A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

06472 Abstracts Collection - XQuery Implementation Paradigms

From 19.11.2006 to 22.11.2006, the Dagstuhl Seminar 06472 ``XQuery Implementation Paradigms'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

AsterixDB: A Scalable, Open Source BDMS

AsterixDB is a new, full-function BDMS (Big Data Management System) with a feature set that distinguishes it from other platforms in today's open source Big Data ecosystem. Its features make it well-suited to applications like web data warehousing, social data storage and analysis, and other use cases related to Big Data. AsterixDB has a flexible NoSQL style data model; a query language that supports a wide range of queries; a scalable runtime; partitioned, LSM-based data storage and indexing (including B+-tree, R-tree, and text indexes); support for external as well as natively stored data; a rich set of built-in types; support for fuzzy, spatial, and temporal types and queries; a built-in notion of data feeds for ingestion of data; and transaction support akin to that of a NoSQL store. Development of AsterixDB began in 2009 and led to a mid-2013 initial open source release. This paper is the first complete description of the resulting open source AsterixDB system. Covered herein are the system's data model, its query language, and its software architecture. Also included are a summary of the current status of the project and a first glimpse into how AsterixDB performs when compared to alternative technologies, including a parallel relational DBMS, a popular NoSQL store, and a popular Hadoop-based SQL data analytics platform, for things that both technologies can do. Also included is a brief description of some initial trials that the system has undergone and the lessons learned (and plans laid) based on those early "customer" engagements

Bridging the Semantic Gap with SQL Query Logs in Natural Language Interfaces to Databases

A critical challenge in constructing a natural language interface to database (NLIDB) is bridging the semantic gap between a natural language query (NLQ) and the underlying data. Two specific ways this challenge exhibits itself is through keyword mapping and join path inference. Keyword mapping is the task of mapping individual keywords in the original NLQ to database elements (such as relations, attributes or values). It is challenging due to the ambiguity in mapping the user's mental model and diction to the schema definition and contents of the underlying database. Join path inference is the process of selecting the relations and join conditions in the FROM clause of the final SQL query, and is difficult because NLIDB users lack the knowledge of the database schema or SQL and therefore cannot explicitly specify the intermediate tables and joins needed to construct a final SQL query. In this paper, we propose leveraging information from the SQL query log of a database to enhance the performance of existing NLIDBs with respect to these challenges. We present a system Templar that can be used to augment existing NLIDBs. Our extensive experimental evaluation demonstrates the effectiveness of our approach, leading up to 138% improvement in top-1 accuracy in existing NLIDBs by leveraging SQL query log information.Comment: Accepted to IEEE International Conference on Data Engineering (ICDE) 201