References Current Trends in <strong>Bio</strong><strong>medical</strong> Data <strong>and</strong> Applications 7 Achard, F., Barillot, E.: Ubiquitous distributed objects with CORBA. In: Pacific Symposium <strong>Bio</strong>computing. World Scientific, London (1997) Achard, F., Dessen, P.: GenXref VI: automatic generation of links between two heterogeneous databases. <strong>Bio</strong>informatics 14, 20–24 (1998) Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropou-Los, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., Kerlavage, A.R., Mccombie, W.R., Venter, J.C.: Complementary DNA sequencing: expressed sequence tags <strong>and</strong> human genome project. Science 252, 1651–1656 (1991) Andrade, M.A., Valencia, A.: Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. In: Gaaster-L<strong>and</strong>, T., Karp, P., Karplus, K., Ouzonis, C., S<strong>and</strong>er, C., Valen-Cia, A. (eds.) 5th International Conference on Intelligent Systems for Molecular <strong>Bio</strong>logy. AAAI, Halkidiki (1997) Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: UniProt: The Universal Protein knowledgebase. Nucleic Acids Research 32, 115–119 (2004) Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence data bank <strong>and</strong> its supplement TrEMBL. Nucleic Acids Research 25, 31–36 (1997) Bairoch, A., Bucher, P., Hofmann, K.: The PROSITE database, its status in 1997. Nucleic Acids Research 25, 217–221 (1997) Barker, W.C., Garavelli, J.S., Haft, D.H., Hunt, L.T., Marzec, C.R., Orcutt, B.C.: The PIR- International Protein Sequence Database. Nucleic Acids Research 26, 27–32 (1998) Bashford, D., Chothia, C., Lesk, A.M.: Determinants of a protein fold: Unique features of the globin amino acid sequences. Journal of Molecular <strong>Bio</strong>logy 196, 199–216 (1987) Ben-Natan, R.: CORBA. McGraw-Hill, New York (1995) Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Rapp, B., Wheeler, D.: GenBank. Nucleic Acids Research 28, 8–15 (2000) Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M.: The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular <strong>Bio</strong>logy 112, 535–542 (1977) Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS- PROT protein knowledgebase <strong>and</strong> its supplement TrEMBL in 2003. Nucleic Acids Research 31, 365–370 (2003) Bork, P., Ouzounis, C., S<strong>and</strong>er, C., Scharf, M., Schneider, R., Sonn-Hammer, E.L.L.: Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science 1, 1677–1690 (1992) Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshp<strong>and</strong>e, N., Feng, Z., Fleri, W., Green, R., Merino-Ott, J.C., Townsend-Merino, W., Weissig, H., Westbrook, J., Berman, H.M.: The distribution <strong>and</strong> query systems of the RCSB Protein Data Bank. Nucleic Acids Research 32, D223–D225 (2004) Casari, G., Ouzounis, C., Valencia, A., S<strong>and</strong>er, C.: GeneQuiz II: automatic function assignment for genome sequence analysis. In: Hunter, L., Klein, T.E. (eds.) 1st Annual Pacific Symposium on <strong>Bio</strong>computing. World Scientific, Hawaii (1996) Cherry, J.M., Ball, C., Weng, S., Juvik, G., Schmidt, R., Adler, C., Dunn, B., Dwight, S., Riles, L., Mortimer, R.K., Botstein, D.: SGD: Saccharomyces Genome Database. Nucleic Acids Research 26, 73–79 (1998)
