The development of semantic meta-database: an ontology based semantic integration of biological databases

Protein sequence annotation is important for the preservation and reuse of knowledge, for content-based queries, and for the understanding of its function. Traditional wet-lab methods are labor intensive and prone to human error. Alternatively, existing tools are time intensive and require high investment in computing facilities for offline usage. On the other hand, these tools are highly dependent on internet stability and speed for online usage. Therefore, a simple and practical computational method that is more accurate, faster, easy to configure and use, and bears low computing cost is needed particularly for offline usage. In this study, a Gene Ontology (GO) based protein sequence annotation tool named extended UTMGO is developed to meet these features. The GO is selected because of its ability to provide dynamic, precisely defined, structured, and controlled terms that describe genes and their functions and products in any organism. Furthermore, the GO terms are linked with gene products and their protein sequences from various species provided by Gene Ontology Annotation (GOA). Thus, assigning highly correlated GO terms of annotated protein sequences to partially annotated or newly discovered protein sequences can be made. The tool comprises two intelligent algorithms. The first algorithm combines parallel genetic algorithm with the split-and-merge algorithm. The idea is to cluster the GO terms into number k of clusters in order to split the monolithic GO RDF/XML file into smaller files. Thus, it enables protein sequences and Inferred from Electronic Annotation (IEA) evidence associations to be included in those files. The second algorithm incorporates parallel genetic algorithm with the semantic similarity measure algorithm. The motive is to search for a set of semantically similar GO terms from the fragmented GO RDF/XML files to a given query. In addition, its basic version which is a GO browser based on semantic similarity search is also introduced to overcome the weaknesses of conventional approach: the keyword matching.

[1]  Christian J. A. Sigrist,et al.  ProRule: a new database containing functional and structural information on PROSITE profiles , 2005, Bioinform..

[2]  Andreas Prlic,et al.  WILMA - automated annotation of protein sequences , 2004, Bioinform..

[3]  Anil K. Jain,et al.  Data clustering: a review , 1999, CSUR.

[4]  Bin Zheng,et al.  BMC Bioinformatics BioMed Central , 2005 .

[5]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[6]  Abraham Duarte,et al.  Improving image segmentation quality through effective region merging using a hierarchical social metaheuristic , 2006, Pattern Recognit. Lett..

[7]  Miquel Sànchez-Marrè,et al.  A comparative study on the use of similarity measures in case-based reasoning to improve the classification of environmental system situations , 2004, Environ. Model. Softw..

[8]  Hai Hu,et al.  Assessing semantic similarity measures for the characterization of human regulatory pathways , 2006, Bioinform..

[9]  Georgios P. Papamichail,et al.  The k-means range algorithm for personalized data clustering in e-commerce , 2007, Eur. J. Oper. Res..

[10]  K. Katayama,et al.  Analysis of crossovers and selections in a coarse-grained parallel genetic algorithm , 2003 .

[11]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[12]  Gertraud Burger,et al.  AutoFACT: An Automatic Functional Annotation and Classification Tool , 2005, BMC Bioinformatics.

[13]  Paul Pavlidis,et al.  ErmineJ: Tool for functional analysis of gene expression data sets , 2005, BMC Bioinformatics.

[14]  Sheldon H. Jacobson,et al.  Optimal search strategies using simultaneous generalized hill climbing algorithms , 2006, Math. Comput. Model..

[15]  Seo Young Kim,et al.  Effect of data normalization on fuzzy clustering of DNA microarray data , 2005, BMC Bioinformatics.

[16]  Chris Walshaw,et al.  Parallel optimisation algorithms for multilevel mesh partitioning , 2000, Parallel Comput..

[17]  Rolf Apweiler,et al.  Bioinformatics database infrastructure for biotechnology research. , 2006, Journal of biotechnology.

[18]  Jean-François Hocquette,et al.  Assessment of hierarchical clustering methodologies for proteomic data mining. , 2007, Journal of proteome research.

[19]  Jennifer Golbeck,et al.  Ontologies for ecoinformatics , 2006, J. Web Semant..

[20]  Hongfang Liu,et al.  DynGO: a tool for visualizing and mining of Gene Ontology and its associations , 2005, BMC Bioinformatics.

