Databases and Information Systems Commons^™

Materials Data Science Ontology (Mds-Onto): Unifying Domain Knowledge In Materials And Applied Data Science, Van D. Tran, Jonathan E. Gordon, Alexander Harding Bradley, Balashanmuga Priyan Rajamohan, Quynh D. Tran, Gabriel Ponón, Yinghui Wu, Laura S. Bruckman, Erika I. Barcelos, Roger H. French

Student Scholarship

Ontologies have gained popularity in the scientific community as a means of standardizing concepts and terminology used in metadata across different institutions to facilitate data comprehension, sharing, and reuse. Despite the existence of frameworks and guidelines for building ontologies, the processes and standards used to develop ontologies still differ significantly, particularly in Materials Science. Our goal with the MDS-Onto Framework is to provide a unified and automated system for ontology development in the Materials and Data Sciences. This framework offers recommendations on where to publish ontologies online, how to best integrate them within the semantic web, and which formats to …

An Automated Method To Enrich And Expand Consumer Health Vocabularies Using Glove Word Embeddings, Mohammed Ibrahim

Graduate Theses and Dissertations

Clear language makes communication easier between any two parties. However, a layman may have difficulty communicating with a professional due to not understanding the specialized terms common to the domain. In healthcare, it is rare to find a layman knowledgeable in medical jargon, which can lead to poor understanding of their condition and/or treatment. To bridge this gap, several professional vocabularies and ontologies have been created to map laymen medical terms to professional medical terms and vice versa. Many of the presented vocabularies are built manually or semi-automatically requiring large investments of time and human effort and consequently the slow …

Empathi: An Ontology For Emergency Managing And Planning About Hazard Crisis, Manas Gaur, Kaeedeh Shekarpour, Amelia Gyrard, Amit P. Sheth

Kno.e.sis Publications

In the domain of emergency management during hazard crises, having sufficient situational awareness information is critical. It requires capturing and integrating information from sources such as satellite images, local sensors and social media content generated by local people.
A bold obstacle to capturing, representing and integrating such heterogeneous and diverse information is lack of a proper ontology which properly conceptualizes this domain, aggregates and unifies datasets. Thus, in this paper, we introduce empathi ontology which conceptualizes the core concepts describing the domain of emergency managing and planning of hazard crises.
Although empathi has a coarse-grained view, it considers the necessary …

Semantic Data Storage In Information Systems, Jean Vincent Fonou Dombeu, Raoul Kwuimi

The African Journal of Information Systems

The storage and retrieval of information are important functions of information systems (IS). These IS functions have been realized for decades, due to the maturity of the relational database technology. In recent years, the concept of Semantic Information System (SIS) has emerged as IS in which information is represented with explicit semantic based on its meaning rather than its syntax to enable its automatic and intelligent processing by computers. At present, there is a shortage of discussions on the topic of semantic data storage in IS as compared to the relational database storage counterpart. This study uses a combination of …

Enhancing The Internet Of Things Architecture With Flow Semantics, Allen Ronald Deserranno

USF Tampa Graduate Theses and Dissertations

Internet of Things (‘IoT’) systems are complex, asynchronous solutions often comprised of various software and hardware components developed in isolation of each other. These components function with different degrees of reliability and performance over an inherently unreliable network, the Internet. Many IoT systems are developed within silos that do not provide the ability to communicate or be interoperable with other systems and platforms. Literature exists on how these systems should be designed, how they should interoperate, and how they could be improved, but practice does not always consult literature.

The work brings together a proposed reference architecture for the IoT …

Development And Semantic Exploitation Of A Relational Data Model For Service Delivery In South African Municipalities, Kgotatso Desmond Mogotlane, Jean Vincent Fonou Dombeu

The African Journal of Information Systems

Relational databases (RDB) are the main sources of structured data for government institutions and businesses. Since these databases are dependent on autonomous hardware and software they create problems of data integration and interoperability. Solutions have been proposed to convert RDB into ontology to enable their sharing, reuse and integration on the Semantic Web. However, the proposed methods and techniques remain highly technical and there is lack of research that focuses on the empirical application of these methods and techniques in information systems (IS) domains. This study develops and semantically exploits a relational data model of the South African Municipalities Information …

The Global Rock-Art Database Project Towards Machine Learning: Building A Collaborative Open Source Platform For Heritage Management From Information Structure To Information Visualization Using Australian Heritage Examples, Robert Haubt

Staff Scholarship - Australia & Dubai

This guest talk, presented at Lava Lab at the University of Hawaiʻi, explores the intersection of collaboration, data ontology, and information visualization in advancing machine learning within the Global Rock Art Database project. Drawing on insights from the project’s first four years, the talk emphasizes the critical need for cultural heritage preservation by systematically recording and structuring global rock art data in accessible and sustainable ways. This effort not only supports public education on rock art but also facilitates scholarly research.

