Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

AKARI-CAS --- Online Service for AKARI All-Sky Catalogues

The AKARI All-Sky Catalogues are an important infrared astronomical database for next-generation astronomy that take over the IRAS catalog. We have developed an online service, AKARI Catalogue Archive Server (AKARI-CAS), for astronomers. The service includes useful and attractive search tools and visual tools. One of the new features of AKARI-CAS is cached SIMBAD/NED entries, which can match AKARI catalogs with other catalogs stored in SIMBAD or NED. To allow advanced queries to the databases, direct input of SQL is also supported. In those queries, fast dynamic cross-identification between registered catalogs is a remarkable feature. In addition, multiwavelength quick-look images are displayed in the visualization tools, which will increase the value of the service. In the construction of our service, we considered a wide variety of astronomers' requirements. As a result of our discussion, we concluded that supporting users' SQL submissions is the best solution for the requirements. Therefore, we implemented an RDBMS layer so that it covered important facilities including the whole processing of tables. We found that PostgreSQL is the best open-source RDBMS products for such purpose, and we wrote codes for both simple and advanced searches into the SQL stored functions. To implement such stored functions for fast radial search and cross-identification with minimum cost, we applied a simple technique that is not based on dividing celestial sphere such as HTM or HEALPix. In contrast, the Web application layer became compact, and was written in simple procedural PHP codes. In total, our system realizes cost-effective maintenance and enhancements.Comment: Yamauchi, C. et al. 2011, PASP..123..852

Italian center for Astronomical Archives publishing solution: modular and distributed

The Italian center for Astronomical Archives tries to provide astronomical data resources as interoperable services based on IVOA standards. Its VO expertise and knowledge comes from active participation within IVOA and VO at European and international level, with a double-fold goal: learn from the collaboration and provide inputs to the community. The first solution to build an easy to configure and maintain resource publisher conformant to VO standards proved to be too optimistic. For this reason it has been necessary to re-think the architecture with a modular system built around the messaging concept, where each modular component speaks to the other interested parties through a system of broker-managed queues. The first implemented protocol, the Simple Cone Search, shows the messaging task architecture connecting the parametric HTTP interface to the database backend access module, the logging module, and allows multiple cone search resources to be managed together through a configuration manager module. Even if relatively young, it already proved the flexibility required by the overall system when the database backend changed from MySQL to PostgreSQL+PgSphere. Another implementation test has been made to leverage task distribution over multiple servers to serve simultaneously: FITS cubes direct linking, cubes cutout and cubes positional merging. Currently the implementation of the SIA-2.0 standard protocol is ongoing while for TAP we will be adapting the TAPlib library. Alongside these tools a first administration tool (TASMAN) has been developed to ease the build up and maintenance of TAP_SCHEMA-ta including also ObsCore maintenance capability. Future work will be devoted at widening the range of VO protocols covered by the set of available modules, improve the configuration management and develop specific purpose modules common to all the service components.Comment: SPIE Astronomical Telescopes + Instrumentation 2018, Software and Cyberinfrastructure for Astronomy V, pre-publishing draft proceeding (reduced abstract

Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

Modeling views in the layered view model for XML using UML

In data engineering, view formalisms are used to provide flexibility to users and user applications by allowing them to extract and elaborate data from the stored data sources. Conversely, since the introduction of Extensible Markup Language (XML), it is fast emerging as the dominant standard for storing, describing, and interchanging data among various web and heterogeneous data sources. In combination with XML Schema, XML provides rich facilities for defining and constraining user-defined data semantics and properties, a feature that is unique to XML. In this context, it is interesting to investigate traditional database features, such as view models and view design techniques for XML. However, traditional view formalisms are strongly coupled to the data language and its syntax, thus it proves to be a difficult task to support views in the case of semi-structured data models. Therefore, in this paper we propose a Layered View Model (LVM) for XML with conceptual and schemata extensions. Here our work is three-fold; first we propose an approach to separate the implementation and conceptual aspects of the views that provides a clear separation of concerns, thus, allowing analysis and design of views to be separated from their implementation. Secondly, we define representations to express and construct these views at the conceptual level. Thirdly, we define a view transformation methodology for XML views in the LVM, which carries out automated transformation to a view schema and a view query expression in an appropriate query language. Also, to validate and apply the LVM concepts, methods and transformations developed, we propose a view-driven application development framework with the flexibility to develop web and database applications for XML, at varying levels of abstraction

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