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revision 1.14, Wed Sep 14 12:10:08 2005 UTC revision 1.15, Wed Oct 12 03:14:27 2005 UTC
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168                      that are encoded as EC numbers.</Notes>                      that are encoded as EC numbers.</Notes>
169                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
170                  </Field>                  </Field>
171                    <Field name="abbr" type="name-string">
172                        <Notes>Abbreviated name for the role, generally non-unique, but useful
173                        in column headings for HTML tables.</Notes>
174                    </Field>
175              </Fields>              </Fields>
176          </Entity>          </Entity>
177          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
# Line 185  Line 189 
189                  </Field>                  </Field>
190              </Fields>              </Fields>
191          </Entity>          </Entity>
192            <Entity name="Reaction" keyType="key-string">
193                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
194                is generally a small number preceded by a letter.</Notes>
195                <Fields>
196                    <Field name="url" type="string" relation="ReactionURL">
197                        <Notes>HTML string containing a link to a web location that describes the
198                        reaction. This field is optional.</Notes>
199                    </Field>
200                    <Field name="rev" type="boolean">
201                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
202                    </Field>
203                </Fields>
204            </Entity>
205            <Entity name="Compound" keyType="name-string">
206                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
207                All compounds have a unique ID and may also have one or more names.</Notes>
208                <Fields>
209                    <Field name="name-priority" type="int" relation="CompoundName">
210                        <Notes>Priority of a compound name. The name with the loweset
211                        priority is the main name of this compound.</Notes>
212                    </Field>
213                    <Field name="name" type="name-string" relation="CompoundName">
214                        <Notes>Descriptive name for the compound. A compound may
215                        have several names.</Notes>
216                    </Field>
217                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
218                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
219                    </Field>
220                </Fields>
221                <Indexes>
222                    <Index>
223                        <Notes>This index allows the user to find the compound corresponding to
224                        the specified name.</Notes>
225                        <IndexFields>
226                            <IndexField name="name" order="ascending" />
227                        </IndexFields>
228                    </Index>
229                    <Index>
230                        <Notes>This index allows the user to access the compound names in
231                        priority order.</Notes>
232                        <IndexFields>
233                            <IndexField name="id" order="ascending" />
234                            <IndexField name="name-priority" order="ascending" />
235                        </IndexFields>
236                    </Index>
237                </Indexes>
238            </Entity>
239          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
240              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
241              is an important tool for recognizing parallel genetic features in different organisms.</Notes>              is an important tool for recognizing parallel genetic features in different organisms.</Notes>
242                <Fields>
243                    <Field name="curator" type="string">
244                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
245                    </Field>
246                    <Field name="notes" type="text">
247                        <Notes>Descriptive notes about the subsystem.</Notes>
248                    </Field>
249                </Fields>
250            </Entity>
251            <Entity name="RoleSubset" keyType="string">
252                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
253                subset names are generally very short, non-unique strings. The ID of the parent
254                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
255            </Entity>
256            <Entity name="GenomeSubset" keyType="string">
257                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
258                in a particular subsystem. The subset names are generally very short, non-unique
259                strings. The ID of the parent subsystem is prefixed to the subset ID in order
260                to make it unique.</Notes>
261          </Entity>          </Entity>
262          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="medium-string">
263              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
# Line 398  Line 468 
468              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
469              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
470              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
471                <Fields>
472                    <Field name="variant-code" type="key-string">
473                        <Notes>Numeric code indicating the subsystem variant to which this
474                        genome belongs. Each subsystem can have multiple variants. A variant
475                        code of [b]-1[/b] indicates that the genome's roles apply to all
476                        variants. A variant code of [b]0[/b] indicates that the genome's
477                        participation is considered iffy.</Notes>
478                    </Field>
479                </Fields>
480                <ToIndex>
481                    <Notes>This index enables the application to find all of the genomes using
482                    a subsystem in order by variant code, which is how we wish to display them
483                    in the spreadsheets.</Notes>
484                    <IndexFields>
485                        <IndexField name="variant-code" order="ascending" />
486                    </IndexFields>
487                </ToIndex>
488          </Relationship>          </Relationship>
489          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
490              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
491                <Fields>
492                    <Field name="column-number" type="int">
493                        <Notes>Column number for this role in the specified subsystem's
494                        spreadsheet.</Notes>
495                    </Field>
496                </Fields>
497                <ToIndex>
498                    <Notes>This index enables the application to see the subsystem roles
499                    in column order. The ordering of the roles is usually significant,
500                    so it is important to preserve it.</Notes>
501                    <IndexFields>
502                        <IndexField name="column-number" order="ascending" />
503                    </IndexFields>
