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Metabolic Pathway Database, 38 Metabolic reconstruction systems, 37–45. See also WIT/WIT2 (What is there?) databases for, 44 30 1 NeuronDB, 106 Nigrostriatal neurons, 111 Nomenclature, in FlyBase, 146 Non-human homolog search, BioKleisli for, Minimization, of dispersion, 93f 208,209 Model-View-Controller (MVC) paradigm, Nonlinear alignment, in GDB, 90,9 1 f 257–258 Nucleic acids tools, in Biology Workbench, ModelDB, 106 243 Models, balancing of, 42 Module use, in biology Workbench, 236 Molecular biology Nucleotide sequences, in SRS, 221 abstraction levels in, 65f integrated research data for, 11–18 O Molecular catalogs, in KEGG, 71 Object class hierarchy, SENSELAB, 11 2 Molecular reactions, in KEGG, 71–72 Object dictionary approach, 107–108 Monotonic chain, longest, 90 Object identifiers, in LabBase, 283 Mouse Genome Database (MGD), 119–126. Object Management Group (OMG), 246 See also Edinburgh Mouse Atlas Object-protocol model, 187–199 beginnings of, 120–122 data management tools of, 190–191 current status of, 122–1 24 database query tools in, 192–194 future of, 126 database query tools in, applications of, web address for, 123f 196–197 Mouse Genome Informatics, 125–1 26 development of, 187–188 Multidatabase tools, in object-protocol model, 194 features of, 188–190 implementation issues in, 198 Multiple object instances, 109–110 multidatabase tools in, 194–196 Mutations, in HGMD, 99–103 multidatabase tools in, applications of, queries in, 190 _196 197–198 N retrofitting tools of, 191–196 Object references, in LabBase, 283 N-ary associations, 108–112 Object-relational mapping, 251 Nackus-Naur Form, 215 Object Request Broker (ORB), 247, 250f National Center for Biotechnology Informa- OdorDB, 106 tion (NCBI), 11–18 Olfactory receptor DB, 105 on ASN.l conversion, 13–14 OMIM (Online Mendelian Inheritance in on data interconnections, 11–12, 12f Man), 77–84 integrating database (ID) in, 16–1 8 allelic variants in, 80 scale-up efforts at, 18 allied resources in, 81–82 sequence identifiers in, 15–16 citations in, 80 sequence record types of, 14–15 clinical synopses in, 79–80 Navigation curation of, 83-84 in Edinburgh Mouse Atlas, 136–1 37 database growth of, 78f with KEGG, 72–73 edit history in, 80 of Mouse Genome Database (MGD), 123f entry identification in, 79 NCBI (National Center for Biotechnology external links in, 81 Information), 11–1 8. See also National future of, 84 Center for Biotechnology Information gene map in, 80 (NCBI) neighboring in, 81 Nervous system, heterogeneous data on, search in, 80–81 105–116. See also SENSELAB update log in, 81 Network comparison, with KEGG, 73 user comments in, 79 Network types, in KEGG data, 66-67 web address of, 77
302 Operands, in SRS, 216–217 in Agricultural Genome Information Sys- OPM, vs. BioKleisli, 210 tem (AGIS), 169–171 ORFs, in metabolic reconstruction, 39, 41 in BioKleisli, 207–208 Ortholog group tables, in KEGG, 70–71 in Biology Workbench, 239f Orthologous genes, in HOVERGEN, 31f in E. Coli Genetic Stock Center Database Orthology, definition of, 22–24 (CGSC), 177–180, 181f in European Bioinformatics Institute (EBI), 249 P in GDB, 86–87 in Genome Database (GDB), 86–87 Painting, in Edinburgh Mouse Atlas, 138 in HOVERGEN, 28–31 Paralogy, definition of, 22–24 in MaizeDB, 160, 161–162 Parsing, in SRS, 214–216 in object-protocol model, 190, 192–194 Paths of reasoning, computation of, 75 in OPM, 192–195 Pathway reconstruction, with KEGG, 73–74 Pathways in EcoCyc, 54 in model balancing, 42 in SRS, 216–218 Periodic computation, in MaizeDB, 157–158 Perl (Practical Extraction and Report Lan- R guage), 236 Reactions, in EcoCyc, 52 Phenome, in FlyBase, 148–149 Real-time computation, in MaizeDB, Phylogenetic trees, and protein multiple 156–157 alignment, 27 Record types, sequence, 14–15 Polymorphism, of protein-coding sequences Redundancy identification, of HOVERGEN, (CDS’s), 26, 27t 24–25 Program input and output, in Biology Work- Relational databases, 202 bench, 236 and CORBA, 251 Protein-2B, of human bone, 23 in KEGG, 69 Protein-coding sequences, in HOVERGEN, vs. ACEDB, 277 24–26 27t Remote Procedure Call (RPC), 247 Protein multiple alignment, and phyloge- Retrieval operations, in EcoCyc, 58 netic trees, 27 Retrofitting tools, in object-protocol model, Protein-role table, 38 191–196 Protein tools, in Biology Workbench, 243 Proteins, in EcoCyc, 52–54 Proteome, in FlyBase, 148–149 Rhamnose catabolism, 55f Protocol classes, 187, 190 Public access, to FlyBase, 145–146 S PubMed, 12 Scale-up efforts, at NCBI, 18 Put and get operations, in LabBase, 284 Schemaeditor, ofOPM, 191 Search, of elements, in KEGG network, 69 Segmented sets, 14 Q SENSELAB, 105–116 data management challenges in, 106–107 Quality control databases of, 105–106 at bioWidget consortium, 261 Entity-Attribute-Value(EAV) design in, in E. Coli Genetic Stock Center Database 113–116 (CGSC), 180, 182 hierarchical associations in, 112 Query(ies) N-ary associations in, 108–112 in Ace database (ACEDB) manager, object class hierarchy in, 112 272–273 object dictionary approach in, 107–108 Sequence identifiers, 15–16
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BIOINFORMATICS: Databases and Syste
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BIOINFORMATICS: Databases and Syste
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To Tish, Emily, Miles and Josephine
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TABLE OF CONTENTS INTRODUCTION ....
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INTRODUCTION Stanley Letovsky Bioin
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for wisdom. Where algorithms tend t
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gain performance by distributing qu
