Analysis of Cancer Omics Data In A Semantic Web Framework

Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancel cell's molecular state and its response to anti-cancer therapy. To study the problem, we have previously focused on data warehousing technologies and statistical data integration. In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology. A key new component presented here is a SPARQL endpoint to our existing data warehouse. This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO). We show how such variegated quantitative and functional data can be integrated and accessed in a universal manner using Semantic Web tools. We also demonstrate how Description Lobic (DL) reasoning can be used to infer previously unstated conclusions from existing knowledge bases. As proof of concept, we illustrate the ability of our setup to answer complex queries on resistance of cancer cells to Decitabine, a demethylating agent

Knowledge and Metadata Integration for Warehousing Complex Data

With the ever-growing availability of so-called complex data, especially on the Web, decision-support systems such as data warehouses must store and process data that are not only numerical or symbolic. Warehousing and analyzing such data requires the joint exploitation of metadata and domain-related knowledge, which must thereby be integrated. In this paper, we survey the types of knowledge and metadata that are needed for managing complex data, discuss the issue of knowledge and metadata integration, and propose a CWM-compliant integration solution that we incorporate into an XML complex data warehousing framework we previously designed.Comment: 6th International Conference on Information Systems Technology and its Applications (ISTA 07), Kharkiv : Ukraine (2007

XML content warehousing: Improving sociological studies of mailing lists and web data

In this paper, we present the guidelines for an XML-based approach for the sociological study of Web data such as the analysis of mailing lists or databases available online. The use of an XML warehouse is a flexible solution for storing and processing this kind of data. We propose an implemented solution and show possible applications with our case study of profiles of experts involved in W3C standard-setting activity. We illustrate the sociological use of semi-structured databases by presenting our XML Schema for mailing-list warehousing. An XML Schema allows many adjunctions or crossings of data sources, without modifying existing data sets, while allowing possible structural evolution. We also show that the existence of hidden data implies increased complexity for traditional SQL users. XML content warehousing allows altogether exhaustive warehousing and recursive queries through contents, with far less dependence on the initial storage. We finally present the possibility of exporting the data stored in the warehouse to commonly-used advanced software devoted to sociological analysis

Pattern tree-based XOLAP rollup operator for XML complex hierarchies

With the rise of XML as a standard for representing business data, XML data warehousing appears as a suitable solution for decision-support applications. In this context, it is necessary to allow OLAP analyses on XML data cubes. Thus, XQuery extensions are needed. To define a formal framework and allow much-needed performance optimizations on analytical queries expressed in XQuery, defining an algebra is desirable. However, XML-OLAP (XOLAP) algebras from the literature still largely rely on the relational model. Hence, we propose in this paper a rollup operator based on a pattern tree in order to handle multidimensional XML data expressed within complex hierarchies