Open Access. Powered by Scholars. Published by Universities.®

Computer Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Computer Science Faculty Research & Creative Works

Discipline
Keyword
Publication Year

Articles 691 - 720 of 919

Full-Text Articles in Computer Sciences

Analysis Of Privacy And Security Policies, Elisa Bertino, Carolyn Brodie, Seraphin Calo, Lorrie Faith Cranor, Clare Marie Karat, John Karat, Ninghui Li, Dan Lin, Jorge Lobo, Qun Ni, Prathima Rao, Xiping Wang Jan 2009

Analysis Of Privacy And Security Policies, Elisa Bertino, Carolyn Brodie, Seraphin Calo, Lorrie Faith Cranor, Clare Marie Karat, John Karat, Ninghui Li, Dan Lin, Jorge Lobo, Qun Ni, Prathima Rao, Xiping Wang

Computer Science Faculty Research & Creative Works

The distributed nature of the environment in which privacy and security policies operate requires tools that help enforce consistency of policy rules across different domains. Furthermore, because changes to policy rules are required as policies evolve over time, such tools can be used by policy administrators to ensure the consistency of policy changes. in this paper, we describe a number of different policy analysis tools and techniques that we have developed over the years and present them in a unified framework in which both privacy and security policies are discussed. We cover dominance analyses of general policies, conflicts among authorizations …


Expressiveness And Effectiveness Of Program Comprehension: Thoughts On Future Research Directions, Jonathan I. Maletic, Huzefa Kagdi Dec 2008

Expressiveness And Effectiveness Of Program Comprehension: Thoughts On Future Research Directions, Jonathan I. Maletic, Huzefa Kagdi

Computer Science Faculty Research & Creative Works

A number of research challenges in the area of program comprehension are presented. the expressiveness and effectiveness of program comprehension are discussed, and research directions are organized along these two axes. Both fundament research issues are raised along with new applications for program comprehension methods. the work advocates the investigation of better measures, further empirical studies, and controlled experiments to assess the effectiveness of program comprehension techniques © 2008 IEEE.


Ttl Based Packet Marking For Ip Traceback, Vamsi Paruchuri, Arjan Durresi, Sriram Chellappan Dec 2008

Ttl Based Packet Marking For Ip Traceback, Vamsi Paruchuri, Arjan Durresi, Sriram Chellappan

Computer Science Faculty Research & Creative Works

Distributed Denial of Service Attacks continue to pose major threats to the Internet. in order to traceback attack sources (i.e., IP addresses), a well-studied approach is Probabilistic Packet Marking (PPM), where each intermediate router of a packet marks it with a certain probability, enabling a victim host to traceback the attack source. in a recent study, we showed how attackers can take advantage of probabilistic nature of packet markings in existing PPM schemes to create spoofed marks, hence compromising traceback. in this paper, we propose a new PPM scheme called TTL-Based PPM (TPM) scheme, where each packet is marked with …


Pas: Predicate-Based Authentication Services Against Powerful Passive Adversaries, Sriram Chellappan, Xiaole Bai, Wenjun Gu, Xun Wang, Dong Xuan, Bin Ma Dec 2008

Pas: Predicate-Based Authentication Services Against Powerful Passive Adversaries, Sriram Chellappan, Xiaole Bai, Wenjun Gu, Xun Wang, Dong Xuan, Bin Ma

Computer Science Faculty Research & Creative Works

Securely authenticating a human user without assistance from any auxiliary device in the presence of powerful passive adversaries is an important and challenging problem. Passive adversaries are those that can passively monitor, intercept, and analyze every part of the authentication procedure, except for an initial secret shared between the user and the server. In this paper, we propose a new secure authentication scheme called predicate-based authentication service (PAS). In this scheme, for the first time, the concept of a predicate is introduced for authentication. We conduct analysis on the proposed scheme and implement its prototype system. Our analytical data and …


Link Rate Allocation Under Bandwidth And Energy Constraints In Sensor Networks, Maggie Cheng, Xuan Gong, Lin Cai Dec 2008

Link Rate Allocation Under Bandwidth And Energy Constraints In Sensor Networks, Maggie Cheng, Xuan Gong, Lin Cai