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systems described (OPM, BioKleisli,
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DATABASES
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1 NCBI: INTEGRATED DATA FOR MOLECUL
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figure 1, and all flows into the ID
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There are other sets of data that c
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2. Explicit declaration by the hist
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2. W. J. Wilbur, A retrieval system
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2 HOVERGEN: COMPARATIVE ANALYSIS OF
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Figure 1: Phylogenetic tree of the
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fragment. In some cases, a same gen
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Figure 2: Distribution of families
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the user can visualize all the anno
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Selecting orthologous genes with HO
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Thus, HOVERGEN allows one to do exh
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21. Saitou, N. Nei, M. The neighbor
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3 WIT/WIT2: METABOLIC RECONSTRUCTIO
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protein sequence are used (e.g., OR
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After we have accumulated an initia
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Coordinating the Development of Met
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Availability of the Pathways, Softw
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4 ECOCYC: THE RESOURCE AND THE LESS
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epresented as an instance of the cl
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The Gene--Reaction Schematic The ma
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EcoCyc contains extensive informati
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within compound windows uses a conc
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Figure 4: The EcoCyc linear map bro
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Figure 5: The software architecture
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6. Karp. Frame representation and r
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Introduction 5 KEGG: FROM GENES TO
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Binary relations Figure 1 : Level o
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hierarchical text. The genome map i
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(2) Java applets to search, compare
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can be used for gene function assig
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influenzae lacks the upper portion
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Future Directions Figure 4. KEGG as
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Introduction 6 OMIM: ONLINE MENDELI
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The Entry Each OMIM entry is assign
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Searching OMIM is as simple as typi
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How OMIM is Curated OMIM is maintai
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7 GDB: INTEGRATING GENOMIC MAPS Int
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in one of two ways: by being wholly
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Figure 3: Universal Coordinate Disp
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Figure 5: Dispersion of linear (lef
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which minimizes dispersion. The opt
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Figure 10: A piece of an "comprehen
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alignments are better for the speci
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Summary 8 HGMD: THE HUMAN GENE MUTA
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Data coverage and structure 101 By
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Conclusions and Outlook 103 Being b
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Introduction 9 SENSELAB: MODELING H
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107 For the purposes of the rest of
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109 users might advocate creating a
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111 The Associations table describe
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Managing the Object Class Hierarchy
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115 In fig. 2, the Objects and Clas
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117 7. Mirsky JS, Nadkarni PM, Hine
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10 THE MOUSE GENOME DATABASE AND TH
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genetics community fostered the ear
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123 Data acquisition for MGD includ
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125 In February 1998, a ‘cDNA and
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Acknowledgments 127 MGD is funded b
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11 THE EDINBURGH MOUSE ATLAS: BASIC
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expression database under developme
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133 For blastocysts the shape of th
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135 which is a cut at an arbitrary
