1,922 research outputs found
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
Query processing of geometric objects with free form boundarie sin spatial databases
The increasing demand for the use of database systems as an integrating
factor in CAD/CAM applications has necessitated the development of database
systems with appropriate modelling and retrieval capabilities. One essential
problem is the treatment of geometric data which has led to the development of
spatial databases. Unfortunately, most proposals only deal with simple geometric
objects like multidimensional points and rectangles. On the other hand, there has
been a rapid development in the field of representing geometric objects with free
form curves or surfaces, initiated by engineering applications such as mechanical
engineering, aviation or astronautics. Therefore, we propose a concept for the realization
of spatial retrieval operations on geometric objects with free form
boundaries, such as B-spline or Bezier curves, which can easily be integrated in
a database management system. The key concept is the encapsulation of geometric
operations in a so-called query processor. First, this enables the definition of
an interface allowing the integration into the data model and the definition of the
query language of a database system for complex objects. Second, the approach
allows the use of an arbitrary representation of the geometric objects. After a
short description of the query processor, we propose some representations for free
form objects determined by B-spline or Bezier curves. The goal of efficient query
processing in a database environment is achieved using a combination of decomposition
techniques and spatial access methods. Finally, we present some experimental
results indicating that the performance of decomposition techniques is
clearly superior to traditional query processing strategies for geometric objects
with free form boundaries
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
An electronic healthcare record server implemented in PostgreSQL
This paper describes the implementation of an Electronic Healthcare Record server inside a PostgreSQL relational database without dependency on any further middleware infrastructure. The five-part international standard for communicating healthcare records (ISO EN 13606) is used as the information basis for the design of the server. We describe some of the features that this standard demands that are provided by the server, and other areas where assumptions about the durability of communications or the presence of middleware lead to a poor fit. Finally, we discuss the use of the server in two real-world scenarios including a commercial application
A standards-based ICT framework to enable a service-oriented approach to clinical decision support
This research provides evidence that standards based Clinical Decision Support (CDS)
at the point of care is an essential ingredient of electronic healthcare service delivery. A
Service Oriented Architecture (SOA) based solution is explored, that serves as a task
management system to coordinate complex distributed and disparate IT systems,
processes and resources (human and computer) to provide standards based CDS.
This research offers a solution to the challenges in implementing computerised CDS such
as integration with heterogeneous legacy systems. Reuse of components and services to
reduce costs and save time. The benefits of a sharable CDS service that can be reused by
different healthcare practitioners to provide collaborative patient care is demonstrated.
This solution provides orchestration among different services by extracting data from
sources like patient databases, clinical knowledge bases and evidence-based clinical
guidelines (CGs) in order to facilitate multiple CDS requests coming from different
healthcare settings. This architecture aims to aid users at different levels of Healthcare
Delivery Organizations (HCOs) to maintain a CDS repository, along with monitoring and
managing services, thus enabling transparency.
The research employs the Design Science research methodology (DSRM) combined with
The Open Group Architecture Framework (TOGAF), an open source group initiative for
Enterprise Architecture Framework (EAF). DSRM’s iterative capability addresses the
rapidly evolving nature of workflows in healthcare. This SOA based solution uses
standards-based open source technologies and platforms, the latest healthcare standards
by HL7 and OMG, Decision Support Service (DSS) and Retrieve, Update Locate Service
(RLUS) standard. Combining business process management (BPM) technologies,
business rules with SOA ensures the HCO’s capability to manage its processes. This
architectural solution is evaluated by successfully implementing evidence based CGs at
the point of care in areas such as; a) Diagnostics (Chronic Obstructive Disease), b) Urgent
Referral (Lung Cancer), c) Genome testing and integration with CDS in screening
(Lynch’s syndrome). In addition to medical care, the CDS solution can benefit
organizational processes for collaborative care delivery by connecting patients,
physicians and other associated members. This framework facilitates integration of
different types of CDS ideal for the different healthcare processes, enabling sharable CDS
capabilities within and across organizations
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