Computer Science Faculty Research & Creative Works

In sensor networks, both energy and band width are scarce resources. in the past, the energy efficient routing problem has been vastly studied in order to maximize network lifetime, but link bandwidth has been optimistically assumed to be abundant. as energy con straint affects how data should be routed, link bandwidth also affects not just the routing topology but also the allowed data rate on each link, which in turn affects lifetime. Previous works that focus on energy efficient operations in sensor networks with the sole objective of maximizing network lifetime only consider the energy constraint and ignore the bandwidth …


Position Transformation: A Location Privacy Protection Method For Moving Objects, Dan Lin, Elisa Bertino, Reynold Cheng, Sunil Prabhakar Dec 2008

Position Transformation: A Location Privacy Protection Method For Moving Objects, Dan Lin, Elisa Bertino, Reynold Cheng, Sunil Prabhakar

Computer Science Faculty Research & Creative Works

The expanding use of location-Based services has profound implications on the privacy of personal information. in this paper, we propose a framework for preserving location privacy based on the idea of sending to the service provider suitably modified location information. Agents execute data transformation, and the service provider directly processes the transformed dataset. Our technique not only prevents the service provider from knowing the exact locations of users, but also protects information about user movements and locations from being disclosed to other users who are not authorized to access this information. We also define a privacy model to analyze our …


A Systematic Framework For Structured Object-Oriented Security Requirements Analysis In Embedded Systems, Sojan Markose, Xiaoqing Frank Liu, Bruce M. Mcmillin Dec 2008

A Systematic Framework For Structured Object-Oriented Security Requirements Analysis In Embedded Systems, Sojan Markose, Xiaoqing Frank Liu, Bruce M. Mcmillin

Computer Science Faculty Research & Creative Works

The primary goal of this paper is to develop a structured objectoriented security requirements analysis methodology for the elicitation and analysis of security requirements in embedded systems. There are several approaches to elicit, analyze and specify security requirements in embedded systems ranging from formal mathematical models for proof of certain security properties to informal methods that are easily understood. Applicability of formal security models is limited because they are complex and it is time consuming to develop. On the other hand, informal security requirements analysis methods are not integrated with conceptual models in requirements analysis, and although both external and …


Implementation And Analysis Of Practical Algorithm For Data Security, Willi Ballenthin, F. Kacani, Julia Albath, Sanjay Kumar Madria Dec 2008

Implementation And Analysis Of Practical Algorithm For Data Security, Willi Ballenthin, F. Kacani, Julia Albath, Sanjay Kumar Madria

Computer Science Faculty Research & Creative Works

In this paper, we present a complete implementation of the Practical Algorithm for Data Security (PADS) proposed by Albath et al., an end-to-end security scheme employing symmetric key encryption. The implementation takes full advantage of the modular design of the TinyOS environment. The simplicity of the algorithm allows for efficient implementation in hardware, a requirement for resource constrained devices. The protocol adds only four bytes of data per packet, on par with industry standards. Simulation and empirical results of the scheme are also provided. The analysis shows that the Practical Algorithm for Data Security is superior to standard security schemes.


Localizing Sensor Networks In Un-Friendly Environments, Sriram Chellappan, Vamsi Paruchuri, Dylan Mcdonald, Arjan Durresi Nov 2008

Localizing Sensor Networks In Un-Friendly Environments, Sriram Chellappan, Vamsi Paruchuri, Dylan Mcdonald, Arjan Durresi

Computer Science Faculty Research & Creative Works

In this paper, we study the issue of defending against a wireless sensor network (WSN) that has been deployed by a malicious enemy agent in an area of interest to us. While there can be many approaches to defend against maliciously deployed WSNs, we propose the design of a localization centric approach. Specifically, the problem we address is: given an enemy deployed WSN in an area of interest to us, how can we determine locations of the sensors without co-operating with the sensors themselves during localization. In our approach, we employ a physically mobile agent called the localizer (e.g., a …


Secure Communications Over Hybrid Military Networks, Vamsi Paruchuri, Arjan Durresi, Sriram Chellappan Nov 2008

Secure Communications Over Hybrid Military Networks, Vamsi Paruchuri, Arjan Durresi, Sriram Chellappan

Computer Science Faculty Research & Creative Works

Stealthiness can be described as a disposition to be sly and to do things surreptitiously. This paper presents a new architecture for flexible and secure networking in battlefields that enables stealthy and covert communication in the presence of node mobility. Our architecture is based on the combination of optical (fiber) and wireless links. Our objective is to be able to carry on undeterred communication without the attack/eavesdropping nodes being able to detect the presence of any communication. This objective is not only crucial for successful completion of the operation, but also for the safety of our mobile nodes, by not …


