tem (AGIS), 166f Abstraction level, in KEGG data, 64, 65f Accessions, gi s Vs, 15 16

Transcription

1 INDEX

2 INDEX A of Agricultural Genome Information Sysof biowidgets, tem (AGIS), 166f Abstraction level, in KEGG data, 64, 65f Accessions, gi s Vs, of Human Gene Mutation Database Ace database (ACEDB) language (HGMD),101 in Agricultural GenomeInformation System (AGIS), 165, , 173f ASCII, 213 of OPM multidatabase tools, 194f vs. biowidgets, 257 ASN. I (Abstract Syntax Notation) conver- Ace database (ACEDB) manager, sion, availability of, 277 and BioKleisli, 205, 207, 208 client server of, Asserted-diagrams table, 39 definition language of, Assignment, in conceptual translations, file format of, history of, performance of, portability of, query language of, vs. other databases, web address of, 277 Associations, multi-axial, Atlas spatial coordinates, in Edinburgh Mouse Atlas, B web interface of, Administration, of SRS, Balancing the model, 42 Agricultural Genome Information System Berkeley Drosophila Genome Project (AGIS), (BDGP), architecture of, 166f Best hit, in metabolic reconstruction, 39 browse mode in, 168 Bidirectional best hit, in metabolic recondatabase links in, 168f struction, 39 databases of, 164t 165t Binary relations future of, 173 in KEGG data, 65, 75 implementation of, object dictionary approach for, main menu of, 167f Bins map strategy, 153 query mode in, Biocatalysis/biodegradation database, 44 table maker mode in, Biochemical pathways, See also web address of, 163 Kyoto Encyclopedia of Genes and Alignment tools, in Biology Workbench, Genomes (KEGG) data organization of, 70 Amino acid sequences, in SRS, 221 Bioinformatics Analysis modules, in Biology Workbench, challenges in, definition of, 2-3 Analysis packages, and biomedical data inte- technology development history of, 1 2 gration, See also BioKleisli BioKleisli, Analysis tools, in Biology Workbench, biomedical queries in, collection programming language (CPL) Annotation, in biowidget displays, 147 in, Annotation classes, in FlyBase, 147 complex type model in, Applets, 256 and CORBA, 210 Application parameters, in SRS, 221, 222f GBD query in, Application programs, in LIMS, as generic driver, Architecture non-human homologsearchin, 208, 209

3 296 as uniform language, 202 vs. OPM, 210 Biology Workbench, analysis modules in, BW.cgi environment in, databases in, 237, HTML environment in, module use in, 236 program input and output in, 236 queries in, 239f rationale for, sessions in, 237 subroutines in, system overview in, CGSC (E. Coli Genetic Stock Center Database), See also E. Coli Genetic Stock Center Database (CGSC) Chemical compounds, in KEGG, 71 Chromosome,canonical, Citrate cycle, 72f Class hierarchy, in EcoCyc data base, 48 _ 49 Classification, of HOVERGEN, Collection programming language (CPL), in BioKleisli, Common Lisp Interface Manager (CLIM), Comparative analysis, of vertebrate genes, tools in, web address of, 234 Complex type model, BioKleisli as, Biomedical data, and analysis packages, Components, in LIMS, See also BioKleisli Compounds, in EcoCyc, Biomedical queries, in BioKleisli, Comprehensive map, 94, 95f, 96f Bioseq sets, Conceptual data model, 249 BioTk, 256 Conceptual translations, BioWidgets, CORBA (Common Request Broker Archi- architecture of, tecture) BioTk in, 256 and BioKleisli, 210 consortium of, 261 in biowidgets, 258 future work of, CORBA prototypes in, 252 genome annotation in, CORBA wrappers in, Java in, 256 and EBI database, (See also users of, European Bioinformatics Institute visualization solutions in, 257 (EBI)) BLAST,23, 144, 207, 221, 223, 238, 256, and IDL interface, in OPM, 198 BMP gene, phylogenetic tree of, 23f in SRS, Boehringer Manheim Biochemical Path- Curation, of data. See Data curation ways, 44 CUSTALW, BRITE, 75 Cystic fibrosis, 82f Browse mode, in Agricultural Genome Infor- mation System (AGIS), 168 BW.cgi environment, D D. Melanogaster, 141 C Data, heterogeneous, See also SENSELAB C-API, 216,218 Data access C ++ programming language, in OPM, 198 in FlyBase, Canonical chromosome, in Human Gene Mutation Database Central repository, of bio Widget consortium, (HGMD), in SRS, 214 CGI (common gateway interface) script Data analysis in Biology Workbench, in Biology Workbench, , in KEGG, and biomedical integration, (See in OPM, 198 also BioKleisli) in SRS, 221

