel methods to understand the action of therapeutic compounds, but require an integrative approach to biological data. Integrated networks can facilitate systems-level analyses by combining multiple sources of evidence to provide a rich description of drugs, their targets and their interactions. Classically, such networks can be mined manually where a skilled person can identify portions of the graph that are indicative of relationships between drugs and highlight possible repositioning opportunities. However, this approach is not scalable. Automated procedures are required to mine integrated networks systematically for these subgraphs and bring them to the attention of the user. The aim of this project was the development of novel computational methods to identify new therapeutic uses for existing drugs (with particular focus on active small molecules) using data integration. A framework for integrating disparate data relevant to drug repositioning, Drug Repositioning Network Integration Framework (DReNInF) was developed as part of this work. This framework includes a high-level ontology, Drug Repositioning Network Integration Ontology (DReNInO), to aid integration and subsequent mining; a suite of parsers; and a generic semantic graph integration platform. This framework enables the production of integrated networks maintaining strict semantics that are important in, but not exclusive to, drug repositioning. The DReNInF is then used to create Drug Repositioning Network Integration (DReNIn), a semantically-rich Resource Description Framework (RDF) dataset. A Web-based front end was developed, which includes a SPARQL Protocol and RDF Query Language (SPARQL) endpoint for querying this dataset. To automate the mining of drug repositioning datasets, a formal framework for the definition of semantic subgraphs was established and a method for Drug Repositioning Semantic Mining (DReSMin) was developed. DReSMin is an algorithm for mining semantically-rich networks for occurrences of a given semantic subgraph. This algorithm allows instances of complex semantic subgraphs that contain data about putative drug repositioning opportunities to be identified in a computationally tractable fashion, scaling close to linearly with network data. The ability of DReSMin to identify novel Drug-Target (D-T) associations was investigated. 9,643,061 putative D-T interactions were identified and ranked, with a strong correlation between highly scored associations and those supported by literature observed. The 20 top ranked associations were analysed in more detail with 14 found to be novel and six found to be supported by the literature. It was also shown that this approach better prioritises known D-T interactions, than other state-of-the-art methodologies. The ability of DReSMin to identify novel Drug-Disease (Dr-D) indications was also investigated. As target-based approaches are utilised heavily in the field of drug discovery, it is necessary to have a systematic method to rank Gene-Disease (G-D) associations. Although methods already exist to collect, integrate and score these associations, these scores are often not a reliable re flection of expert knowledge. Therefore, an integrated data-driven approach to drug repositioning was developed using a Bayesian statistics approach and applied to rank 309,885 G-D associations using existing knowledge. Ranked associations were then integrated with other biological data to produce a semantically-rich drug discovery network. Using this network it was shown that diseases of the central nervous system (CNS) provide an area of interest. The network was then systematically mined for semantic subgraphs that capture novel Dr-D relations. 275,934 Dr-D associations were identified and ranked, with those more likely to be side-effects filtered. Work presented here includes novel tools and algorithms to enable research within the field of drug repositioning. DReNIn, for example, includes data that previous comparable datasets relevant to drug repositioning have neglected, such as clinical trial data and drug indications. Furthermore, the dataset may be easily extended using DReNInF to include future data as and when it becomes available, such as G-D association directionality (i.e. is the mutation a loss-of-function or gain-of-function). Unlike other algorithms and approaches developed for drug repositioning, DReSMin can be used to infer any types of associations captured in the target semantic network. Moreover, the approaches presented here should be more generically applicable to other fields that require algorithms for the integration and mining of semantically rich networks.European and Physical Sciences Research Council (EPSRC) and GS

Exploiting multimedia in creating and analysing multimedia Web archives

The data contained on the web and the social web are inherently multimedia and consist of a mixture of textual, visual and audio modalities. Community memories embodied on the web and social web contain a rich mixture of data from these modalities. In many ways, the web is the greatest resource ever created by human-kind. However, due to the dynamic and distributed nature of the web, its content changes, appears and disappears on a daily basis. Web archiving provides a way of capturing snapshots of (parts of) the web for preservation and future analysis. This paper provides an overview of techniques we have developed within the context of the EU funded ARCOMEM (ARchiving COmmunity MEMories) project to allow multimedia web content to be leveraged during the archival process and for post-archival analysis. Through a set of use cases, we explore several practical applications of multimedia analytics within the realm of web archiving, web archive analysis and multimedia data on the web in general

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

Finding Patterns in a Knowledge Base using Keywords to Compose Table Answers

We aim to provide table answers to keyword queries against knowledge bases. For queries referring to multiple entities, like "Washington cities population" and "Mel Gibson movies", it is better to represent each relevant answer as a table which aggregates a set of entities or entity-joins within the same table scheme or pattern. In this paper, we study how to find highly relevant patterns in a knowledge base for user-given keyword queries to compose table answers. A knowledge base can be modeled as a directed graph called knowledge graph, where nodes represent entities in the knowledge base and edges represent the relationships among them. Each node/edge is labeled with type and text. A pattern is an aggregation of subtrees which contain all keywords in the texts and have the same structure and types on node/edges. We propose efficient algorithms to find patterns that are relevant to the query for a class of scoring functions. We show the hardness of the problem in theory, and propose path-based indexes that are affordable in memory. Two query-processing algorithms are proposed: one is fast in practice for small queries (with small patterns as answers) by utilizing the indexes; and the other one is better in theory, with running time linear in the sizes of indexes and answers, which can handle large queries better. We also conduct extensive experimental study to compare our approaches with a naive adaption of known techniques.Comment: VLDB 201

On construction, performance, and diversification for structured queries on the semantic desktop

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