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The Gene--Reaction Schematic The many-to-many relationships among genes, enzymes, and reactions can be complex. An enzyme composed of several subunits might catalyze more than one reaction, and a given reaction might be catalyzed by multiple enzymes. The Gene— Reaction Schematic depicts the relationships among a set of genes, enzymes, and reactions (see Figure 2). It is generated by starting with the object that is the focus of the current window (which is highlighted in the schematic), and then recursively traversing KB relationships from that object to related objects, such as from a gene to its product, or from a reaction to the enzyme(s) that catalyzes it. The schematic summarizes these complex relationships succinctly, and also constitutes a navigational aid—the user can click on an object in the schematic to cause EcoCyc to display that object. The first schematic in Figure 2 means that the trpA gene encodes a polypeptide (the circle to the left of the box for the trpA gene) that forms a heterotetramer (the next circle to the left —the 2 indicates two copies) that also contains two copies of the product of the trpB gene. That complex in turn catalyzes reaction 4.2.1.20. The second schematic (reading down the column) depicts three isozymes (two homodimers and a homotetramer) that catalyze reaction 4.2.1.2. The third schematic depicts a bifunctional polypeptide, and the fourth schematic depicts a case where a homodimer of the TrpD polypeptide catalyzes one reaction, and a heterotetramer of TrpD and TrpE catalyzes a second reaction. The fourth schematic depicts two isozymes that each are heterotetramers. The fifth schematic depicts the ATP synthase protein, which consists of a large complex containing two subcomplexes. Schematics also include modified forms of a protein (or tRNA) when relevant. For example, the schematic for the acyl carrier protein shows both a yellow circle for the unmodified form of the protein, and 13 orange circles, which represent different modified forms of the protein. 51
52 Figure 2: A set of gene--reaction schematics. Some of the reactions in the largest schematic have no assigned EC number. The boxes to the left represent reactions, the boxes on the right represent genes, and the circles in the middle represent proteins. The lines indicate relationships among these objects. The schematic is drawn in gene windows, reaction windows, and protein windows. Reactions The reactions within EcoCyc were gathered from biomedical literature on E.coli. In addition, we incorporated many non-E. coli reactions and 269 reaction classes that constitute the enzyme classification system [21] from the ENZYME DB [l]. EcoCyc therefore contains many reactions not found in E.coli, for reference purposes. EcoCyc reaction windows state whether or not we have evidence that a given reaction occurs in E.coli. The reaction display window shows the class(es) containing the reaction within the classification of reactions. It shows the one or more enzymes that catalyze the reaction, the gene(s) that code for the enzymes, and the pathway that contains the reaction. The display shows the EC number for the reaction, and the reaction equation. Note that there exists a one-to-one mapping between EC numbers and reactions, but not between EC numbers and enzymes [11], therefore, we label reactions, and not enzymes, with the EC number. The standard change in Gibbs free energy of the reaction is listed when known. Proteins
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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 ....
Page 10 and 11: INTRODUCTION Stanley Letovsky Bioin
Page 12 and 13: for wisdom. Where algorithms tend t
Page 14 and 15: gain performance by distributing qu
Page 16 and 17: systems described (OPM, BioKleisli,
Page 18 and 19: DATABASES
Page 20 and 21: 1 NCBI: INTEGRATED DATA FOR MOLECUL
Page 22 and 23: figure 1, and all flows into the ID
Page 24 and 25: There are other sets of data that c
Page 26 and 27: 2. Explicit declaration by the hist
Page 28 and 29: 2. W. J. Wilbur, A retrieval system
Page 30 and 31: 2 HOVERGEN: COMPARATIVE ANALYSIS OF
Page 32 and 33: Figure 1: Phylogenetic tree of the
Page 34 and 35: fragment. In some cases, a same gen
Page 36 and 37: Figure 2: Distribution of families
Page 38 and 39: the user can visualize all the anno
Page 40 and 41: Selecting orthologous genes with HO
Page 42 and 43: Thus, HOVERGEN allows one to do exh
Page 44 and 45: 21. Saitou, N. Nei, M. The neighbor
Page 46 and 47: 3 WIT/WIT2: METABOLIC RECONSTRUCTIO
Page 48 and 49: protein sequence are used (e.g., OR
Page 50 and 51: After we have accumulated an initia
Page 52 and 53: Coordinating the Development of Met
Page 54 and 55: Availability of the Pathways, Softw
Page 56 and 57: 4 ECOCYC: THE RESOURCE AND THE LESS
Page 58 and 59: epresented as an instance of the cl
Page 62 and 63: EcoCyc contains extensive informati
Page 64 and 65: within compound windows uses a conc
Page 66 and 67: Figure 4: The EcoCyc linear map bro
Page 68 and 69: Figure 5: The software architecture
Page 70 and 71: 6. Karp. Frame representation and r
Page 72 and 73: Introduction 5 KEGG: FROM GENES TO
Page 74 and 75: Binary relations Figure 1 : Level o
Page 76 and 77: hierarchical text. The genome map i
Page 78 and 79: (2) Java applets to search, compare
Page 80 and 81: can be used for gene function assig
Page 82 and 83: influenzae lacks the upper portion
Page 84 and 85: Future Directions Figure 4. KEGG as
Page 86 and 87: Introduction 6 OMIM: ONLINE MENDELI
Page 88 and 89: The Entry Each OMIM entry is assign
Page 90 and 91: Searching OMIM is as simple as typi
Page 92 and 93: How OMIM is Curated OMIM is maintai
Page 94 and 95: 7 GDB: INTEGRATING GENOMIC MAPS Int
Page 96 and 97: in one of two ways: by being wholly
Page 98 and 99: Figure 3: Universal Coordinate Disp
Page 100 and 101: Figure 5: Dispersion of linear (lef
Page 102 and 103: which minimizes dispersion. The opt
Page 104 and 105: Figure 10: A piece of an "comprehen
Page 106 and 107: alignments are better for the speci
Page 108 and 109: 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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251 Wrappers with and without State
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Discussion 25 3 CORBA and IDL minim
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Introduction 21 BIOWIDGETS:REUSABLE
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Visualization Solutions 257 Turnkey
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259 The architecture also exploits
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possible because the bioWidget arch
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263 4. Gish, Warren (1994-1997). un
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22 ACEDB: THE ACE DATABASE MANAGER
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267 On the other hand, most users c
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269 Street, City and State into "ma
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27 1 to a running database after ed
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273 database the class Map refers t
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275 were waiting for the Biowidget
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277 table of 13 columns and 1 milli
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Introduction 23 LABBASE: DATA AND W
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28 1 We will use as a running examp
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LabBase Details 283 A LabBase objec
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When the procedure completes, LabFl
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287 sequence-assembly Worker in our
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289 The Worker converts the object
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291 Genome Research and are beginni
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INDEX
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INDEX A of Agricultural Genome Info
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of vertebrate genes, 21-33 developm
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GenBank database query software of,
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Metabolic Pathway Database, 38 Meta
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conversion to ‘gi’ identifiers
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