12,845 research outputs found
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
Visual exploration and retrieval of XML document collections with the generic system X2
This article reports on the XML retrieval system X2 which has been developed at the University of Munich over the last five years. In a typical session with X2, the user
first browses a structural summary of the XML database in order to select interesting elements and keywords occurring in documents. Using this intermediate result, queries combining structure and textual references are composed semiautomatically.
After query evaluation, the full set of answers is presented in a visual and structured way. X2 largely exploits the structure found in documents, queries and answers to enable new interactive visualization and exploration techniques that support mixed IR and database-oriented querying, thus bridging the gap between these three views on the data to be retrieved. Another salient characteristic of X2 which distinguishes it from other visual query systems for XML is that it supports various degrees of detailedness in the presentation of answers, as well as techniques for dynamically reordering and grouping retrieved elements once the complete answer set has been computed
SWI-Prolog and the Web
Where Prolog is commonly seen as a component in a Web application that is
either embedded or communicates using a proprietary protocol, we propose an
architecture where Prolog communicates to other components in a Web application
using the standard HTTP protocol. By avoiding embedding in external Web servers
development and deployment become much easier. To support this architecture, in
addition to the transfer protocol, we must also support parsing, representing
and generating the key Web document types such as HTML, XML and RDF.
This paper motivates the design decisions in the libraries and extensions to
Prolog for handling Web documents and protocols. The design has been guided by
the requirement to handle large documents efficiently. The described libraries
support a wide range of Web applications ranging from HTML and XML documents to
Semantic Web RDF processing.
To appear in Theory and Practice of Logic Programming (TPLP)Comment: 31 pages, 24 figures and 2 tables. To appear in Theory and Practice
of Logic Programming (TPLP
Tangos: the agile numerical galaxy organization system
We present Tangos, a Python framework and web interface for database-driven
analysis of numerical structure formation simulations. To understand the role
that such a tool can play, consider constructing a history for the absolute
magnitude of each galaxy within a simulation. The magnitudes must first be
calculated for all halos at all timesteps and then linked using a merger tree;
folding the required information into a final analysis can entail significant
effort. Tangos is a generic solution to this information organization problem,
aiming to free users from the details of data management. At the querying
stage, our example of gathering properties over history is reduced to a few
clicks or a simple, single-line Python command. The framework is highly
extensible; in particular, users are expected to define their own properties
which tangos will write into the database. A variety of parallelization options
are available and the raw simulation data can be read using existing libraries
such as pynbody or yt. Finally, tangos-based databases and analysis pipelines
can easily be shared with collaborators or the broader community to ensure
reproducibility. User documentation is provided separately.Comment: Clarified various points and further improved code performance;
accepted for publication in ApJS. Tutorials (including video) at
http://tiny.cc/tango
Security-oriented data grids for microarray expression profiles
Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results
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