Abstract: The most important property of the Gene Ontology is
the terms. These control vocabularies are defined to provide
consistent descriptions of gene products that are shareable and
computationally accessible by humans, software agent, or other
machine-readable meta-data. Each term is associated with
information such as definition, synonyms, database references, amino
acid sequences, and relationships to other terms. This information has
made the Gene Ontology broadly applied in microarray and
proteomic analysis. However, the process of searching the terms is
still carried out using traditional approach which is based on keyword
matching. The weaknesses of this approach are: ignoring semantic
relationships between terms, and highly depending on a specialist to
find similar terms. Therefore, this study combines semantic similarity
measure and genetic algorithm to perform a better retrieval process
for searching semantically similar terms. The semantic similarity
measure is used to compute similitude strength between two terms.
Then, the genetic algorithm is employed to perform batch retrievals
and to handle the situation of the large search space of the Gene
Ontology graph. The computational results are presented to show the
effectiveness of the proposed algorithm.
Abstract: Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.
Abstract: Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.
Abstract: Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.
Abstract: Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.
Abstract: Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.
Abstract: The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.
Abstract: Requirements are critical to system validation as they guide all subsequent stages of systems development. Inadequately specified requirements generate systems that require major revisions or cause system failure entirely. Use Cases have become the main vehicle for requirements capture in many current Object Oriented (OO) development methodologies, and a means for developers to communicate with different stakeholders. In this paper we present the results of a laboratory experiment that explored whether different types of use case format are equally effective in facilitating high knowledge user-s understanding. Results showed that the provision of diagrams along with the textual use case descriptions significantly improved user comprehension of system requirements in both familiar and unfamiliar application domains. However, when comparing groups that received models of textual description accompanied with diagrams of different level of details (simple and detailed) we found no significant difference in performance.
Abstract: Understanding proteins functions is a major goal in
the post-genomic era. Proteins usually work in context of other
proteins and rarely function alone. Therefore, it is highly relevant to
study the interaction partners of a protein in order to understand its
function. Machine learning techniques have been widely applied to
predict protein-protein interactions. Kernel functions play an
important role for a successful machine learning technique. Choosing
the appropriate kernel function can lead to a better accuracy in a
binary classifier such as the support vector machines. In this paper,
we describe a Bayesian kernel for the support vector machine to
predict protein-protein interactions. The use of Bayesian kernel can
improve the classifier performance by incorporating the probability
characteristic of the available experimental protein-protein
interactions data that were compiled from different sources. In
addition, the probabilistic output from the Bayesian kernel can assist
biologists to conduct more research on the highly predicted
interactions. The results show that the accuracy of the classifier has
been improved using the Bayesian kernel compared to the standard
SVM kernels. These results imply that protein-protein interaction can
be predicted using Bayesian kernel with better accuracy compared to
the standard SVM kernels.
Abstract: The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.