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Figure 7. A SWISS-PROT entry with its sequence shown by a Java applet as a hydropathicity plot. The applet can be controlled to display other amino acid properties or to show the curve with a larger scale. 225 Since a single root entry may be linked to many leaf entries it is sometimes useful to have only the number of linked entries displayed. The SRSWWW server shows this number as a hypertext link that when clicked retrieves the list of leaf entries. The number is of value itself and can be used for statistics. For instance, using an example of a link from the TAXONOMY [16] databank to GENBANK one could obtain a table of taxa together with the number of GENBANK entries that exist for all organisms each taxon represents. SRS World Wide: The Databank of DATABANKS Locating an appropriate server is only the first problem users face when exploring new databases, since there are as many different query interfaces as there are databanks. Documentation relating to the databanks and manuals describing the interfaces vary greatly in content and form, and are often not easily obtained. In this section we focus on a newly added component within SRS version 5.1 [ 17] which generates DATAB ANKS, a database of databanks, by traversing public SRS servers around the world. In SRS, the documentation for each databank can be viewed as the respective ‘databank information page’ via the SRSWWW interface. The databank information page has a standardized layout for easy reference and also includes server status data on indexing of the respective databank. Both the parser and the databank documentation files can be requested from SRS for reuse at other sites. By pooling the knowledge gathered at these worldwide sites, SRS now provides both a unified method for direct access to around 250 different databases and a standard framework for their documentation. Automated nightly compilation of the data guarantees that the overview is up to date. The documentation collected in DATABANKS is written by the community of SRS server administrators. In a collaborative effort, it is regularly updated and extended in a distributed manner.
226 New Functionality for the User DATABANKS gives the user a single uniform entry point for browsing or searching particular databanks, and optionally leads directly to the respective databank query forms. DATABANKS is typically searched by databank name or description. More generally, any fields of the databank information pages as well as site and server characteristics can be used in a query. The results of such a search show all the databanks that matched the search request and at which sites they are available. For convenience, the list of results offers direct links to their remote SRS query forms. For example, figure 8 shows the result of a request for databanks named ‘ENZYME’. As in most cases, more than one server maintains a copy of the databank, and the list shows alternative sites. The number of indexed entries and the release number (where assigned by the server maintainers) help in choosing a nearby site with a current version of the databank. When searching for a particular database, it often helps to first restrict the search to a subset of DATABANKS which includes only one site from each group of alternatives. Currently, this representative site is chosen as the site with the most extensive databank information page.
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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
Page 184 and 185: 15 CGSC: THE E.COLI GENETIC STOCK C
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Page 188 and 189: FIGURE 1. A Query for an hsdR- recA
Page 190 and 191: FIGURE 2. A Query for a lacZ-(amber
Page 192 and 193: 183 These are suggestions that dese
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Page 196 and 197: Introduction 16 OPM: OBJECT-PROTOCO
Page 198 and 199: 189 OPM is a data model whose objec
Page 200 and 201: The OPM Database Development Tools
Page 202 and 203: ased on this query tree. Further qu
Page 204 and 205: 195 Interface, except that one can
Page 206 and 207: 197 Our strategy of providing suppo
Page 208 and 209: Acknowledgments 199 Between 1992 an
Page 210 and 211: Introduction 17 BIOKLEISLI:INTEGRAT
Page 212 and 213: 203 In the remainder of this chapte
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Page 216 and 217: BioKleisli in Action: Querying Biom
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Page 220 and 221: References 211 13. NCBI ASN. 1 Spec
Page 222 and 223: Introduction 18 SRS: ANALYZING AND
Page 224 and 225: 215 In SRS, databank structures are
Page 226 and 227: 217 Operands also include named set
Page 228 and 229: Figure 1. The SRS Top Page. Figure
Page 230 and 231: Analyzing Data in SRS with Applicat
Page 232 and 233: 223 other databanks, and define spe
Page 236 and 237: Figure 8. The results of a query fo
Page 238 and 239: parser and documentation files, and
Page 240 and 241: 23 1 12. Altschul, S.F., Gish, W.,
Page 242 and 243: Introduction 19 BIOLOGY WORKBENCH:
Page 244 and 245: Figure 1. Organization and Flow of
Page 246 and 247: 237 In order to make wrapper develo
Page 248 and 249: the browser window containing a men
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Page 252 and 253: PROFILESCAN Comparison of protein o
Page 254 and 255: 20 EBI: CORBA AND THE EBI DATABASES
Page 256 and 257: 247 the Object Request Broker (ORB)
Page 258 and 259: 249 Every database entry is represe
Page 260 and 261: 251 Wrappers with and without State
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
Page 268 and 269: 259 The architecture also exploits
Page 270 and 271: possible because the bioWidget arch
Page 272 and 273: 263 4. Gish, Warren (1994-1997). un
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Page 276 and 277: 267 On the other hand, most users c
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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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