8 A.S. Sidhu, M. Bellgard, <strong>and</strong> T.S. Dillon Dayhoff, M.O., Eck, R.V., Chang, M.A., Sochard, M.R.: Atlas of Protein Sequence <strong>and</strong> Structure. National <strong>Bio</strong><strong>medical</strong> Research Foundation, USA (1965) Des Jardins, M., Karp, P., Krummenacker, M., Lee, T.J., Ouzounis, C.: Prediction of enzyme classification from protein sequence without the use of sequence similarity. In: Gaasterl<strong>and</strong>, T., Karp, P., Karplus, K., Ouzonis, C., S<strong>and</strong>er, C., Valencia, A. (eds.) 5th International Conference on Intelligent Systems for Molecular <strong>Bio</strong>logy. AAAI, Halkidiki (1997) Dodge, C., Schneider, R., S<strong>and</strong>er, C.: The HSSP database of protein structure-sequence alignments <strong>and</strong> family profiles. Nucleic Acids Research 26, 313–315 (1998) Eckman, B.A., Aaronson, J.S., Borkowski, J.A., Bailey, W.J., Elliston, K.O., Williamson, A.R., Blevins, R.A.: The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization <strong>and</strong> EST data mining. <strong>Bio</strong>informatics 14, 2– 13 (1997) Etzold, T., Argos, P.: SRS: An Indexing <strong>and</strong> Retrieval Tool for Flat File Data Libraries. Computer Application of <strong>Bio</strong>sciences 9, 49–57 (1993) Frishman, D., Mewes, H.W.: PEDANTic genome analysis. Trends in Genetics 13, 415–416 (1997) Gaasterl<strong>and</strong>, T., Sensen, C.W.: MAGPIE: automated genome interpretation. Trends in Genetics 12, 76–78 (1996) Gelbart, W.M., Crosby, M., Matthews, B., Rindone, W.P., Chillemi, J., Twombly, S.R., Emmert, D., Bayraktaroglu, L.: FlyBase: a Drosophila database. Nucleic Acids Research 26, 85–88 (1998) George, D.G., Mewes, H.-W., Kihara, H.: A st<strong>and</strong>ardized format for sequence data exchange. Protein Seq. Data Anal. 1, 27–29 (1987) Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G.: ACNUC–a portable retrieval system for nucleic acid sequence databases: logical <strong>and</strong> physical designs <strong>and</strong> usage. Computer applications in the biosciences 1, 167–172 (1985) Henikoff, S., Pietrokovski, S., Henikoff, J.G.: Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Research 26, 309–312 (1998) Hide, W., Burke, J., Christoffels, A., Miller, R.: Toward automated prediction of protein function from microbial genomic sequences. In: Miyano, S., Takagi, T. (eds.) Genome Informatics. Universal Academy Press, Tokyo (1997) Hooft, R.W., S<strong>and</strong>er, C., Vriend, G.: Objectively judging the quality of a protein structure from a Ramach<strong>and</strong>ran plot. Computer Application of <strong>Bio</strong>sciences 13, 425–430 (1997) Karp, P.D.: A strategy for database interoperation. Journal of Computational <strong>Bio</strong>logy 2, 573–583 (1996) Koonin, E.V., Galperin, M.Y.: Prokaryotic genomes: the emerging paradigm of genomebased microbiology. Current Opinons in Genetic Development 7, 757–763 (1997) Maidak, B.L., Olsen, G.J., Larsen, N., Overbeek, R., Mccaughey, M.J., Woese, C.R.: The ribosomal database project (RDP). Nucleic Acids Research 24, 82–85 (1996) Maxam, A.M., Gilbert, W.: A new method for sequencing DNA. In: Proceedings of National Academic of Science, vol. 74, pp. 560–564 (1977) Mckusick, V.A.: Mendelian Inheritance in Man. In: A Catalog of Human Genes <strong>and</strong> Genetic Disorders. Johns Hopkins University Press, Baltimore (1998) Miyazaki, S., Sugawara, H., Gojobori, T., Tateno, Y.: DNA Databank of Japan (DDBJ) in XML. Nucleic Acids Research 31, 13–16 (2003) Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences <strong>and</strong> Structures. Journal of Molecular <strong>Bio</strong>logy 247, 536–540 (1995)
- Page 1 and 2: Amandeep S. Sidhu and Tharam S. Dil
- Page 3 and 4: Amandeep S. Sidhu and Tharam S. Dil
- Page 5 and 6: Preface The molecular biology commu
- Page 7 and 8: Preface VII biomedical systems, and
- Page 9 and 10: X Contents Mining Clinical, Immunol
- Page 11 and 12: 2 A.S. Sidhu, M. Bellgard, and T.S.