4 297 of vertebrate genes, development lessons in, CGSC in, Data coordination in FlyBase, 144 of MaizeDB, in WIT/WIT2 (What is there?), 43 Database directory and schema library, 191 Data curation Database links of E. Coli Genetic Stock Center Database of Agricultural Genome Information Sysof CGSC, 177 (CGSC),180, 182 tem (AGIS), 168f in FlyBase, 143 in Maize DB, of FlyBase, 144 in OMIM (Online Mendelian Inheritance of MaizeDB, in Man), of National Center for Biotechnology Information (NCBI), 11 12, 12f Data extensions, in Edinburgh Mouse Atlas, 139 ofomom, 81 Data formats of SRS, 220 ASN.l in, Database management incompatibility of, 234, 245 LabBase in, (See also LabBase) tag-value format in, 13 Object Management Group (OMG) in, 246 Data interconnections. See also Database object-protocol model tools for, links in SENSELAB, National Center for Biotechnology Infor- sequence management tools in, of Biolmation (NCBI) on, 11 12, 12f ogy Workbench, 242 Data management. See Database manage- of SRS, ment Database management, in KEGG, Data management tools, object-protocol DBGET/LinkDB system in, 67 _ 68 model as, See also Objectprotocol model relational database system in, 69 KEGG system in, Data model, conceptual, 249 Database query software, of HOVERGEN, Data organization. See also Database struc ture Database query tools, in object-protocol in EcoCyc, model, 192 _ 194 in KEGG, Database structure Data representation, in KEGG, of Agricultural Genome Information Sysof biowidgets, abstraction level in, 64, 65f tem (AGIS), 166f binary relations in, 65 network types in, of Edinburgh Mouse Atlas, 131 Data structure of Human Gene Mutation Database of Agricultural Genome Information Sys- (HGMD), 101 tem (AGIS), 166f of OPM multidatabase tools, 194f of biowidgets, Databases of Human Gene Mutation Database in Biology Workbench, 237, (HGMD), 101 organization of, 59 of OPM multidatabase tools, 194f DBGETLinkDBsystem,67 68 Data submission, in Edinburgh Mouse Atlas, Dehydrogenase, Derivation rules, of object-protocol model, Data treatment, of HOVERGEN, Data views Diagram-role table, 38 in Edinburgh Mouse Atlas, Dispersion measurement, in GDB, inflybase, Distributed structure, in FlyBase, 142 in SRS, Domain Tack Forces (DTF), 253 table view in, Drosophilidae, data base for, See DATABANKS, 225, 228f also FlyBase Database design. See also Database structure

5 298 E European Bioinformatics Institute (EBI), E. coli conceptual data model in, 249 database website for, 44 CORBA interface in, EcoCyc data base of, (See also Eco- CORBA prototypes in, 252 Cyc) CORBA wrappers in, E. Coli Genetic Stock Center Database generic approach in, 249 (CGSC), queries in, 249 curation in, 180, 182 strategy of, 246 developmentof, European Drosophila Genome Project features of, (EDGP), lessons learned from, European Molecular Biology Laboratory quality control in, 180, 182 (EMBL), 213 query examples in, , 18 1 f Expressed sequence tag (EST), 15 reusable parts of, 177 External use, vs. internal use, web address of, 175 EcoCyc, compounds in, F data of, 4748 data organization of, FASTA, 23,223,238,260 gene-reaction schematic in, 51,52f Federation, vs. warehousing, 4 5 genes of, 50 Fetch-and-store -interface, 284 genomic-map displays in, Flat files, graphical user interface of, 48 FlyBase, lessons learned from, metabolic-map overview in, pathways in, 54 proteins in, reactions in, 52 retrieval operations in, 58 software architecture and distribution in, annotation classes in, 147 consolidated data bases of, data coordination within, 144 data curation in, 143 data responsibility subdivisions in, 142 data views in, database links in, external, hyperlinks in, 148 web address of, 44 literature database in, , 144 Edinburgh Mouse Atlas, public access to, atlas spatial coordinates in, sequence representations in, atlas temporal coordinates in, server update schedule in, 146 data extensions in, 139 Forced parsing, data submission in, Formats, data database structure in, 13 1 ASN.1 in, navigation in, incompatibility of, 234, 245 overview of, tag-value format in, 13 painting in, 138 Frame knowledge representation system viewing coordinates in, (FRS), 4849 voxel model in, 13 1 Function diagrams, for metabolism reprewarping in, sentation, 38 Element search, in KEGG network, 69 EMBL, homology information of, Entity-Attribute-Value (EAV), in SENSE- LAB, ENTREZ, vs. HOVERGEN, 32 Enzymatic reactions, in KEGG, 71 Eshcerichia coli. See E. Coli Eulerian angles, G GAIA system, GBD query, in BioKleisli, GDB (Genome Database), See also Genome Database (GDB)

