Databases and Systems

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