Who Can Help Me With This Source Code Change, Huzefa Kagdi, Maen Hammad, Jonathan I. Maletic Oct 2008

Who Can Help Me With This Source Code Change, Huzefa Kagdi, Maen Hammad, Jonathan I. Maletic

Computer Science Faculty Research & Creative Works

An approach to recommend a ranked list of developers to assist in performing software changes to a particular file is presented. The ranking is based on change expertise, experience, and contributions of developers, as derived from the analysis of the previous commits involving the specific file in question. The commits are obtained from a software system's version control repositories (e.g., Subversion). The basic premise is that a developer who has substantially contributed changes to specific files in the past is likely to best assist for their current or future change. Evaluation of the approach on a number of open source …


Automated Code Generation For Industrial-Strength Systems, Thomas Weigert, Frank Weil, Aswin Van Den Berg, Paul Dietz, Kevin Marth Aug 2008

Automated Code Generation For Industrial-Strength Systems, Thomas Weigert, Frank Weil, Aswin Van Den Berg, Paul Dietz, Kevin Marth

Computer Science Faculty Research & Creative Works

Model-driven engineering proposes to develop software systems by first creating an executable model of the system design and then transforming this model into an implementation. This paper discusses the design of an automatic code generation system that transforms such models into product implementations for highly reliable, industrial-strength systems. It provides insights, practical considerations, and lessons learned when developing code generators for applications that must conform to the constraints imposed by real-world, high-performance systems. Automatic code generation has played a large part in dramatically increasing both the quality and the reliability of software for these systems.


An Open Framework For Highly Concurrent Real-Time Hardware-In-The-Loop Simulation, Ryan C. Underwood, Bruce M. Mcmillin, Mariesa Crow Aug 2008

An Open Framework For Highly Concurrent Real-Time Hardware-In-The-Loop Simulation, Ryan C. Underwood, Bruce M. Mcmillin, Mariesa Crow

Computer Science Faculty Research & Creative Works

Hardware-in-the-loop (HIL) real-time simulation is becoming a significant tool in prototyping complex, highly available systems. The HIL approach permits testing of hardware prototypes of components that would be extremely costly or difficult to test in the deployed environment. In power system simulation, key issues are the ability to wrap the systems of equations (such as Partial Differential Equations) describing the deployed environment into real-time software models, provide low synchronization overhead between the hardware and software, and reduce reliance on proprietary platforms. This paper introduces an open source HIL simulation framework that can be ported to any standard Unix-like system on …


Security Property Violation In Cps Through Timing, Han Tang, Bruce M. Mcmillin Jul 2008

Security Property Violation In Cps Through Timing, Han Tang, Bruce M. Mcmillin

Computer Science Faculty Research & Creative Works

Security in a cyber-physical system (CPS) is not well understood. Interactions between components in the cyber and physical domains lead to unintended information flow. This paper makes use of formal information flow models to describe leakage in a model CPS, the Cooperating FACTS Power System. Results show that while a casual observer cannot ascertain confidential internal information, when application semantics, including timing, are considered, this confidentiality is lost. Model checking is used to verify the result. The significance of the paper is in showing an example of the complex interactions that occur between the Cyber and Physical domains and their …


Transactional Agents For Pervasive Computing, Machigar Ongtang, A. R. Hurson, Yu Jiao Jul 2008

Transactional Agents For Pervasive Computing, Machigar Ongtang, A. R. Hurson, Yu Jiao

Computer Science Faculty Research & Creative Works

Pervasive computing enables seamless integration of computing technology into everyday life to make upto- date information and services proactively available to the users based on their needs and behaviors. We aim to develop a transaction management scheme as a pertinent component for such environment supported by either structured or ad hoc networks. We propose Transactional Agents for Pervasive COmputing (TAPCO), which utilizes a dynamic hierarchical meta data structure that captures the semantic contents of the underlying heterogeneous data sources. Mobile agents process the transactions collaboratively, to preserve ACID properties without violating local autonomy of the data sources. TAPCO is simulated …