Key discussions include advancements in data ontology using the CIDOC Conceptual Reference Model (CIDOC CRM) for semantic data management …

A Scalable Backward Chaining-Based Reasoner For A Semantic Web, Hui Shi, Kurt Maly, Steven Zeil

Computer Science Faculty Publications

In this paper we consider knowledge bases that organize information using ontologies. Specifically, we investigate reasoning over a semantic web where the underlying knowledge base covers linked data about science research that are being harvested from the Web and are supplemented and edited by community members. In the semantic web over which we want to reason, frequent changes occur in the underlying knowledge base, and less frequent changes occur in the underlying ontology or the rule set that governs the reasoning. Interposing a backward chaining reasoner between a knowledge base and a query manager yields an architecture that can support …

Semantic Assistance For Data Utilization And Curation, Brian J. Becker

LSU New Orleans Theses and Dissertations

We propose that most data stores for large organizations are ill-designed for the future, due to limited searchability of the databases. The study of the Semantic Web has been an emerging technology since first proposed by Berners-Lee. New vocabularies have emerged, such as FOAF, Dublin Core, and PROV-O ontologies. These vocabularies, combined, can relate people, places, things, and events. Technologies developed for the Semantic Web, namely the standardized vocabularies for expressing metadata, will make data easier to utilize. We gathered use cases for various data sources, from human resources to big enterprise. Most of our use cases reflect real-world data. …

A Hybrid Approach To Finding Relevant Social Media Content For Complex Domain Specific Information Needs, Delroy H. Cameron, Amit P. Sheth, Nishita Jaykumar, Gaurish Anand, Krishnaprasad Thirunarayan, Gary Alan Smith

Kno.e.sis Publications

While contemporary semantic search systems offer to improve classical keyword-based search, they are not always adequate for complex, domain specific information needs. Some complex search situations require knowledge of both ontological concepts as well as 'intelligible constructs' not typically modeled in ontologies. Intelligible constructs convey essential information, which may be important to the holistic information needs of information seekers. Such constructs may include notions of intensity, frequency, interval, dosage, emotion, sentiment, equivalence, synonymy, negation, parts-of-speech, etc. However, few search systems utilize both structured background knowledge (ontologies) and the aforementioned knowledge for query interpretation in domain specific searches. Instead, there is …

Advancing Data Reuse In Phyloinformatics Using An Ontology-Driven Semantic Web Approach, Maryam Panahiazar, Amit P. Sheth, Ajith Harshana Ranabahu, Rutger Vos, Jim Leebens-Mack

Kno.e.sis Publications

Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web …

Ontology–Based Representation Of Simulation Models, Katarina Grolinger, Miriam A.M. Capretz, José R. Marti, Krishan D. Srivastava

Electrical and Computer Engineering Publications

Ontologies have been used in a variety of domains for multiple purposes such as establishing common terminology, organizing domain knowledge and describing domain in a machine-readable form. Moreover, ontologies are the foundation of the Semantic Web and often semantic integration is achieved using ontology. Even though simulation demonstrates a number of similar characteristics to Semantic Web or semantic integration, including heterogeneity in the simulation domain, representation and semantics, the application of ontology in the simulation domain is still in its infancy. This paper proposes an ontology-based representation of simulation models. The goal of this research is to facilitate comparison among …

Key Ingredients For Your Next Semantics Elevator Talk, Krzysztof Janowicz, Pascal Hitzler

Computer Science and Engineering Faculty Publications

2012 brought a major change to the semantics research community. Discussions on the use and benefits of semantic technologies are shifting away from the why to the how. Surprisingly this more in stakeholder interest is not accompanied by a more detailed understanding of what semantics research is about. Instead of blaming others for their (wrong) expectations, we need to learn how to emphasize the paradigm shift proposed by semantics research while abstracting from technical details and advocate the added value in a way that relates to the immediate needs of individual stakeholders without overselling. This paper highlights some of …

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

Department of Computer Electronics and 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 …

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 …

Biomedical Ontologies For Parasite Research, Vinh Nguyen, Satya S. Sahoo, Priti Parikh, Todd Minning, Brent Weatherly, Flora Logan, Amit P. Sheth, Rick Tarleton