[21]  Angel Rubio,et al.  Correlation between gene expression and GO semantic similarity , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[22]  Jih-Jeng Huang,et al.  Marketing segmentation using support vector clustering , 2007, Expert Syst. Appl..

[23]  KöhlerJacob,et al.  Ontology based text indexing and querying for the semantic web , 2006 .

[24]  Anbupalam Thalamuthu,et al.  Gene expression Evaluation and comparison of gene clustering methods in microarray analysis , 2006 .

[25]  D.M. Mount,et al.  An Efficient k-Means Clustering Algorithm: Analysis and Implementation , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[26]  R. Apweiler.  Protein sequence databases. , 2000, Advances in protein chemistry.

[27]  Cheng-Jye Luh,et al.  Generating page clippings from web search results using a dynamically terminated genetic algorithm , 2005, Inf. Syst..

[28]  Susmita Datta,et al.  Evaluation of clustering algorithms for gene expression data , 2006, BMC Bioinformatics.

[29]  Witold Pedrycz,et al.  Rough–Fuzzy Collaborative Clustering , 2006, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[30]  Liping Wei,et al.  Genome comparison using Gene Ontology (GO) with statistical testing , 2006, BMC Bioinformatics.

[31]  Chittibabu Guda,et al.  Predicting the Subcellular Localization of Human Proteins Using Machine Learning and Exploratory Data Analysis , 2006, Genom. Proteom. Bioinform..

[32]  Wing-Kin Sung,et al.  Probabilistic prediction of protein-protein interactions from the protein sequences , 2006, Comput. Biol. Medicine.

[33]  Mark E. Bastin,et al.  Improved segmentation reproducibility in group tractography using a quantitative tract similarity measure , 2006, NeuroImage.

[34]  Wolfgang Marquardt,et al.  OntoCAPE - A large-scale ontology for chemical process engineering , 2007, Eng. Appl. Artif. Intell..

[35]  Yu-Dong Cai,et al.  Predicting protease types by hybridizing gene ontology and pseudo amino acid composition , 2006, Proteins.

[36]  Horst Bunke,et al.  Validation indices for graph clustering , 2003, Pattern Recognit. Lett..

[37]  Melba M. Crawford,et al.  Unsupervised multistage image classification using hierarchical clustering with a bayesian similarity measure , 2005, IEEE Transactions on Image Processing.

[38]  Margarida Moz,et al.  A genetic algorithm approach to a nurse rerostering problem , 2007, Comput. Oper. Res..

[39]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[40]  Midori A. Harris,et al.  The Gene Ontology project , 2005 .

[41]  Minghe Sun.  Solving the uncapacitated facility location problem using tabu search , 2006, Comput. Oper. Res..

[42]  Chris Walshaw,et al.  Mesh Partitioning: A Multilevel Balancing and Refinement Algorithm , 2000, SIAM J. Sci. Comput..

[43]  Mário J. Silva,et al.  Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors , 2005, CIKM '05.

[44]  Safaai Deris,et al.  UTMGO: A Tool for Searching a Group of Semantically Related Gene Ontology Terms and Application to Annotation of Anonymous Protein Sequence , 2007 .

[45]  David W. Conrath,et al.  Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.

[46]  Emily Dimmer,et al.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology , 2004, Nucleic Acids Res..

[47]  Xiaomei Wu,et al.  Prediction of yeast protein–protein interaction network: insights from the Gene Ontology and annotations , 2006, Nucleic acids research.

[48]  Christel Daniel-Le Bozec,et al.  Computation of semantic similarity within an ontology of breast pathology to assist inter-observer consensus , 2006, Comput. Biol. Medicine.

[49]  Michael Schroeder,et al.  SCOPPI: a structural classification of protein–protein interfaces , 2005, Nucleic Acids Res..

[50]  Martin Chodorow,et al.  Combining local context and wordnet similarity for word sense identification , 1998 .

[51]  Frank Klawonn,et al.  JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information , 2006, Nucleic Acids Res..

[52]  Yuxin Peng,et al.  Clip-based similarity measure for query-dependent clip retrieval and video summarization , 2006, IEEE Trans. Circuits Syst. Video Technol..

[53]  Enrico Zio,et al.  Evolutionary fuzzy clustering for the Classification of transients in nuclear components , 2005 .

