8,596 research outputs found
bdbms -- A Database Management System for Biological Data
Biologists are increasingly using databases for storing and managing their
data. Biological databases typically consist of a mixture of raw data,
metadata, sequences, annotations, and related data obtained from various
sources. Current database technology lacks several functionalities that are
needed by biological databases. In this paper, we introduce bdbms, an
extensible prototype database management system for supporting biological data.
bdbms extends the functionalities of current DBMSs to include: (1) Annotation
and provenance management including storage, indexing, manipulation, and
querying of annotation and provenance as first class objects in bdbms, (2)
Local dependency tracking to track the dependencies and derivations among data
items, (3) Update authorization to support data curation via content-based
authorization, in contrast to identity-based authorization, and (4) New access
methods and their supporting operators that support pattern matching on various
types of compressed biological data types. This paper presents the design of
bdbms along with the techniques proposed to support these functionalities
including an extension to SQL. We also outline some open issues in building
bdbms.Comment: This article is published under a Creative Commons License Agreement
(http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute,
display, and perform the work, make derivative works and make commercial use
of the work, but, you must attribute the work to the author and CIDR 2007.
3rd Biennial Conference on Innovative Data Systems Research (CIDR) January
710, 2007, Asilomar, California, US
Using Ontologies for the Design of Data Warehouses
Obtaining an implementation of a data warehouse is a complex task that forces
designers to acquire wide knowledge of the domain, thus requiring a high level
of expertise and becoming it a prone-to-fail task. Based on our experience, we
have detected a set of situations we have faced up with in real-world projects
in which we believe that the use of ontologies will improve several aspects of
the design of data warehouses. The aim of this article is to describe several
shortcomings of current data warehouse design approaches and discuss the
benefit of using ontologies to overcome them. This work is a starting point for
discussing the convenience of using ontologies in data warehouse design.Comment: 15 pages, 2 figure
Digital Image Access & Retrieval
The 33th Annual Clinic on Library Applications of Data Processing, held at the University of Illinois at Urbana-Champaign in March of 1996, addressed the theme of "Digital Image Access & Retrieval." The papers from this conference cover a wide range of topics concerning digital imaging technology for visual resource collections. Papers covered three general areas: (1) systems, planning, and implementation; (2) automatic and semi-automatic indexing; and (3) preservation with the bulk of the conference focusing on indexing and retrieval.published or submitted for publicatio
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights
With an unprecedented growth in the biomedical literature, keeping up to date with
the new developments presents an immense challenge. Publications are often studied
in isolation of the established literature, with interpretation being subjective and
often introducing human bias. With ontology-driven annotation of biomedical data
gaining popularity in recent years and online databases offering metatags with rich
textual information, it is now possible to automatically text-mine ontological terms
and complement the laborious task of manual management, interpretation, and
analysis of the accumulated literature with downstream statistical analysis. In this
paper, we have formulated an automated workflow through which we have identified
ontological information, including nutrition-related terms in PubMed abstracts
(from 1991 to 2016) for two main types of Inflammatory Bowel Diseases: Crohn’s
Disease and Ulcerative Colitis; and two other gastrointestinal (GI) diseases, namely,
Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering
patterns as well as spatial and temporal trends inherent to the considered GI diseases
in terms of literature that has been accumulated so far. Although automated
interpretation cannot replace human judgement, the developed workflow shows
promising results and can be a useful tool in systematic literature reviews. The
workflow is available at https://github.com/KociOrges/pytag
Towards a query language for annotation graphs
The multidimensional, heterogeneous, and temporal nature of speech databases
raises interesting challenges for representation and query. Recently,
annotation graphs have been proposed as a general-purpose representational
framework for speech databases. Typical queries on annotation graphs require
path expressions similar to those used in semistructured query languages.
However, the underlying model is rather different from the customary graph
models for semistructured data: the graph is acyclic and unrooted, and both
temporal and inclusion relationships are important. We develop a query language
and describe optimization techniques for an underlying relational
representation.Comment: 8 pages, 10 figure
Mining Event Logs to Support Workflow Resource Allocation
Workflow technology is widely used to facilitate the business process in
enterprise information systems (EIS), and it has the potential to reduce design
time, enhance product quality and decrease product cost. However, significant
limitations still exist: as an important task in the context of workflow, many
present resource allocation operations are still performed manually, which are
time-consuming. This paper presents a data mining approach to address the
resource allocation problem (RAP) and improve the productivity of workflow
resource management. Specifically, an Apriori-like algorithm is used to find
the frequent patterns from the event log, and association rules are generated
according to predefined resource allocation constraints. Subsequently, a
correlation measure named lift is utilized to annotate the negatively
correlated resource allocation rules for resource reservation. Finally, the
rules are ranked using the confidence measures as resource allocation rules.
Comparative experiments are performed using C4.5, SVM, ID3, Na\"ive Bayes and
the presented approach, and the results show that the presented approach is
effective in both accuracy and candidate resource recommendations.Comment: T. Liu et al., Mining event logs to support workflow resource
allocation, Knowl. Based Syst. (2012), http://dx.doi.org/
10.1016/j.knosys.2012.05.01
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