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revision 1.47, Tue Feb 5 05:04:26 2008 UTC revision 1.49, Tue Sep 16 18:53:28 2008 UTC
# Line 121  Line 121 
121    
122  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.  Loads B<Genome>, B<HasContig>, B<Contig>, B<IsMadeUpOf>, and B<Sequence>.
123    
 =item Feature  
   
 Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,  
 B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,  
 B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,  
 B<CDD>, and B<IsPresentOnProteinOf>  
   
124  =item Subsystem  =item Subsystem
125    
126  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
127  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
128  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,  B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
129  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>, B<Diagram>,
130  B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>,  B<RoleOccursIn>, B<SubSystemClass>, B<RoleEC>, B<IsIdentifiedByEC>, and
131  B<ContainsFeature>.  B<ContainsFeature>.
132    
133  =item Annotation  =item Annotation
134    
135  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>,  Loads B<SproutUser>, B<UserAccess>, B<Annotation>, B<IsTargetOfAnnotation>, and
136  B<MadeAnnotation>.  B<MadeAnnotation>.
137    
138  =item Property  =item Property
139    
140  Loads B<Property>, B<HasProperty>.  Loads B<Property>, and B<HasProperty>.
   
 =item Group  
   
 Loads B<GenomeGroups>.  
141    
142  =item Source  =item Source
143    
144  Loads B<Source>, B<ComesFrom>, B<SourceURL>.  Loads B<Source>, B<ComesFrom>, and B<SourceURL>.
   
 =item External  
   
 Loads B<ExternalAliasOrg>, B<ExternalAliasFunc>.  
145    
146  =item Reaction  =item Reaction
147    
148  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
149  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>, B<Scenario>, B<IsInputFor>,
150    B<IsOutputOf>, B<IsOnDiagram>, and B<Catalyzes>.
151    
152  =item Synonym  =item Synonym
153    
# Line 175  Line 161 
161    
162  Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.  Loads B<PDB>, B<DocksWith>, C<IsProteinForFeature>, and C<Ligand>.
163    
164    =item Feature
165    
166    Loads B<Feature>, B<FeatureAlias>, B<FeatureTranslation>, B<FeatureUpstream>,
167    B<IsLocatedIn>, B<FeatureLink>, B<IsAliasOf>, B<CDD>, B<HasFeature>,
168    B<HasRoleInSubsystem>, B<FeatureEssential>, B<FeatureVirulent>, B<FeatureIEDB>,
169    B<CDD>, B<IsPresentOnProteinOf>, and B<Keyword>.
170    
171  =item *  =item *
172    
173  Loads all of the above tables.  Loads all of the above tables.
# Line 255  Line 248 
248    
249  # This is a list of the load groups in their natural order. We'll go through these in sequence, processing  # This is a list of the load groups in their natural order. We'll go through these in sequence, processing
250  # the ones the user asks for.  # the ones the user asks for.
251  my @LoadGroups = qw(Genome Feature Subsystem Property Annotation Source External Reaction Synonym Family Drug);  my @LoadGroups = qw(Genome Subsystem Property Annotation Source Reaction Synonym Family Drug Feature);
252    
253  # Get the command-line parameters and options.  # Get the command-line parameters and options.
254  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',  my ($options, @parameters) = StandardSetup(['SproutLoad', 'ERDBLoad', 'Stats',
# Line 267  Line 260 
260                                                loadOnly => [0, "load the database from previously generated files"],                                                loadOnly => [0, "load the database from previously generated files"],
261                                                resume => [0, "resume a complete load starting with the first group specified in the parameter list"],                                                resume => [0, "resume a complete load starting with the first group specified in the parameter list"],
262                                                phone => ["", "phone number (international format) to call when load finishes"],                                                phone => ["", "phone number (international format) to call when load finishes"],
263                                                  trace => [3, "trace level"],
264                                              },                                              },
265                                              "<group1> <group2> ...",                                              "<group1> <group2> ...",
266                                              @ARGV);                                              @ARGV);

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