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137 This defines a viewing directio
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139 plate spline [19] or polynomial
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12 FLYBASE: GENOMIC AND POST- GENOM
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143 Genes, including links via publ
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Public Access to FlyBase Data The c
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147 There are two classes of annota
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149 screens to identify direct or i
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13 MAIZEDB: THE MAIZE GENOME DATABA
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The bins map strategy has been empl
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Clicking on one of the orthologous
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* hyper-text linked to MaizeDB enti
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DISSEMINATION TO EXTERNAL DATABASES
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Appendix 2: part of the Query Form
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Introduction 14 AGIS: USING THE AGR
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Horn Fly--Haematobia Screwworm--Coc
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Figure 2 : Main AGIS Menu 167
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Figure 4 : Available Classes and Su
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Figure 6 : Query by Example and Que
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Figure 8 : Hypertext ACEDB Object a
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15 CGSC: THE E.COLI GENETIC STOCK C
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177 described once for that gene an
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FIGURE 1. A Query for an hsdR- recA
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FIGURE 2. A Query for a lacZ-(amber
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183 These are suggestions that dese
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SYSTEMS
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Introduction 16 OPM: OBJECT-PROTOCO
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189 OPM is a data model whose objec
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The OPM Database Development Tools
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ased on this query tree. Further qu
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195 Interface, except that one can
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197 Our strategy of providing suppo
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Acknowledgments 199 Between 1992 an
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Introduction 17 BIOKLEISLI:INTEGRAT
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203 In the remainder of this chapte
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pages : “4267-4274", abstract:
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BioKleisli in Action: Querying Biom
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209 savings in execution time is si
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References 211 13. NCBI ASN. 1 Spec
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Introduction 18 SRS: ANALYZING AND
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215 In SRS, databank structures are
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217 Operands also include named set
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Figure 1. The SRS Top Page. Figure
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Analyzing Data in SRS with Applicat
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223 other databanks, and define spe
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Figure 7. A SWISS-PROT entry with i
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Figure 8. The results of a query fo
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parser and documentation files, and
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23 1 12. Altschul, S.F., Gish, W.,
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Introduction 19 BIOLOGY WORKBENCH:
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Figure 1. Organization and Flow of
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237 In order to make wrapper develo
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the browser window containing a men
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either during the current Workbench
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PROFILESCAN Comparison of protein o
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20 EBI: CORBA AND THE EBI DATABASES
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247 the Object Request Broker (ORB)
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249 Every database entry is represe
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Page 262 and 263: Discussion 25 3 CORBA and IDL minim
Page 264 and 265: Introduction 21 BIOWIDGETS:REUSABLE
Page 266 and 267: Visualization Solutions 257 Turnkey
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Page 276 and 277: 267 On the other hand, most users c
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Page 288 and 289: Introduction 23 LABBASE: DATA AND W
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Page 292 and 293: LabBase Details 283 A LabBase objec
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Page 302 and 303: INDEX
Page 304 and 305: INDEX A of Agricultural Genome Info
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