504                </ToIndex>
505          </Relationship>          </Relationship>
506          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
507              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 413  Line 514 
514          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
515              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
516              features assigned to it.</Notes>              features assigned to it.</Notes>
517                <Fields>
518                    <Field name="cluster-number" type="int">
519                        <Notes>ID of this feature's cluster. Clusters represent families of
520                        related proteins participating in a subsystem.</Notes>
521                    </Field>
522                </Fields>
523            </Relationship>
524            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
525                <Notes>This relationship connects a reaction to the compounds that participate
526                in it.</Notes>
527                <Fields>
528                    <Field name="product" type="boolean">
529                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
530                        it is a substrate. When a reaction is written on paper in
531                        chemical notation, the substrates are left of the arrow and the
532                        products are to the right. Sorting on this field will cause
533                        the substrates to appear first, followed by the products. If the
534                        reaction is reversible, then the notion of substrates and products
535                        is not at intuitive; however, a value here of FALSE still puts the
536                        compound left of the arrow and a value of TRUE still puts it to the
537                        right.</Notes>
538                    </Field>
539                    <Field name="stoichometry" type="int">
540                        <Notes>Number of molecules of the compound that participate in a
541                        single instance of the reaction. For example, if a reaction
542                        produces two water molecules, the stoichometry of water for the
543                        reaction would be two. When a reaction is written on paper in
544                        chemical notation, the stoichometry is the number next to the
545                        chemical formula of the compound.</Notes>
546                    </Field>
547                    <Field name="main" type="boolean">
548                        <Notes>TRUE if this compound is one of the main participants in
549                        the reaction, else FALSE. It is permissible for none of the
550                        compounds in the reaction to be considered main, in which
551                        case this value would be FALSE for all of the relevant
552                        compounds.</Notes>
553                    </Field>
554                    <Field name="loc" type="key-string">
555                        <Notes>An optional character string that indicates the relative
556                        position of this compound in the reaction's chemical formula. The
557                        location affects the way the compounds present as we cross the
558                        relationship from the reaction side. The product/substrate flag
559                        comes first, then the value of this field, then the main flag.
560                        The default value is an empty string; however, the empty string
561                        sorts first, so if this field is used, it should probably be
562                        used for every compound in the reaction.</Notes>
563                    </Field>
564                </Fields>
565                <ToIndex>
566                    <Notes>This index presents the compounds in the reaction in the
567                    order they should be displayed when writing it in chemical notation.
568                    All the substrates appear before all the products, and within that
569                    ordering, the main compounds appear first.</Notes>
570                    <IndexField name="product" order="ascending" />
571                    <IndexField name="loc" order="ascending" />
572                    <IndexField name="main" order="descending" />
573                </ToIndex>
574          </Relationship>          </Relationship>
575          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
576              <Notes>This relationship connects a feature to the contig segments that work together              <Notes>This relationship connects a feature to the contig segments that work together
# Line 512  Line 670 
670              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
671              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
672          </Relationship>          </Relationship>
673            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
674                <Notes>This relationship connects a role subset to the roles that it covers.
675                A subset is, essentially, a named group of roles belonging to a specific
676                subsystem, and this relationship effects that. Note that will a role
677                may belong to many subsystems, a subset belongs to only one subsystem,
678                and all roles in the subset must have that subsystem in common.</Notes>
679            </Relationship>
680            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
681                <Notes>This relationship connects a subset to the genomes that it covers.
682                A subset is, essentially, a named group of genomes participating in a specific
683                subsystem, and this relationship effects that. Note that while a genome
684                may belong to many subsystems, a subset belongs to only one subsystem,
685                and all genomes in the subset must have that subsystem in common.</Notes>
686            </Relationship>
687            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
688                <Notes>This relationship connects a subsystem to its constituent
689                role subsets. Note that some roles in a subsystem may not belong to a
690                subset, so the relationship between roles and subsystems cannot be
691                derived from the relationships going through the subset.</Notes>
692            </Relationship>
693            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
694                <Notes>This relationship connects a subsystem to its constituent
695                genome subsets. Note that some genomes in a subsystem may not belong to a
696                subset, so the relationship between genomes and subsystems cannot be
697                derived from the relationships going through the subset.</Notes>
698            </Relationship>
699            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
700                <Notes>This relationship connects a role to the reactions it catalyzes.
701                The purpose of a role is to create proteins that trigger certain
702                chemical reactions. A single reaction can be triggered by many roles,
703                and a role can trigger many reactions.</Notes>
704            </Relationship>
705      </Relationships>      </Relationships>
706  </Database>  </Database>

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