Kno.e.sis Publications

Trypanosoma cruzi is a protozoan parasite that causes Chagas disease or American trypanosomiasis, which is the leading cause of death in Latin America. The primary objective of this study is to create an ontology-driven information infrastructure to support parasite researchers in identifying gene knockout, vaccination, or drug targets for T. cruzi. This involves querying across multiple datasets from diverse sources, such as proteome, pathway, internal lab data, etc. that are often represented in heterogeneous formats. To address this, a multi-ontology parasite knowledge repository (PKR) is being created with an intuitive graphical query interface called Cuebee. The PKR is underpinned by …

Provenance Management In Parasite Research, Vinh Nguyen, Priti Parikh, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

The objective of this research is to create a semantic problem solving environment (PSE) for human parasite Trypanosoma cruzi. As a part of the PSE, we are trying to manage provenance of the experiment data as it is generated. It requires to capture the provenance which is often collected through web forms used by biologists to input the information about experiments they conduct. We have created Parasite Experiment Ontology (PEO) that represents provenance information used in the project. We have modified the back end which processes the data gathered from biologists, generates RDF triples and serializes them into the triple …

Wikipedia2onto: Building Concept Ontology Automatically, Experimenting With Web Image Retrieval, Huan Wang, Xing Jiang, Liang-Tien Chia, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Given its effectiveness to better understand data, ontology has been used in various domains including artificial intelligence, biomedical informatics and library science. What we have tried to promote is the use of ontology to better understand media (in particular, images) on the World Wide Web. This paper describes our preliminary attempt to construct a large-scale multi-modality ontology, called AutoMMOnto, for web image classification. Particularly, to enable the automation of text ontology construction, we take advantage of both structural and content features of Wikipedia and formalize real world objects in terms of concepts and relationships. For visual part, we train classifiers …

An Ontological Representation Of Time Series Observations On The Semantic Sensor Web, Cory Andrew Henson, Holger Neuhaus, Amit P. Sheth, Krishnaprasad Thirunarayan, Rajkumar Buyya

Kno.e.sis Publications

Time series observations are a common method of collecting sensor data. The Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) provides a standard representation for time series observations within the Observations and Measurements language, and therefore is in heavy use on the Sensor Web. By providing a common model, Observations and Measurements (O&M) facilitates syntax-level integration, but lacks the ability to facilitate semantic-level integration. This inability can cause problems with interoperability between disparate sensor networks that may have subtle variations in their sensing methods. An ontological representation of time series observations could provide a more expressive model and resolve problems …

Ontology Enhanced Web Image Retrieval: Aided By Wikipedia And Spreading Activation Theory, Huan Wang, Xing Jiang, Liang-Tien Chia, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Ontology, as an efective approach to bridge the semantic gap in various domains, has attracted a lot of interests from multimedia researchers. Among the numerous possibilities enabled by ontology, we are particularly interested in exploiting ontology for a better understanding of media task (particularly, images) on the World Wide Web. To achieve our goal, two open issues are inevitably involved: 1) How to avoid the tedious manual work for ontology construction? 2) What are the effective inference models when using an ontology? Recent works about ontology learned from Wikipedia has been reported in conferences targeting the areas of knowledge management …

A Framework To Support Spatial, Temporal And Thematic Analytics Over Semantic Web Data, Matthew Perry, Amit P. Sheth

Kno.e.sis Publications

Spatial and temporal data are critical components in many applications. This is especially true in analytical applications ranging from scientific discovery to national security and criminal investigation. The analytical process often requires uncovering and analyzing complex thematic relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful for this purpose. However, these analysis mechanisms are primarily intended for thematic relationships. In this paper, we describe a framework built around the RDF data model for analysis of thematic, spatial and temporal relationships between …

Supporting Complex Thematic, Spatial And Temporal Queries Over Semantic Web Data, Matthew Perry, Amit P. Sheth, Farshad Hakimpour, Prateek Jain

Kno.e.sis Publications

Spatial and temporal data are critical components in many applications. This is especially true in analytical domains such as national security and criminal investigation. Often, the analytical process requires uncovering and analyzing complex thematic relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful for this purpose. However, these analysis mechanisms are primarily intended for thematic relationships. In this paper, we describe a framework built around the RDF metadata model for analysis of thematic, spatial and temporal relationships between named entities. We …

What, Where And When: Supporting Semantic, Spatial And Temporal Queries In A Dbms, Matthew Perry, Amit P. Sheth, Farshad Hakimpour, Prateek Jain

Kno.e.sis Publications

Spatial and temporal data are critical components in many applications. This is especially true in analytical domains such as national security and criminal investigation. The outcome of the analytical process in these applications often hinges on uncovering and analyzing complex relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful in these applications. However, these analysis mechanisms are primarily intended for thematic relationships. We describe a framework built around the RDF metadata model for analysis of thematic, spatial and temporal relationships between …