[54]  S. Mitra,et al.  Bioinformatics with soft computing , 2006, IEEE Transactions on Systems, Man, and Cybernetics, Part C (Applications and Reviews).

[55]  Ibrahim Kushchu,et al.  Web-based evolutionary and adaptive information retrieval , 2005, IEEE Transactions on Evolutionary Computation.

[56]  Matthias Mann,et al.  NOPdb: Nucleolar Proteome Database , 2005, Nucleic Acids Res..

[57]  F. Meer.  The effectiveness of spectral similarity measures for the analysis of hyperspectral imagery , 2006 .

[58]  Spiros Mancoridis,et al.  On the automatic modularization of software systems using the Bunch tool , 2006, IEEE Transactions on Software Engineering.

[59]  Mohand Boughanem,et al.  Multiple query evaluation based on an enhanced genetic algorithm , 2003, Inf. Process. Manag..

[60]  Xinjian Chen,et al.  A new algorithm for distorted fingerprints matching based on normalized fuzzy similarity measure , 2006, IEEE Trans. Image Process..

[61]  Youssef Saab,et al.  An effective multilevel algorithm for bisecting graphs and hypergraphs , 2004, IEEE Transactions on Computers.

[62]  Eytan Domany,et al.  Coupled Two-way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data , 2002, Bioinform..

[63]  Michael Specht,et al.  Ontology based text indexing and querying for the semantic web , 2006, Knowl. Based Syst..

[64]  Michel Dumontier,et al.  CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules , 2005, FEBS letters.

[65]  Zalmiyah Zakaria,et al.  Automatic clustering of gene ontology by genetic algorithm , 2007 .

[66]  Byung Ro Moon,et al.  Genetic Algorithm and Graph Partitioning , 1996, IEEE Trans. Computers.

[67]  K. Chang,et al.  Integration of Self-Organizing Feature Maps and Genetic-Algorithm-Based Clustering Method for Market Segmentation , 2004, J. Organ. Comput. Electron. Commer..

[68]  R. Garduno-Ramirez,et al.  Multiobjective control of power plants using particle swarm optimization techniques , 2006, IEEE Transactions on Energy Conversion.

[69]  Basheer M. Khumawala,et al.  An empirical comparison of tabu search, simulated annealing, and genetic algorithms for facilities location problems , 1997 .

[70]  Ulrich Elsner,et al.  Graph partitioning - a survey , 2005 .

[71]  Duane Szafron,et al.  PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization , 2004, Nucleic Acids Res..

[72]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[73]  Jan Morbach,et al.  OntoCAPE: A Re-Usable Ontology for Chemical Process Engineering , 2009 .

[74]  Rolf Apweiler,et al.  Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT , 2001, Bioinform..

[75]  Pavel Berkhin,et al.  A Survey of Clustering Data Mining Techniques , 2006, Grouping Multidimensional Data.

[76]  Yongchuan Tang,et al.  Linguistic modelling based on semantic similarity relation among linguistic labels , 2006, Fuzzy Sets Syst..

[77]  Christoph Schlieder,et al.  Ontology-based verification of core model conformity in conceptual modeling , 2006, Comput. Environ. Urban Syst..

[78]  Christopher W. V. Hogue,et al.  Domain-based small molecule binding site annotation , 2006, BMC Bioinformatics.

[79]  Julia V Ponomarenko,et al.  Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology , 2005, Proteins.

[80]  Safaai Deris,et al.  A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences , 2008, J. Biomed. Informatics.

[81]  S. Kotsiantis,et al.  Recent Advances in Clustering : A Brief Survey , 2004 .

[82]  Hans Lehrach,et al.  GOblet: a platform for Gene Ontology annotation of anonymous sequence data , 2004, Nucleic Acids Res..

[83]  Cathy H. Wu,et al.  Protein family classification and functional annotation , 2003, Comput. Biol. Chem..

[84]  L. You,et al.  Assessing the spatial distribution of crop areas using a cross-entropy method , 2005 .

[85]  Yi Pan,et al.  Clustering support vector machines for protein local structure prediction , 2007, Expert Syst. Appl..

[86]  Mark Craven,et al.  Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text , 2005, BMC Bioinformatics.

[87]  Michael E. Wall,et al.  Galib: a c++ library of genetic algorithm components , 1996 .