Incorporation Of Evidences Into An Intelligent Computational Argumentation Network For A Web-Based Collaborative Engineering Design System, Xiaoqing Frank Liu, Ekta Khudkhudia, Ming-Chuan Leu May 2008

Incorporation Of Evidences Into An Intelligent Computational Argumentation Network For A Web-Based Collaborative Engineering Design System, Xiaoqing Frank Liu, Ekta Khudkhudia, Ming-Chuan Leu

Computer Science Faculty Research & Creative Works

Conflicts among the stakeholders are unavoidable in the process of collaborative engineering design. Resolution of these conflicts is a challenging task. In our previous research, a web based intelligent collaborative system was developed which provides decision-making support, using computational argumentation techniques. Enhancements were done to this system to incorporate the priorities of the stakeholders and to detect arguments that self conflict. As an effort to make this system more effective and more objective in the process of decision making, we develop a method to assess the effect of evidences in the argumentation network, using Dempster-Shafer theory of evidence and fuzzy …


Updated Data Dissemination For Applications With Time Constraints In Mobile Ad Hoc Networks, Takahiro Hara, Sanjay Kumar Madria Apr 2008

Updated Data Dissemination For Applications With Time Constraints In Mobile Ad Hoc Networks, Takahiro Hara, Sanjay Kumar Madria

Computer Science Faculty Research & Creative Works

In our previous work, we proposed few updated data dissemination methods to refresh old replicas efficiently in mobile ad hoc networks. These methods disseminate updated data items every time when owners of original data items update the items or every time two mobile hosts are newly connected with each other and this causes heavy traffic in the entire network. In this paper, we assume applications that periodically execute read operations with strict deadlines to data items and propose few alternative updated data dissemination methods. These methods reduces the traffic for data dissemination while keeping a high success ratio for read …


Economic-Based Incentive Schemes For Dynamic Data Management In Mobile P2p Computing, Sanjay Kumar Madria, Anirban Mondal Apr 2008

Economic-Based Incentive Schemes For Dynamic Data Management In Mobile P2p Computing, Sanjay Kumar Madria, Anirban Mondal

Computer Science Faculty Research & Creative Works

Data management in mobile peer to peer (M-P2P) systems needs dynamic data management due to mobility and fragile wireless connection connecting resource constraint devices. Traditional methods of data management and services in mobile P2P environment generally assume all peers to cooperate. Since peer activities in M-P2P are not generally monitored, users assume that they are free to use the resources anyway they like. Under this feeling of freedom, a subset of users (free riders) begins to consume much more resources available on M-P2P than they wish to contribute. In addition, due to the dynamic nature of moving hosts, topology changes …


Garuda: Achieving Effective Reliability For Downstream Communication In Wireless Sensor Networks, Seung Jong Park, Ramanuja Vedantham, Raghupathy Sivakumar, Ian F. Akyildiz Feb 2008

Garuda: Achieving Effective Reliability For Downstream Communication In Wireless Sensor Networks, Seung Jong Park, Ramanuja Vedantham, Raghupathy Sivakumar, Ian F. Akyildiz

Computer Science Faculty Research & Creative Works

There exist several applications of sensor networks where the reliability of data delivery can be critical. Although the redundancy inherent in a sensor network might increase the degree of reliability, it by no means can provide any guaranteed reliability semantics. In this paper, we consider the problem of reliable sink-to-sensors data delivery. We first identify several fundamental challenges that need to be addressed and are unique to the environment of wireless sensor networks. We then propose a scalable framework for reliable downstream data delivery that is specifically designed to both address and leverage the characteristics of the wireless sensor networks …


Web-Based Service Exchange System For Agents And Humans Alike, Evens Jean, Machigar Ongtang, A. R. Hurson Jan 2008

Web-Based Service Exchange System For Agents And Humans Alike, Evens Jean, Machigar Ongtang, A. R. Hurson

Computer Science Faculty Research & Creative Works

Semantic Web research aims at bridging the gap between how humans and agents process information readily available on the Internet. One of the great challenges to this goal lies in the fact that humans, contrary to agents, can extract the meaning of words based on its context. This work introduces a service exchange system for the Web that allows agents to intelligently process information, as would humans. This is achieved by the use of thesauri to help agents resolve semantic heterogeneity in the information being processed. The framework for the exchange system has been realized under the aglet platform on …


Energy Efficient Correlated Data Aggregation For Wireless Sensor Networks, Seung Jong Park, Raghupathy Sivakumar Jan 2008