- Page 13 and 14: 4 A.S. Sidhu, M. Bellgard, and T.S.
- Page 15: 6 A.S. Sidhu, M. Bellgard, and T.S.
- Page 19 and 20: Towards Bioinformatics Resourceomes
- Page 21 and 22: Towards Bioinformatics Resourceomes
- Page 23 and 24: Towards Bioinformatics Resourceomes
- Page 25 and 26: 2 The New Waves Towards Bioinformat
- Page 27 and 28: 2.4 Semantic Web Towards Bioinforma
- Page 29 and 30: Towards Bioinformatics Resourceomes
- Page 31 and 32: Towards Bioinformatics Resourceomes
- Page 33 and 34: Towards Bioinformatics Resourceomes
- Page 35 and 36: Towards Bioinformatics Resourceomes
- Page 37 and 38: Towards Bioinformatics Resourceomes
- Page 39 and 40: Towards Bioinformatics Resourceomes
- Page 41 and 42: Towards Bioinformatics Resourceomes
- Page 43 and 44: A Summary of Genomic Databases: Ove
- Page 45 and 46: A Summary of Genomic Databases: Ove
- Page 47 and 48: A Summary of Genomic Databases: Ove
- Page 49 and 50: A Summary of Genomic Databases: Ove
- Page 51 and 52: A Summary of Genomic Databases: Ove
- Page 53 and 54: A Summary of Genomic Databases: Ove
- Page 55 and 56: A Summary of Genomic Databases: Ove
- Page 57 and 58: A Summary of Genomic Databases: Ove
- Page 59 and 60: Appendix A Summary of Genomic Datab
- Page 61 and 62: Protein Data Integration Problem Am
- Page 63 and 64: Protein Data Integration Problem 57
- Page 65 and 66: Protein Data Integration Problem 59
- Page 67 and 68:
Protein Data Integration Problem 61
- Page 69 and 70:
Fig. 3. Class Hierarchy of Protein
- Page 71 and 72:
Protein Data Integration Problem 65
- Page 73 and 74:
Protein Data Integration Problem 67
- Page 75 and 76:
Protein Data Integration Problem 69
- Page 77 and 78:
72 L. Stanescu, D. Dan Burdescu, an
- Page 79 and 80:
74 L. Stanescu, D. Dan Burdescu, an
- Page 81 and 82:
76 L. Stanescu, D. Dan Burdescu, an
- Page 83 and 84:
78 L. Stanescu, D. Dan Burdescu, an
- Page 85 and 86:
80 L. Stanescu, D. Dan Burdescu, an
- Page 87 and 88:
82 L. Stanescu, D. Dan Burdescu, an
- Page 89 and 90:
84 L. Stanescu, D. Dan Burdescu, an
- Page 91 and 92:
86 L. Stanescu, D. Dan Burdescu, an
- Page 93 and 94:
88 L. Stanescu, D. Dan Burdescu, an
- Page 95 and 96:
90 L. Stanescu, D. Dan Burdescu, an
- Page 97 and 98:
92 L. Stanescu, D. Dan Burdescu, an
- Page 99 and 100:
94 L. Stanescu, D. Dan Burdescu, an
- Page 101 and 102:
96 L. Stanescu, D. Dan Burdescu, an
- Page 103 and 104:
98 L. Stanescu, D. Dan Burdescu, an
- Page 105 and 106:
100 L. Stanescu, D. Dan Burdescu, a
- Page 107 and 108:
102 L. Stanescu, D. Dan Burdescu, a
- Page 109 and 110:
104 L. Stanescu, D. Dan Burdescu, a
- Page 111 and 112:
106 L. Stanescu, D. Dan Burdescu, a
- Page 113 and 114:
108 L. Stanescu, D. Dan Burdescu, a
- Page 115 and 116:
110 L. Stanescu, D. Dan Burdescu, a
- Page 117 and 118:
112 L. Stanescu, D. Dan Burdescu, a
- Page 119 and 120:
114 L. Stanescu, D. Dan Burdescu, a
- Page 121 and 122:
116 L. Stanescu, D. Dan Burdescu, a
- Page 123 and 124:
118 L. Stanescu, D. Dan Burdescu, a
- Page 125 and 126:
120 L. Stanescu, D. Dan Burdescu, a
- Page 127 and 128:
122 L. Stanescu, D. Dan Burdescu, a
- Page 129 and 130:
124 L. Stanescu, D. Dan Burdescu, a
- Page 131 and 132:
126 L. Stanescu, D. Dan Burdescu, a
- Page 133 and 134:
128 L. Stanescu, D. Dan Burdescu, a
- Page 135 and 136:
130 L. Stanescu, D. Dan Burdescu, a
- Page 137 and 138:
132 L. Stanescu, D. Dan Burdescu, a
- Page 139 and 140:
134 L. Stanescu, D. Dan Burdescu, a
- Page 141 and 142:
136 L. Stanescu, D. Dan Burdescu, a
- Page 143 and 144:
138 L. Stanescu, D. Dan Burdescu, a
- Page 145 and 146:
140 L. Stanescu, D. Dan Burdescu, a
- Page 147 and 148:
Bio-medical Ontologies Maintenance
- Page 149 and 150:
Bio-medical Ontologies Maintenance
- Page 151 and 152:
Bio-medical Ontologies Maintenance
- Page 153 and 154:
Bio-medical Ontologies Maintenance
- Page 155 and 156:
Bio-medical Ontologies Maintenance
- Page 157 and 158:
Bio-medical Ontologies Maintenance
- Page 159 and 160:
TextToOnto (Maedche and Volz 2001)
- Page 161 and 162:
Bio-medical Ontologies Maintenance
- Page 163 and 164:
Bio-medical Ontologies Maintenance
- Page 165 and 166:
Bio-medical Ontologies Maintenance
- Page 167 and 168:
Bio-medical Ontologies Maintenance
- Page 169 and 170:
Bio-medical Ontologies Maintenance
- Page 171 and 172:
Bio-medical Ontologies Maintenance
- Page 173 and 174:
Extraction of Constraints from Biol
- Page 175 and 176:
Extraction of Constraints from Biol
- Page 177 and 178:
Extraction of Constraints from Biol
- Page 179 and 180:
Extraction of Constraints from Biol
- Page 181 and 182:
Extraction of Constraints from Biol
- Page 183 and 184:
Extraction of Constraints from Biol
- Page 185 and 186:
Extraction of Constraints from Biol
- Page 187 and 188:
Extraction of Constraints from Biol
- Page 189 and 190:
Extraction of Constraints from Biol
- Page 191 and 192:
Classifying Patterns in Bioinformat
- Page 193 and 194:
Classifying Patterns in Bioinformat
- Page 195 and 196:
Classifying Patterns in Bioinformat
- Page 197 and 198:
Classifying Patterns in Bioinformat
- Page 199 and 200:
Classifying Patterns in Bioinformat
- Page 201 and 202:
Classifying Patterns in Bioinformat
- Page 203 and 204:
Classifying Patterns in Bioinformat
- Page 205 and 206:
Classifying Patterns in Bioinformat
- Page 207 and 208:
Classifying Patterns in Bioinformat
- Page 209 and 210:
Classifying Patterns in Bioinformat
- Page 211 and 212:
Classifying Patterns in Bioinformat
- Page 213 and 214:
Classifying Patterns in Bioinformat
- Page 215 and 216:
Mining Clinical, Immunological, and
- Page 217 and 218:
Mining Clinical, Immunological, and
- Page 219 and 220:
Mining Clinical, Immunological, and
- Page 221 and 222:
Mining Clinical, Immunological, and
- Page 223 and 224:
Mining Clinical, Immunological, and
- Page 225 and 226:
Mining Clinical, Immunological, and
- Page 227 and 228:
Mining Clinical, Immunological, and
- Page 229 and 230:
Mining Clinical, Immunological, and
- Page 231 and 232:
Mining Clinical, Immunological, and
- Page 233 and 234:
Mining Clinical, Immunological, and