Active Semantic Electronic Medical Record, Amit P. Sheth, Sangeeta Agrawal, Jonathan Lathem, Nicole Oldham, H. Wingate, K. Gallagher

Kno.e.sis Publications

The healthcare industry is rapidly advancing towards the widespread use of electronic medical records systems to manage the increasingly large amount of patient data and reduce medical errors. In addition to patient data there is a large amount of data describing procedures, treatments, diagnoses, drugs, insurance plans, coverage, formularies and the relationships between these data sets. While practices have benefited from the use of EMRs, infusing these essential programs with rich domain knowledge and rules can greatly enhance their performance and ability to support clinical decisions. Active Semantic Electronic Medical Record (ASEMR) application discussed here uses Semantic Web technologies to …

A Component Based Formal Ontology Model, A Method For Evaluating Such A Model, And The Results Of An Application Of That Method, Charles Tumitsa

Computational Modeling & Simulation Engineering Theses & Dissertations

For systems to truly communicate effectively, more than just data interchange is necessary. The systems must achieve conceptual interoperability, which implies communicating with understanding.

The LCIM (Levels of Conceptual Interoperability Model) describes a number of levels of interoperability, each of which shows systems with an increased amount of conceptual understanding of the other systems they are communicating with. The lowest levels of this model, technical and syntactic interoperability, are achieved (and there are many existing examples) via data exchange in a number of different ways. Research has shown, however, that to attain higher levels of conceptual understanding, that there must …

Predicting Domain Specific Entities With Limited Background Knowledge, Christopher Thomas, Amit P. Sheth

Kno.e.sis Publications

This paper proposes a framework for automatic recognition of domain-specific entities from text, given limited background knowledge, e.g. in form of an ontology. The algorithm exploits several lightweight natural language processing techniques, such as tokenization and stemming, as well as statistical techniques, such as singular value decomposition (SVD) to suggest domain relatedness of unknown entities.

Intelligent Resource Discovery Using Ontology-Based Resource Profiles, J. Steven Hughes, Dan Crichton, Sean Kelly, Chris A. Mattmann, Jerry Crichton, Thuy Tran

Copyright, Fair Use, Scholarly Communication, etc.

Successful resource discovery across heterogeneous repositories is highly dependent on the semantic and syntactic homogeneity of the associated resource descriptions in each repository. Ideally, consistent resource descriptions are easily extracted from each repository, expressed using standard syntactic and semantic structures, and managed and accessed within a distributed, flexible, and scalable software framework. In practice however, seldom do all three of these elements exist. To help address this situation, the Object Oriented Data Technology (OODT) project at the Jet Propulsion Laboratory has developed an extensible, standards-based resource description scheme that provides the necessary description and management facilities for the discovery of …

Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza

Kno.e.sis Publications

As the Semantic Web gains importance for sharing knowledge on the Internet this has lead to the development and publishing of many ontologies in different domains. When trying to reuse existing ontologies into their applications, users are faced with the problem of determining if an ontology is suitable for their needs. In this paper, we introduce OntoQA, an approach that analyzes ontology schemas and their populations (i.e. knowledgebases) and describes them through a well defined set of metrics. These metrics can highlight key characteristics of an ontology schema as well as its population and enable users to make an informed …

Opems: Online Peer-To-Peer Expertise Matching System, Sharifullah Khan, S.M. Nabeel

International Conference on Information and Communication Technologies

Internet is a vital source to disseminate and share information to the masses. This has made information available in abundance on the Web. However, finding relevant information is difficult if not impossible. This difficulty is bilateral between information providers and seekers in terms of information presentation and accessibility respectively. This paper proposed an online Peer-to-Peer Expertise Matching system. The approach provides a highly scalable and self-organizing system and helps individuals in presenting and accessing the information in a consistent format on the Web. This makes the sharing of information among the autonomous organizations successful.

Meteor-S Wsdi: A Scalable P2p Infrastructure Of Registries For Semantic Publication And Discovery Of Web Services, Kunal Verma, Kaarthik Sivashanmugam, Amit P. Sheth, Abhijit Patil, Swapna Oundhakar, John Miller

Kno.e.sis Publications

Web services are the new paradigm for distributed computing. They have much to offer towards interoperability of applications and integration of large scale distributed systems. To make Web services accessible to users, service providers use Web service registries to publish them. Current infrastructure of registries requires replication of all Web service publications in all Universal Business Registries. Large growth in number of Web services as well as the growth in the number of registries would make this replication impractical. In addition, the current Web service discovery mechanism is inefficient, as it does not support discovery based on the capabilities of …