6 299 GenBank database query software of, homology information of, and databases, other, 32 sequence identifiers in, 15 growth rate of, 28f Gene catalogs, in KEGG, 70 limitations of, Gene Expression Database (GXD), perspectives of, 33 Genera software, 177, 182 scope and content of, 24 Genes. See also specific types, e.g., BMP sequence selection of, gene sequence type definitions of, in biochemical pathways, ( See also similarity search of, Kyoto Encyclopedia of Genes and HTML, in Biology Workbench, Genomes (KEGG)) Human bone protein-2b (BMP2B), 23 symbols for, in HGMD, Human Gene Mutation Database (HGMD), Genetics, OMIM in, Genome, annotation of, Genome Database (GDB), dispersion measurement in, linear alignment in, map display in, 94 95, 96f map integration in, map query in, nonlinear alignment in, 90, 91f OPM tools for, 196 data access in, 102 data coverage and structure in, 101 outlook for, 103 utility of, web address of, 99 Hyperlinks. See also Links, database in FlyBase, 148 in SRS, 220 Hypertext navigation, 58 Hypertext objects, in Agricultural Genome Information System (AGIS), 173 Genome maps, in KEGG, 70 Genome project, NCBI scale-up efforts for, 18 GenomeNet, 64t, 68t Genomic-map displays, in EcoCyc, I Gi s Vs accessions, GKB Editor, 50 Icarus, Grammars, 215 Identifiers Graphical interface, of HOVERGEN, in LabBase, 283 Graphical user interface in metabolic reconstruction system, 38 of biowidgets, of National Center for Biotechnology Inof sequence, of EcoCyc, 48 formation (NCBI), 13 Grasper-CL, 58f, 59 Implementation issues, in object-protocol model, 198 H Indexing, in SRS, Integrated data, for molecular biology re- H. influenzae, in EcoCyc data base, 48 search, H. pylori, in EcoCyc data base, 48 Integrating database (ID), of NCBI, Heterogeneous textual databanks, 192, Interfaces See also Sequence Retrieval of Biology Workbench, 234 System (SRS) of biowidgets, Hierarchical associations, Common Lisp Interface Manager (CLIM) Homologous sequences, of vertebrate genes, as, CORBA as, Homology, definition of, of EcoCyc, 48 HOVERGEN, of HOVERGEN, application examples of, 32 IDL as, availability of, 33 Java as, 258 classification of, of KEGG, data treatment of, of LabBase, 284

