GXQuery: Extending XQuery for Querying Graph-structured XML Data

XML data can be naturally modeled as a graph. Existing query languages to XML can only express queries of matching XML document with a tree-structured schema with structural and value constraints without the consideration of graph features. The ability of such query languages cannot satisfy various requirements of querying graph-structured XML data. In this paper, GXQuery is presented as an extension of XQuery, an XML query language recommended byW3C, to express more flexible query on graph-structured XML. GXQuery expressions can match XML documentwith graph-structured schema with not only structural and value constraints, but also topological constraints

An annotation database for multimodal scientific data

Cristina Bogdanschi, Simone Santini, "An annotation database for multimodal scientific data", Proc. SPIE 7255, Multimedia Content Access: Algorithms and Systems III, 72550G (2009). Copyright 2009 Society of Photo‑Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.In many collaborative research environments novel tools and techniques allow researchers to generate data from experiments and observations at a staggering rate. Researchers in these areas are now facing the strong need for querying, sharing and exchanging these data in a uniform and transparent fashion. However, due to the nature of the various types of heterogeneous data and lack of local and global database structures, standard data integration approaches fail or are not applicable. A viable solution to this problem is the extensive use of metadata. In this paper we present the model of an annotation management system suitable for such research environments, and discuss some aspects of its implementation. Annotations provide rich linkage structure between data and between themselves that translates in a complex graph structure of which annotations and data are the nodes. We show how annotations are managed and used for data retrieval and outline some of the query techniques used in the system

Network Analytics ER Model - Towards a Conceptual View of Network Analytics

This paper proposes a conceptual modelling paradigm for network analysis applications, called the Network Analytics ER model (NAER). Not only data requirements but also query requirements are captured by the conceptual description of network analysis applications. This unified analytical framework allows us to flexibly build a number of topology schemas on the basis of the underlying core schema, together with a collection of query topics that describe topological results of interest. In doing so, we can alleviate many issues in network analysis, such as performance, semantic integrity and dynamics of analysis

STRG-QL: Spatio-Temporal Region Graph Query Language for Video Databases

Copyright 2008 Society of Photo-Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.In this paper, we present a new graph-based query language and its query processing for a Graph-based Video Database Management System (GVDBMS). Although extensive researches have proposed various query languages for video databases, most of them have the limitation in handling general-purpose video queries. Each method can handle specific data model, query type or application. In order to develop a general-purpose video query language, we first produce Spatio-Temporal Region Graph (STRG) for each video, which represents spatial and temporal information of video objects. An STRG data model is generated from the STRG by exploiting object-oriented model. Based on the STRG data model, we propose a new graph-based query language named STRG-QL, which supports various types of video query. To process the proposed STRG-QL, we introduce a rule-based query optimization that considers the characteristics of video data, i.e., the hierarchical correlations among video segments. The results of our extensive experimental study show that the proposed STRG-QL is promising in terms of accuracy and cost.http://dx.doi.org/10.1117/12.76553

PathCase-SB architecture and database design

<p>Abstract</p> <p>Background</p> <p>Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.</p> <p>Description</p> <p>PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.</p> <p>Conclusions</p> <p>PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.</p

Temporal Representation in Semantic Graphs

A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs

Context-Sensitive Control Flow Graph

Control Flow Graph (CFG) is known to be essential in compiler optimizations and quite useful in program comprehension. But visualizing and understanding CFG is hard because the CFG is often too large. The problem becomes harder if one were to understand inter-procedural CFG. Often the user wants to understand specific aspects of the CFG; hence, omitting parts of CFG irrelevant to the user\u27s current interest becomes a desirable approach in working with CFG. We formalize an approach of constructing and visualizing CFG that takes users\u27 interests into account. Users have to specify the program artifacts that are of interest to them, then we define the Context-Sensitive CFG that is relevant to the artifacts. The Context-Sensitive CFG is much smaller in size. The actual compression depends on the context and its spread in the given code. We show some results using the XINU operating system code as the test case. While the Context-Sensitive CFG captures only the relevant details, it could still be of substantial size and complexity. We propose query capability as a next step to help the user by extracting details related to a specific question. For example, the user can apply a query to check if there is an execution path in the CFG along which there is a missing memory deallocation and thus a possible memory leak. This thesis only implements queries that operate solely within the scope of a method (intra-procedural). We have built a proof-of-concept tool that allows the user to visualize Context-Sensitive CFG and make queries