[88]  Ismail H. Toroslu,et al.  Genetic algorithm for the personnel assignment problem with multiple objectives , 2007, Inf. Sci..

[89]  Jingyu Wang,et al.  Ant colony optimization for the nonlinear resource allocation problem , 2006, Appl. Math. Comput..

[90]  Miguel García-Remesal,et al.  ONTOFUSION: Ontology-based integration of genomic and clinical databases , 2006, Comput. Biol. Medicine.

[91]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[92]  Sim Heng Ong,et al.  A Luminance- and Contrast-Invariant Edge-Similarity Measure , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[93]  Weiguo Sheng,et al.  A weighted sum validity function for clustering with a hybrid niching genetic algorithm , 2005, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[94]  Greg Hamerly,et al.  Learning the k in k-means , 2003, NIPS.

[95]  Duane Szafron,et al.  The Path-A metabolic pathway prediction web server , 2006, Nucleic Acids Res..

[96]  Georg Peters,et al.  Some refinements of rough k-means clustering , 2006, Pattern Recognit..

[97]  S. Bandyopadhyay,et al.  Nonparametric genetic clustering: comparison of validity indices , 2001, IEEE Trans. Syst. Man Cybern. Syst..

[98]  Jitendra Malik,et al.  Normalized cuts and image segmentation , 1997, Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition.

[99]  Gong-Xin Yu,et al.  Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations , 2004, J. Bioinform. Comput. Biol..

[100]  Barry Smith,et al.  Biodynamic ontology: applying BFO in the biomedical domain. , 2004, Studies in health technology and informatics.

[101]  Patrice Koehl,et al.  MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences , 2005, Nucleic acids research.

[102]  Carl J. Schmidt,et al.  GoFigure: Automated Gene OntologyTM annotation , 2003, Bioinform..

[103]  Carole A. Goble,et al.  A short study on the success of the Gene Ontology , 2004, J. Web Semant..

[104]  Limin Fu,et al.  FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data , 2007, BMC Bioinformatics.

[105]  Anne-Lise Veuthey,et al.  Automated annotation of microbial proteomes in SWISS-PROT , 2003, Comput. Biol. Chem..

[106]  Ge Gao,et al.  DRTF: a database of rice transcription factors , 2006, Bioinform..

[107]  H. Iba,et al.  Gene selection for classification of cancers using probabilistic model building genetic algorithm. , 2005, Bio Systems.

[108]  Chun Zhou,et al.  MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation , 2006, Bioinform..

[109]  Yskandar Hamam,et al.  Task allocation for maximizing reliability of distributed systems: A simulated annealing approach , 2006, J. Parallel Distributed Comput..

[110]  Xin Yao,et al.  An evolutionary clustering algorithm for gene expression microarray data analysis , 2006, IEEE Transactions on Evolutionary Computation.

[111]  Rajan Batta,et al.  A simulated annealing approach to police district design , 2002, Comput. Oper. Res..

[112]  Abdulkadir Sengür,et al.  Comparison of clustering algorithms for analog modulation classification , 2006, Expert Syst. Appl..

[113]  Kam-Fai Wong,et al.  A genetic algorithm-based clustering approach for database partitioning , 2002, IEEE Trans. Syst. Man Cybern. Part C.

[114]  Robert P. W. Duin,et al.  Building Road-Sign Classifiers Using a Trainable Similarity Measure , 2006, IEEE Transactions on Intelligent Transportation Systems.

[115]  Giorgio Parisi,et al.  Physica A: Statistical Mechanics and its Applications: Editorial note , 2005 .

[116]  Kengo Katayama,et al.  Performance of a genetic algorithm for the graph partitioning problem , 2003 .

[117]  Ujjwal Maulik,et al.  Performance Evaluation of Some Clustering Algorithms and Validity Indices , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[118]  Nikola K. Kasabov,et al.  An efficient greedy K-means algorithm for global gene trajectory clustering , 2006, Expert Syst. Appl..

[119]  Gene Ontology Consortium,et al.  The Gene Ontology (GO) project in 2006 , 2005, Nucleic Acids Res..

[120]  Donald E. Grierson,et al.  Comparison among five evolutionary-based optimization algorithms , 2005, Adv. Eng. Informatics.