7 300 of OPM, , 198 of SRS, Interpretation free, 13 1 ISMAP graphics, 173 J LabFlow execution engine in, LabFlow management system in, protocols in, Launching, in SRS, 221, 222f Linear alignment, in GDB, Linear map browser, in EcoCyc, 57f Linking, in SRS, , 220 Links, database of Agricultural Genome Information System (AGIS), 168f Japanese GenomeNet Service, 64t DBGET/Link in, 68t Java, 256, of CGSC, 177 JavaBeans TM, 259 of FlyBase, 144 of MaizeDB, of National Center for Biotechnology Inof OMIM, 81 K formation (NCBI), 11 12, 12f KEGG (Kyoto Encyclopedia of Genes and of SRS, 220 Genomes), See also Kyoto En- Locuslite query, MaizeDB, cyclopedia of Genes and Genomes Longest monotonic chain, 90 (KEGG) Knowledge acquisition problem, Kyoto Encyclopedia of Genes and Genomes M (KEGG), abstraction level in, 64,65f Main menu, of Agricultural Genome Inforbinary relations in, 65 mation System (AGIS), 167f data organization in, MaizeDB, data representation in, data content of, database management systems in, data entry in, future directions in, database design of, navigation with, database links in, external, network comparison with, 73 future directions in, 159 network types in, locuslite query in, objectives of, periodic computation in, pathway reconstruction with, from binary real-timecomputation in, relations, 74 short locus query form in, 160 pathway reconstruction with, references web address of, 44, 152 in, Management, of database web addresses for, 64t Object Management Group (OMG) in, 246 object-protocol model tools for, in SENSELAB, sequence management tools in, of Biol- L ogy Workbench, 242 SRS in, LabBase, management system of, object typing in, 283 protocols for, put and get operations in, 284 LabFlow, 284,285f, Laboratory information management system (LIMS) LabBase management system in, LabBase objects in, Map browser, linear, in EcoCyc, 57f Map display, in GDB, 94 95, 96f Map integration, in GDB, Map query, in GDB, Map strategy, bins, 153 Mapping, object-relational, 25 1 MEDLINE, 12 Mendelian Inheritance in Man, 77 Message definition, asn.all in, Metabolic-map, of EcoCyc, 55 56

8 30 1 Metabolic Pathway Database, 38 Metabolic reconstruction systems, See also WIT/WIT2 (What is there?) databases for, 44 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 Nucleic acids tools, in Biology Workbench, ModelDB, Models, balancing of, 42 Nucleotide sequences, in SRS, 221 Module use, in biology Workbench, 236 Molecular biology abstraction levels in, 65f integrated research data for, Molecular catalogs, in KEGG, 71 Molecular reactions, in KEGG, Monotonic chain, longest, 90 Mouse Genome Database (MGD), See also Edinburgh Mouse Atlas beginnings of, current status of, future of, 126 web address for, 123f Mouse Genome Informatics, Multidatabase tools, in object-protocol model, 194 _ 196 Multiple object instances, Mutations, in HGMD, O Object class hierarchy, SENSELAB, 11 2 Object dictionary approach, Object identifiers, in LabBase, 283 Object Management Group (OMG), 246 Object-protocol model, data management tools of, database query tools in, database query tools in, applications of, development of, features of, implementation issues in, 198 multidatabase tools in, multidatabase tools in, applications of, queries in, 190 N retrofitting tools of, Object references, in LabBase, 283 N-ary associations, Object-relational mapping, 251 Nackus-Naur Form, 215 Object Request Broker (ORB), 247, 250f National Center for Biotechnology Informa- OdorDB, 106 tion (NCBI), Olfactory receptor DB, 105 on ASN.l conversion, OMIM (Online Mendelian Inheritance in on data interconnections, 11 12, 12f Man), integrating database (ID) in, allelic variants in, 80 scale-up efforts at, 18 allied resources in, sequence identifiers in, citations in, 80 sequence record types of, clinical synopses in, Navigation curation of, in Edinburgh Mouse Atlas, with KEGG, of Mouse Genome Database (MGD), 123f NCBI (National Center for Biotechnology Information), See also National Center for Biotechnology Information gene map in, 80 (NCBI) neighboring in, 81 Nervous system, heterogeneous data on, See also SENSELAB Network comparison, with KEGG, 73 Network types, in KEGG data, database growth of, 78f edit history in, 80 entry identification in, 79 external links in, 81 future of, 84 search in, update log in, 81 user comments in, 79 web address of, 77

