Physical Sciences and Mathematics Commons^™

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Computer and Electronics Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Using Semantic Templates To Study Vulnerabilities Recorded In Large Software Repositories, Yan Wu

Student Work

Software vulnerabilities allow an attacker to reduce a system's Confidentiality, Availability, and Integrity by exposing information, executing malicious code, and undermine system functionalities that contribute to the overall system purpose and need. With new vulnerabilities discovered everyday in a variety of applications and user environments, a systematic study of their characteristics is a subject of immediate need for the following reasons:

• The high rate in which information about past and new vulnerabilities are accumulated makes it difficult to absorb and comprehend.
• Rather than learning from past mistakes, similar types of vulnerabilities are observed repeatedly.
• As the scale and complexity of …

Extensions Of Snomed Taxonomy Abstraction Networks Supporting Auditing And Complexity Analysis, Duo Wei

Dissertations

The Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT) has been widely used as a standard terminology in various biomedical domains. The enhancement of the quality of SNOMED contributes to the improvement of the medical systems that it supports.

In previous work, the Structural Analysis of Biomedical Ontologies Center (SABOC) team has defined the partial-area taxonomy, a hierarchical abstraction network consisting of units called partial-areas. Each partial-area comprises a set of SNOMED concepts exhibiting a particular relationship structure and being distinguished by a unique root concept. In this dissertation, some extensions and applications of the taxonomy framework are considered. …

Comparison Of Clustered Rdf Data Stores, Venkata Patchigolla

Purdue Polytechnic Masters Theses

Storing data in RDF format helps in simpler data interchange among different researchers compared to present approaches. There has been tremendous increase in the applications that use RDF data. The nature of RDF data is such that it tends to increase explosively. This makes it necessary to consider the time for retrieval and scalability of data while selecting a suitable RDF data store for developing applications. The research concentrates on comparing BigOWLIM. Bigdata, 4store and Virtuoso RDF stores on basis of their scalability and performance of storing and retrieving cancer proteomics and mass spectrometry data using SPARQL queries. In this …

Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge. …

From Glossaries To Ontologies: Disaster Management Domain, Katarina Grolinger, Kevin P. Brown, Miriam A.M. Capretz

Electrical and Computer Engineering Publications

Our society’s reliance on a variety of critical infrastructures (CI) presents significant challenges for disaster preparedness, response and recovery. Experts from different domains including police, paramedics, firefighters and various other CI teams are involved in the fast paced response to a disaster, increasing the risk of miscommunication. To ensure clear communication, as well as to facilitate CI software interoperability, a common disaster ontology is needed. We propose using the knowledge stored in domain glossaries, vocabularies and dictionaries for the creation of a lightweight disaster management domain ontology. Glossaries, vocabularies and dictionaries are semi structured representations of domain knowledge, where significant …

Federated Critical Infrastructure Simulators: Towards Ontologies For Support Of Collaboration, Katarina Grolinger, Miriam Am Capretz, Adam Shypanski, Gagandeep S. Gill

Electrical and Computer Engineering Publications

Our society relies greatly on a variety of critical infrastructures (CI), such as power system networks, water distribution, oil and natural gas systems, telecommunication networks and others. Interdependency between those systems is high and may result in cascading failures spanning different infrastructures. Behavior of each CI can be observed and analyzed through the use of domain simulators, but this does not account for their interdependency. To explore CI interdependencies, domain simulators need to be integrated in a federation where they can collaborate.

This paper explores three different simulators: the EPANET water distribution simulator, the PSCAD power system simulator and the …