Energy Efficient Correlated Data Aggregation For Wireless Sensor Networks, Seung Jong Park, Raghupathy Sivakumar

Computer Science Faculty Research & Creative Works

Data aggregations from Sensors to a sink in wireless sensor networks (WSNs) are typically characterized by correlation along the spatial, semantic, and temporal dimensions. Exploiting such correlation when performing data aggregation can result in considerable improvements in the bandwidth and energy performance of WSNs. For the sensors-to-sink data delivery, we first explore two theoretical solutions: the shortest path tree (SPT) and the minimum spanning tree (MST) approaches. To approximate the optimal solution (MST) in case of perfect correlation among data, we propose a new aggregation which combines the minimum dominating set (MDS) with the shortest path tree (SPT) in order …


Enlightened Computing: An Architecture For Co-Allocating Network, Compute, And Other Grid Resources For High-End Applications, Lina Battestilli, Andrei Hutanut, Gigi Karmous-Edwards, Daniel S. Katz, Jon Maclarent, Joe Mambretti, John H. Moore, Seung Jong Park, Harry G. Perros, Syam Sundar, Savera Tanwir, Steven R. Thorpe, Yufeng Xin Dec 2007

Enlightened Computing: An Architecture For Co-Allocating Network, Compute, And Other Grid Resources For High-End Applications, Lina Battestilli, Andrei Hutanut, Gigi Karmous-Edwards, Daniel S. Katz, Jon Maclarent, Joe Mambretti, John H. Moore, Seung Jong Park, Harry G. Perros, Syam Sundar, Savera Tanwir, Steven R. Thorpe, Yufeng Xin

Computer Science Faculty Research & Creative Works

Many emerging high-performance applications require distributed infrastructure that is significantly more powerful and flexible than traditional Grids. Such applications require the optimization, close integration, and control of all Grid resources, including networks. The EnLIGHTened (ENL) Computing Project has designed an architectural framework that allows Grid applications to dynamically request (in-advance or on-demand) any type of Grid resource: computers, storage, instruments, and deterministic, high-bandwidth network paths, including lightpaths. Based on application requirements, the ENL middleware communicates with Grid resource managers and, when availability is verified, co-allocates all the necessary resources. ENL's Domain Network Manager controls all network resource allocations to dynamically …


Research Issues And Overview Of Economic Models In Mobile-P2p Networks, Anirban Mondal, Sanjay Kumar Madria, Masaru Kitsuregawa Dec 2007

Research Issues And Overview Of Economic Models In Mobile-P2p Networks, Anirban Mondal, Sanjay Kumar Madria, Masaru Kitsuregawa

Computer Science Faculty Research & Creative Works

The mobile-P2P paradigm is becoming increasingly popular. Existing mobile-P2P solutions largely do not consider economic incentive models for enticing peer participation without eliminating free-riders and for effectively handling mobile resource constraints such as energy. This paper presents an executive summary of the existing solutions and an overview of some of the important issues for handling problems in mobile-P2P networks using economic models. We also present our perspectives on building 'real' mobile-P2P applications using economic models. © 2007 IEEE.


Time-Adaptive Numerical Simulation For High Speed Networks, Suman Kumar, Seung Jong Park, S. Sitharama Iyengar, Jung Han Kimn Dec 2007

Time-Adaptive Numerical Simulation For High Speed Networks, Suman Kumar, Seung Jong Park, S. Sitharama Iyengar, Jung Han Kimn

Computer Science Faculty Research & Creative Works

As the bandwidth of networks is increasing exponentially, the computational cost to simulate such type of networks is also growing in a similar fashion. This paper presents a scalable simulation method, called time-adaptive numerical simulation, which can be used to represent dynamics of high-speed networks using fluid-based models. The new method dynamically adjusts the size of a time step for a numerical solver which solves a system of differential equations representing dynamics of protocols and nodes' behaviors. The simulation results show that the time-adaptive-method reduces the computational time while achieving the same accuracy compared to that of a fixed step-size …


Sybil Attack Detection In A Hierarchical Sensor Network, Jian Yin, Sanjay Kumar Madria Dec 2007

Sybil Attack Detection In A Hierarchical Sensor Network, Jian Yin, Sanjay Kumar Madria

