Bobby McKnight - Research

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Research Interests

My primary research interest is the semantic web. I am concerned mainly with the query aspect of large-scale information systems, usually in the domain of life sciences. This includes using semantics as a method to build intuitive query systems that allow users to query advanced relationships without schema and formal query language knowledge, using ontologies as an umbrella for integration of heterogeneous data, and novel results visualization methods.

Graduate Dissertation

From a Genome Database to a Semantic Knowledge Base

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Referred Conference Publications

Bobby McKnight and I. Budak Arpinar. Linking and Querying Genomic Datasets Using Natural Language. The IEEE International Conference on Bioinformatics and Biomedicine 2012. Philadelphia, USA. October 2012

Samir Tartir, Bobby McKnight, and I. Budak Arpinar. SemanticQA: Exploiting Semantic Associations for Cross-Document Question Answering. Fourth International Symposium on Innovation in Information & Communication Technology, Aman, Jordan, November 2011.

Samir Tartir, Bobby McKnight, and I. Budak Arpinar. SemanticQA: Web-Based Ontology-Driven Question Answering. In the 24th Annual ACM Symposium on Applied Computing, Waikiki Beach, Honolulu, Hawaii, USA, March 2009.

Pablo N. Mendes, Bobby McKnight, Amit P. Sheth, Jessica C. Kissinger. Enabling Complex Queries for Genome Data Exploration. IEEE Second International Conference on Semantic Computing. Santa Clara, California. August 2008.

Current Research Projects


Knoesis Lab at Wright State University, LSDIS Lab at the University of Georgia, and The Jessica Kissinger Lab at the University of Georgia

The association of experimental data with domain knowledge expressed in ontologies facilitates information aggregation, meaningful querying and knowledge discovery to aid in the process of analyzing the extensive amount of interconnected data available for genome projects. TcruziKB is an ontology-based system to describe and provide access to the data available for the project TcruziDB, a genome database for the parasitic agent Trypanosoma cruzi. TcruziKB uses Cuebee as its query interface and D2R Server as the relational-to-RDF mapper.

Semantically Enhanced Quesiton Answering

Using ontologies and natural language parsing to assist in finding answers in the World Wide Web. Transforming natural English queries into formal SPARQL queries using unrestricted English parsing for querying semantic knowlegebases. Hybrid methods fusing IR and the web with structued data queries are also being explored as a part of this work.

Previous Projects

Relaxing MD5 for Mission Critical Systems

Bobby McKnight, Kang Li

Bloom Filter with Cross Referencing

A comparison of Bloom Filter variants in terms of spacial requirements and false positives. Research conducted under the direction of Professor Kang Li.

Geo Temporal Semantics for Integrated Geographical Information Systems

In association with Oakridge Labs, Wright State University, and the University of Georgia

Presentations Given

Towards a Semantic Google

Computer Science Department, UGA. October 12th, 2007.


With the current World Wide Web a search engine may never really give you the results you are looking for. This is due to the fact that documents on the web are made for humans to view and are just a jumble of meaningless characters to a computer. To further complicate the problem, the data on the web is inherently ambiguous because, again, it is human language. Search engines rely largely on basic keyword matching of these strings with no sense of their meaning or their relationship to other terms in the document will often return undesired results. The Semantic Web attempts to change these limitations by making the documents on the web computer understandable. The realization of the Semantic Web could revolutionize search engines, improve data mining, and greatly enhance automation of web based transactions by allowing computers to do processing on the data that would be impossible with the current web. In this seminar I will cover the basics of the Semantic Web, showing that is more than a buzzword. I will also give a vision of a fully realized Semantic Web, describing how the Google of tomorrow will operate as well as the challenges and open problems that are to be faced. Finally, I will conclude with my research in the area: applying Semantic Web techniques on domain specific applications to enhance the query process.

Harnessing Semantics for Bioinformatics

Computer Science Department/Institute for Bioinformatics, UGA. March 19th, 2007.


With the recent explosion in the amount of biological data available the need for systems that can organize, integrate, and analyze the data becomes more important than ever. It is in these areas that bioinformaticians can look toward the advances in the Semantic Web for a solution. The semantic web offers methods for integrating heterogeneous data via federated database and web services, the elimination of redundant data via ambiguity resolution, and advanced analysis tools via inference models and formal query languages. In this talk I will explore current tools available to biologist to bring the power of the semantic web to their research as well as what the future holds in the area.

Other Publications

Plantation Management Research Cooperative Database

PMRC Online 

Integrated forestry measurements from over 20 years available as a public access database that can be mined or referenced for advancement of forest research.

Faculty Activity Reporting


A novel and user friendly approach for generating faculty reports. Features include automatic parsing of CV and resumes, intuitive data editing and management, and easily printable hard copies. Currently in use in the Warnell School of Forest Resources at the University of Georgia.