- Page 235 and 236:
Mining Clinical, Immunological, and
- Page 237 and 238:
Mining Clinical, Immunological, and
- Page 239 and 240:
Mining Clinical, Immunological, and
- Page 241 and 242:
Substructure Analysis of Metabolic
- Page 243 and 244:
Substructure Analysis of Metabolic
- Page 245 and 246:
Substructure Analysis of Metabolic
- Page 247 and 248:
Substructure Analysis of Metabolic
- Page 249 and 250:
Substructure Analysis of Metabolic
- Page 251 and 252:
Substructure Analysis of Metabolic
- Page 253 and 254:
entry compound relation subtype com
- Page 255 and 256:
Substructure Analysis of Metabolic
- Page 257 and 258:
Running Time 4500 4000 3500 3000 25
- Page 259 and 260:
Substructure Analysis of Metabolic
- Page 261 and 262:
Substructure Analysis of Metabolic
- Page 263 and 264:
6 Conclusion Substructure Analysis
- Page 265 and 266:
Substructure Analysis of Metabolic
- Page 267 and 268:
266 J.Y. Chen, S. Taduri, and F. Ll
- Page 269 and 270:
268 J.Y. Chen, S. Taduri, and F. Ll
- Page 271 and 272:
270 J.Y. Chen, S. Taduri, and F. Ll
- Page 273 and 274:
272 J.Y. Chen, S. Taduri, and F. Ll
- Page 275 and 276:
274 J.Y. Chen, S. Taduri, and F. Ll
- Page 277 and 278:
276 J.Y. Chen, S. Taduri, and F. Ll
- Page 279 and 280:
278 J.Y. Chen, S. Taduri, and F. Ll
- Page 281 and 282:
Completing the Total Wellbeing Puzz
- Page 283 and 284:
Completing the Total Wellbeing Puzz
- Page 285 and 286:
Completing the Total Wellbeing Puzz
- Page 287 and 288:
Completing the Total Wellbeing Puzz
- Page 289 and 290:
Completing the Total Wellbeing Puzz
- Page 291 and 292:
Completing the Total Wellbeing Puzz
- Page 293 and 294:
Completing the Total Wellbeing Puzz
- Page 295 and 296:
296 M. Fernandez, M. Villasana, and
- Page 297 and 298:
298 M. Fernandez, M. Villasana, and
- Page 299 and 300:
300 M. Fernandez, M. Villasana, and
- Page 301 and 302:
302 M. Fernandez, M. Villasana, and
- Page 303 and 304:
304 M. Fernandez, M. Villasana, and
- Page 305 and 306:
306 M. Fernandez, M. Villasana, and
- Page 307 and 308:
308 M. Fernandez, M. Villasana, and
- Page 309 and 310:
310 M. Fernandez, M. Villasana, and
- Page 311 and 312:
312 M. Fernandez, M. Villasana, and
- Page 313 and 314:
314 M. Fernandez, M. Villasana, and
- Page 315 and 316:
Genetic Algorithm in Ab Initio Prot
- Page 317 and 318:
Genetic Algorithm in Ab Initio Prot
- Page 319 and 320:
Genetic Algorithm in Ab Initio Prot
- Page 321 and 322:
Genetic Algorithm in Ab Initio Prot
- Page 323 and 324:
Genetic Algorithm in Ab Initio Prot
- Page 325 and 326:
Genetic Algorithm in Ab Initio Prot
- Page 327 and 328:
Genetic Algorithm in Ab Initio Prot
- Page 329 and 330:
Genetic Algorithm in Ab Initio Prot
- Page 331 and 332:
Genetic Algorithm in Ab Initio Prot
- Page 333 and 334:
Genetic Algorithm in Ab Initio Prot
- Page 335 and 336:
Genetic Algorithm in Ab Initio Prot
- Page 337 and 338:
Genetic Algorithm in Ab Initio Prot
- Page 339 and 340:
Genetic Algorithm in Ab Initio Prot
- Page 341:
Author Index Apiletti, Daniele 169