Computer Science Faculty Research & Creative Works

The Sybil attack is a particularly harmful threat to sensor networks where a single sensor node illegitimately claims multiple identities. a malicious node may generate an arbitrary number of additional node identities using only one physical device. the Sybil attack can disrupt normal functioning of the sensor network, such as the multipath routing, used to explore the multiple disjoint paths between source-destination pairs. But the Sybil attack can disrupt it when a single adversary presents multiple identities, which appear on the multiple paths. Digital certificates are a way to prove identities, but they are not suitable for the sensor network …


Transmission Scheduling In Sensor Networks Via Directed Edge Coloring, Maggie Xiaioyan Cheng, Li Yin Dec 2007

Transmission Scheduling In Sensor Networks Via Directed Edge Coloring, Maggie Xiaioyan Cheng, Li Yin

Computer Science Faculty Research & Creative Works

This paper presents a transmission scheduling scheme in sensor networks. Each node is assigned a list of time slots to use for unicasting and broadcast communication. the algorithm employs edge coloring on a directed graph for transmission scheduling. It is different from previous works that use vertex coloring of a graph for node scheduling, or those that use edge coloring of undirected graphs for link scheduling. the proposed algorithm uses the least number of time slots compared to its counterparts and it avoids both the hidden terminal problem and the exposed terminal problem in both unicast and broadcast communication. ©2007 …


Journal Of Combinatorial Optimization, Special Issue On Communication Networks And Internet Applications, Maggie Xiaoyan Cheng Nov 2007

Journal Of Combinatorial Optimization, Special Issue On Communication Networks And Internet Applications, Maggie Xiaoyan Cheng

Computer Science Faculty Research & Creative Works

No abstract provided.


Electrostatic Force Microscopy Studies Of Boron-Doped Diamond Films, Santosh Gupta, O. A. Williams, Eric W. Bohannan Nov 2007

Electrostatic Force Microscopy Studies Of Boron-Doped Diamond Films, Santosh Gupta, O. A. Williams, Eric W. Bohannan

Computer Science Faculty Research & Creative Works

Much has been learned from electrochemical properties of boron-doped diamond (BDD) thin films synthesized using microwave plasma-assisted chemical vapor deposition about the factors influencing electrochemical activity, but some characteristics are still not entirely understood, such as its electrical conductivity in relation with microscale structure. Therefore, to effectively utilize these materials, understanding both the microscopic structure and physical (electrical, in particular) properties becomes indispensable. in addition to topography using atomic force microscopy, electrostatic force microscopy (EFM) in phase mode measuring the long-range electrostatic force gradients, helps to map the electrical conductivity heterogeneity of boron-doped micro-/nanocrystalline diamond surfaces. the mapping of electrical …


Alternative Splicing: Associating Frequency With Isoforms, Anuradha Roy, Jennifer Leopold, Anne M. Maglia Oct 2007

Alternative Splicing: Associating Frequency With Isoforms, Anuradha Roy, Jennifer Leopold, Anne M. Maglia

Computer Science Faculty Research & Creative Works

In the simplest model of protein production, a gene gives rise to a single protein; DNA is transcribed to form pre-mRNA, which is converted to mRNA by splicing or removing introns. The result is a chain of exons that is translated to form a protein. Alternative splicing of exons may result in the formation of multiple proteins from the same gene sequence. However, not all of these proteins may be functional. Thus, we ask whether we can predict and rank (in order of frequency of occurrence and functional importance) the set of possible proteins for a gene. Herein we describe …


Determining Domain Similarity And Domain-Protein Similarity Using Functional Similarity Measurements Of Gene Ontology Terms, Lisa Michelle Guntly, Jennifer Leopold, Anne M. Maglia Oct 2007

Determining Domain Similarity And Domain-Protein Similarity Using Functional Similarity Measurements Of Gene Ontology Terms, Lisa Michelle Guntly, Jennifer Leopold, Anne M. Maglia

Computer Science Faculty Research & Creative Works

Protein domains typically correspond to major functional sites of a protein. Therefore, determining similarity between domains can aid in the comparison of protein functions, and can provide a basis for grouping domains based on function. One strategy for comparing domain similarity and domain-protein similarity is to use similarity measurements of annotation terms from the Gene Ontology (GO). In this paper five methods are analyzed in terms of their usefulness for comparing domains, and comparing domains to proteins based on GO terms.