2,504 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
Agents in Bioinformatics
The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions
An extensible web interface for databases and its application to storing biochemical data
This paper presents a generic web-based database interface implemented in
Prolog. We discuss the advantages of the implementation platform and
demonstrate the system's applicability in providing access to integrated
biochemical data. Our system exploits two libraries of SWI-Prolog to create a
schema-transparent interface within a relational setting. As is expected in
declarative programming, the interface was written with minimal programming
effort due to the high level of the language and its suitability to the task.
We highlight two of Prolog's features that are well suited to the task at hand:
term representation of structured documents and relational nature of Prolog
which facilitates transparent integration of relational databases. Although we
developed the system for accessing in-house biochemical and genomic data the
interface is generic and provides a number of extensible features. We describe
some of these features with references to our research databases. Finally we
outline an in-house library that facilitates interaction between Prolog and the
R statistical package. We describe how it has been employed in the present
context to store output from statistical analysis on to the database.Comment: Online proceedings of the Joint Workshop on Implementation of
Constraint Logic Programming Systems and Logic-based Methods in Programming
Environments (CICLOPS-WLPE 2010), Edinburgh, Scotland, U.K., July 15, 201
kLog: A Language for Logical and Relational Learning with Kernels
We introduce kLog, a novel approach to statistical relational learning.
Unlike standard approaches, kLog does not represent a probability distribution
directly. It is rather a language to perform kernel-based learning on
expressive logical and relational representations. kLog allows users to specify
learning problems declaratively. It builds on simple but powerful concepts:
learning from interpretations, entity/relationship data modeling, logic
programming, and deductive databases. Access by the kernel to the rich
representation is mediated by a technique we call graphicalization: the
relational representation is first transformed into a graph --- in particular,
a grounded entity/relationship diagram. Subsequently, a choice of graph kernel
defines the feature space. kLog supports mixed numerical and symbolic data, as
well as background knowledge in the form of Prolog or Datalog programs as in
inductive logic programming systems. The kLog framework can be applied to
tackle the same range of tasks that has made statistical relational learning so
popular, including classification, regression, multitask learning, and
collective classification. We also report about empirical comparisons, showing
that kLog can be either more accurate, or much faster at the same level of
accuracy, than Tilde and Alchemy. kLog is GPLv3 licensed and is available at
http://klog.dinfo.unifi.it along with tutorials
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
A Semantic Framework for Declarative and Procedural Knowledge
In any scientic domain, the full set of data and programs has reached an-ome status, i.e. it has grown massively. The original article on the Semantic Web describes the evolution of a Web of actionable information, i.e.\ud
information derived from data through a semantic theory for interpreting the symbols. In a Semantic Web, methodologies are studied for describing, managing and analyzing both resources (domain knowledge) and applications (operational knowledge) - without any restriction on what and where they\ud
are respectively suitable and available in the Web - as well as for realizing automatic and semantic-driven work\ud
ows of Web applications elaborating Web resources.\ud
This thesis attempts to provide a synthesis among Semantic Web technologies, Ontology Research, Knowledge and Work\ud
ow Management. Such a synthesis is represented by Resourceome, a Web-based framework consisting of two components which strictly interact with each other: an ontology-based and domain-independent knowledge manager system (Resourceome KMS) - relying on a knowledge model where resource and operational knowledge are contextualized in any domain - and a semantic-driven work ow editor, manager and agent-based execution system (Resourceome WMS).\ud
The Resourceome KMS and the Resourceome WMS are exploited in order to realize semantic-driven formulations of work\ud
ows, where activities are semantically linked to any involved resource. In the whole, combining the use of domain ontologies and work ow techniques, Resourceome provides a exible domain and operational knowledge organization, a powerful engine for semantic-driven work\ud
ow composition, and a distributed, automatic and\ud
transparent environment for work ow execution
The Family of MapReduce and Large Scale Data Processing Systems
In the last two decades, the continuous increase of computational power has
produced an overwhelming flow of data which has called for a paradigm shift in
the computing architecture and large scale data processing mechanisms.
MapReduce is a simple and powerful programming model that enables easy
development of scalable parallel applications to process vast amounts of data
on large clusters of commodity machines. It isolates the application from the
details of running a distributed program such as issues on data distribution,
scheduling and fault tolerance. However, the original implementation of the
MapReduce framework had some limitations that have been tackled by many
research efforts in several followup works after its introduction. This article
provides a comprehensive survey for a family of approaches and mechanisms of
large scale data processing mechanisms that have been implemented based on the
original idea of the MapReduce framework and are currently gaining a lot of
momentum in both research and industrial communities. We also cover a set of
introduced systems that have been implemented to provide declarative
programming interfaces on top of the MapReduce framework. In addition, we
review several large scale data processing systems that resemble some of the
ideas of the MapReduce framework for different purposes and application
scenarios. Finally, we discuss some of the future research directions for
implementing the next generation of MapReduce-like solutions.Comment: arXiv admin note: text overlap with arXiv:1105.4252 by other author
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