[121]  Rahul,et al.  Optimization of FRP composites against impact induced failure using island model parallel genetic algorithm , 2005 .

[122]  K. E. Ravikumar,et al.  An online literature mining tool for protein phosphorylation , 2006, Bioinform..

[123]  James M. Keller,et al.  Fuzzy Measures on the Gene Ontology for Gene Product Similarity , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[124]  S. Kannan,et al.  Application and comparison of metaheuristic techniques to generation expansion planning problem , 2005, IEEE Transactions on Power Systems.

[125]  Roland Eils,et al.  GOPET: A tool for automated predictions of Gene Ontology terms , 2006, BMC Bioinformatics.

[126]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[127]  Bonnie L. Webber,et al.  COBrA: a bio-ontology editor , 2005, Bioinform..

[128]  Naoki Shibata,et al.  Techniques to improve exploration efficiency of parallel self-adaptive genetic algorithms by dispensing with iteration and synchronization , 2006 .

[129]  Naoki Shibata,et al.  Techniques to improve exploration efficiency of parallel self-adaptive genetic algorithms by dispensing with iteration and synchronization , 2006, Systems and Computers in Japan.

[130]  J. Grabowski,et al.  The permutation flow shop problem with blocking. A tabu search approach , 2007 .

[131]  Lin Fang,et al.  WEGO: a web tool for plotting GO annotations , 2006, Nucleic Acids Res..

[132]  Geoffrey J. Barton,et al.  GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes , 2004, BMC Bioinformatics.

[133]  Uwe Reyle,et al.  Developing a Protein-Interactions Ontology , 2003, Comparative and functional genomics.

[134]  Dekang Lin,et al.  An Information-Theoretic Definition of Similarity , 1998, ICML.

[135]  Ali Kaveh,et al.  A hybrid graph-genetic method for domain decomposition , 2000 .

[136]  Manoj Kumar Tiwari,et al.  Solving Part-Type Selection and Operation Allocation Problems in an FMS: An Approach Using Constraints-Based Fast Simulated Annealing Algorithm , 2006, IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans.

[137]  Graeme Hirst,et al.  Evaluating WordNet-based Measures of Lexical Semantic Relatedness , 2006, CL.

[138]  Gultekin Özsoyoglu,et al.  Annotating proteins by mining protein interaction networks , 2006, ISMB.

[139]  Bidyut Baran Chaudhuri,et al.  A novel genetic algorithm for automatic clustering , 2004, Pattern Recognit. Lett..

[140]  Lin-Yu Tseng,et al.  A genetic approach to the automatic clustering problem , 2001, Pattern Recognit..

[141]  Catherine Brooksbank,et al.  The European Bioinformatics Institute's data resources: towards systems biology , 2004, Nucleic Acids Res..

[142]  Abdulkadir Sengur,et al.  Comparison of clustering algorithms for analog modulation classification , 2006 .

[143]  Ute Baumann,et al.  BMC Bioinformatics BioMed Central Methodology article Automated methods of predicting the function of biological sequences using GO and BLAST , 2005 .

[144]  Thomas E. Potok,et al.  A flocking based algorithm for document clustering analysis , 2006, J. Syst. Archit..

[145]  Rolf Apweiler,et al.  Automatic rule generation for protein annotation with the C4.5 data-mining algorithm applied on peptides in Ensembl , 2001, German Conference on Bioinformatics.

[146]  Michel C. A. Klein,et al.  Structure-Based Partitioning of Large Concept Hierarchies , 2004, SEMWEB.

[147]  Horst Bunke,et al.  Self-organizing map for clustering in the graph domain , 2002, Pattern Recognit. Lett..

[148]  A. C. Martínez-Estudillo,et al.  Hybridization of evolutionary algorithms and local search by means of a clustering method , 2005, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[149]  Bostjan Likar,et al.  A protocol for evaluation of similarity measures for rigid registration , 2006, IEEE Transactions on Medical Imaging.

[150]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[151]  Berkant Barla Cambazoglu,et al.  Adaptive decomposition and remapping algorithms for object-space-parallel direct volume rendering of unstructured grids , 2007, J. Parallel Distributed Comput..

[152]  Philip Resnik,et al.  Using Information Content to Evaluate Semantic Similarity in a Taxonomy , 1995, IJCAI.