9 302 Operands, in SRS, in Agricultural Genome Information Sys- OPM, vs. BioKleisli, 210 tem (AGIS), ORFs, in metabolic reconstruction, 39, 41 in BioKleisli, Ortholog group tables, in KEGG, in Biology Workbench, 239f Orthologous genes, in HOVERGEN, 31f in E. Coli Genetic Stock Center Database Orthology, definition of, (CGSC), , 181f in European Bioinformatics Institute (EBI), 249 P in GDB, in Genome Database (GDB), Painting, in Edinburgh Mouse Atlas, 138 in HOVERGEN, Paralogy,definition of, in MaizeDB, 160, Parsing, in SRS, in object-protocol model, 190, Paths of reasoning, computation of, 75 in OPM, Pathway reconstruction, with KEGG, in SRS, Pathways in EcoCyc, 54 in model balancing, 42 Periodiccomputation, in MaizeDB, R Perl (Practical Extraction and Report Language), 236 Reactions, in EcoCyc, 52 Phenome, in FlyBase, Real-time computation, in MaizeDB, Phylogenetic trees, and protein multiple alignment, 27 Record types, sequence, Polymorphism, of protein-coding sequences Redundancy identification, of HOVERGEN, (CDS s), 26, 27t Programinputandoutput, in BiologyWork- Relational databases, 202 bench, 236 and CORBA, 251 Protein-2B, of human bone, 23 in KEGG, 69 Protein-coding sequences, in HOVERGEN, vs. ACEDB, t 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, Protein tools, in Biology Workbench, 243 Rhamnose catabolism, 55f Proteins, in EcoCyc, Proteome, in FlyBase, Protocol classes, 187, 190 S Public access, to FlyBase, PubMed, 12 Put and get operations, in LabBase, 284 Scale-up efforts, at NCBI, 18 Schemaeditor, ofopm, 191 Search, of elements, in KEGG network, 69 Segmented sets, 14 Q SENSELAB, data management challenges in, Quality control databases of, at biowidget consortium, 261 Entity-Attribute-Value(EAV) design in, in E. Coli Genetic Stock Center Database (CGSC), 180, 182 hierarchical associations in, 112 Query(ies) N-ary associations in, in Ace database (ACEDB) manager, object class hierarchy in, object dictionary approach in, Sequence identifiers, 15 16

10 303 conversion to gi identifiers in, Sequence management tools, in Biology Workbench, 242 Sequence record types, Sequence representations, in FlyBase, T Sequence retrieval, in HOVERGEN, 28 Sequence Retrieval System (SRS), 192, administration of, application parameters in, 221,222f application results in, processing of, application results in, viewing of, core features of, 214 data analysis in, 221 DATABANKS featureof, 225, 228f development history of, 213 future works of, indexing in, interfaces of, 218 launching in, 221,222f U linking in, parsing in, querying in, UNIX, 234 servers of, 229 user functionality of, ,228f web interface of, Sequence selection, of HOVERGEN, Serls, D., 256 Servers, of SRS, 229 Servers, updates of in BioKleisli, 207 in CGSC database, 176 Table maker mode, in Agricultural Genome Information System (AGIS), Table view, Tag-value format, 13 TCA cycle, 72f, 73 Temporal coordinates, in Edinburgh Mouse Atlas, Theiler stages, 134 Time scales, 133 Token list, Tracking, in conceptual translations, 1617 Type constructors, in LabBase, 283 Universal coordinate system, Updates, of servers in FlyBase, 146 inomim,81 in SRS, 225 User functionality, of SRS, , 228f in FlyBase, 146 V in OMIM, 81 in SRS, 225 Vertebrate genes, comparative analysis of, Short locus query form, in MaizeDB, Similarity search, of HOVERGEN, View, in SRS, Similarity search programs, 23 Viewing coordinates, in Edinburgh Mouse Site mirrors, Atlas, Visualization components, Visualization tools, of EcoCyc, 50 Voxel model, 13 1 Software architecture, in EcoCyc, SoyBase, 44 Spatial coordinates, in Edinburgh Mouse Atlas, Stanford RH map, 88f Star schema, Storage capacity, of ACEDB, 277 Strainquery, in CGSC, , 181f Subroutines, in Biology Workbench, Warehousing, vs. federation, 4 5 Warping,in Edinburgh Mouse Atlas, Substrates, in model balancing, 42 Web address(es) Swiss Protein Data Bank, in metabolic recon- of ace database (ACEDB) manager, 277 struction systems, 38 of Agricultural Genome Information Sys- Sybase, 280 tem (AGIS), 163 W

11 304 of Biology Workbench, 234