[153]  Christiane Fellbaum,et al.  Combining Local Context and Wordnet Similarity for Word Sense Identification , 1998 .

[154]  Scott Vandenberg,et al.  Comparing the protein expression profiles of human mesenchymal stem cells and human osteoblasts using gene ontologies. , 2005, Stem cells and development.

[155]  John R. Smith,et al.  Large-scale concept ontology for multimedia , 2006, IEEE MultiMedia.

[156]  Miodrag Potkonjak,et al.  Watermarking graph partitioning solutions , 2002, IEEE Trans. Comput. Aided Des. Integr. Circuits Syst..

[157]  Safaai Deris,et al.  Computational Method for Annotation of Protein Sequence According to Gene Ontology Terms , 2007 .

[158]  Jane Lomax,et al.  Get ready to GO! A biologist's guide to the Gene Ontology , 2005, Briefings Bioinform..

[159]  Alan L. Porter,et al.  R&D Cluster Quality Measures and Technology Maturity , 2003 .

[160]  Andrew W. Moore,et al.  X-means: Extending K-means with Efficient Estimation of the Number of Clusters , 2000, ICML.

[161]  Alex Pentland,et al.  A Bayesian similarity measure for deformable image matching , 2001, Image Vis. Comput..

[162]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[163]  Michael J. Laszlo,et al.  A genetic algorithm using hyper-quadtrees for low-dimensional k-means clustering , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[164]  Javier Garcia-Frías,et al.  A novel HMM-based clustering algorithm for the analysis of gene expression time-course data , 2006, Comput. Stat. Data Anal..

[165]  Angus R. Simpson,et al.  Application of two ant colony optimisation algorithms to water distribution system optimisation , 2006, Math. Comput. Model..

[166]  Mark Gerstein,et al.  The Database of Macromolecular Motions: new features added at the decade mark , 2005, Nucleic Acids Res..

[167]  Rolf Apweiler,et al.  A novel method for automatic functional annotation of proteins , 1999, Bioinform..

[168]  H. Torresa,et al.  Self-organizing map clustering based on continuous multiresolution entropy , 2005 .

[169]  Vladimir Pavlovic,et al.  Protein classification using probabilistic chain graphs and the Gene Ontology structure , 2006, Bioinform..

[170]  Sueli Aparecida Mingoti,et al.  Comparing SOM neural network with Fuzzy c , 2006, Eur. J. Oper. Res..

[171]  Jean-Michel Claverie,et al.  Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes , 2003, Nucleic Acids Res..

[172]  James C. Bezdek,et al.  Fuzzy c-means clustering of incomplete data , 2001, IEEE Trans. Syst. Man Cybern. Part B.

[173]  Adam Godzik,et al.  JAFA: a protein function annotation meta-server , 2006, Nucleic Acids Res..

[174]  M. Andrea Rodríguez,et al.  A genetic algorithm for searching spatial configurations , 2005, IEEE Transactions on Evolutionary Computation.

[175]  Safaai Deris,et al.  Incorporating Semantic Similarity Measure in Genetic Algorithm: An Approach for Searching the Gene Ontology Terms , 2007 .

[176]  Vito Di Gesù,et al.  GenClust: A genetic algorithm for clustering gene expression data , 2005, BMC Bioinformatics.

[177]  William S Maki,et al.  An efficient method for estimating semantic similarity based on feature overlap: Reliability and validity of semantic feature ratings , 2006, Behavior research methods.

[178]  Jung-Hsien Chiang,et al.  Literature Extraction of Protein Functions Using Sentence Pattern Mining , 2005, IEEE Trans. Knowl. Data Eng..

[179]  Yan Li.  Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core , 2006, J. Chem. Inf. Model..

[180]  Alex Lewin,et al.  BMC Bioinformatics BioMed Central Methodology article Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data , 2006 .

[181]  Sankar K. Pal,et al.  Web mining in soft computing framework: relevance, state of the art and future directions , 2002, IEEE Trans. Neural Networks.

[182]  D. Barrell,et al.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. , 2003, Genome research.

[183]  Shantanu Dutt,et al.  Probability-based approaches to VLSI circuit partitioning , 2000, IEEE Trans. Comput. Aided Des. Integr. Circuits Syst..