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revision 1.12, Tue Sep 13 03:50:59 2005 UTC revision 1.22, Wed Apr 19 03:34:15 2006 UTC
# Line 121  Line 121 
121                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
122                      <DataGen>RandParam('peg','rna')</DataGen>                      <DataGen>RandParam('peg','rna')</DataGen>
123                  </Field>                  </Field>
124                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
125                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
126                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
127                  </Field>                  </Field>
# Line 163  Line 163 
163              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
164              One of the main goals of the database is to record the roles of the various features.</Notes>              One of the main goals of the database is to record the roles of the various features.</Notes>
165              <Fields>              <Fields>
166                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
167                      <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>EC code for this role.</Notes>
                     that are encoded as EC numbers.</Notes>  
168                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
169                  </Field>                  </Field>
170                    <Field name="abbr" type="name-string">
171                        <Notes>Abbreviated name for the role, generally non-unique, but useful
172                        in column headings for HTML tables.</Notes>
173                    </Field>
174              </Fields>              </Fields>
175                <Indexes>
176                    <Index>
177                        <Notes>This index allows the user to find the role corresponding to
178                        an EC number.</Notes>
179                        <IndexFields>
180                            <IndexField name="EC" order="ascending" />
181                        </IndexFields>
182                    </Index>
183                </Indexes>
184          </Entity>          </Entity>
185          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
186              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
187              are currently the only objects that may be inserted directly into the database. All other              are currently the only objects that may be inserted directly into the database. All other
188              information is loaded from data exported by the SEED.              information is loaded from data exported by the SEED.</Notes>
             [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation  
             is the target feature ID followed by a timestamp.</Notes>  
189              <Fields>              <Fields>
190                  <Field name="time" type="date">                  <Field name="time" type="date">
191                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 185  Line 195 
195                  </Field>                  </Field>
196              </Fields>              </Fields>
197          </Entity>          </Entity>
198            <Entity name="Reaction" keyType="key-string">
199                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
200                is generally a small number preceded by a letter.</Notes>
201                <Fields>
202                    <Field name="url" type="string" relation="ReactionURL">
203                        <Notes>HTML string containing a link to a web location that describes the
204                        reaction. This field is optional.</Notes>
205                    </Field>
206                    <Field name="rev" type="boolean">
207                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
208                    </Field>
209                </Fields>
210            </Entity>
211            <Entity name="Compound" keyType="name-string">
212                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
213                All compounds have a unique ID and may also have one or more names.</Notes>
214                <Fields>
215                    <Field name="name-priority" type="int" relation="CompoundName">
216                        <Notes>Priority of a compound name. The name with the loweset
217                        priority is the main name of this compound.</Notes>
218                    </Field>
219                    <Field name="name" type="name-string" relation="CompoundName">
220                        <Notes>Descriptive name for the compound. A compound may
221                        have several names.</Notes>
222                    </Field>
223                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
224                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
225                    </Field>
226                    <Field name="label" type="name-string">
227                        <Notes>Name used in reaction display strings.
228                        It is the same as the name possessing a priority of 1, but it is placed
229                        here to speed up the query used to create the display strings.</Notes>
230                    </Field>
231                </Fields>
232                <Indexes>
233                    <Index>
234                        <Notes>This index allows the user to find the compound corresponding to
235                        the specified name.</Notes>
236                        <IndexFields>
237                            <IndexField name="name" order="ascending" />
238                        </IndexFields>
239                    </Index>
240                    <Index>
241                        <Notes>This index allows the user to find the compound corresponding to
242                        the specified CAS ID.</Notes>
243                        <IndexFields>
244                            <IndexField name="cas-id" order="ascending" />
245                        </IndexFields>
246                    </Index>
247                    <Index>
248                        <Notes>This index allows the user to access the compound names in
249                        priority order.</Notes>
250                        <IndexFields>
251                            <IndexField name="id" order="ascending" />
252                            <IndexField name="name-priority" order="ascending" />
253                        </IndexFields>
254                    </Index>
255                </Indexes>
256            </Entity>
257          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
258              <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
259              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>
260                <Fields>
261                    <Field name="curator" type="string">
262                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
263                    </Field>
264                    <Field name="notes" type="text">
265                        <Notes>Descriptive notes about the subsystem.</Notes>
266                    </Field>
267                </Fields>
268            </Entity>
269            <Entity name="RoleSubset" keyType="string">
270                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
271                subset names are generally very short, non-unique strings. The ID of the parent
272                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
273            </Entity>
274            <Entity name="GenomeSubset" keyType="string">
275                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
276                in a particular subsystem. The subset names are generally very short, non-unique
277                strings. The ID of the parent subsystem is prefixed to the subset ID in order
278                to make it unique.</Notes>
279          </Entity>          </Entity>
280          <Entity name="SSCell" keyType="name-string">          <Entity name="SSCell" keyType="hash-string">
281              <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
282              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
283              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 270  Line 358 
358                      </Field>                      </Field>
359                  </Fields>                  </Fields>
360          </Entity>          </Entity>
361          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="hash-string">
362              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
363              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
364              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 286  Line 374 
374                  </Field>                  </Field>
375              </Fields>              </Fields>
376          </Entity>          </Entity>
377          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="hash-string">
378              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
379              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
380              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 328  Line 416 
416                  </IndexFields>                  </IndexFields>
417              </ToIndex>              </ToIndex>
418          </Relationship>          </Relationship>
419            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
420                <Notes>This relationship connects a genome to all of its features. This
421                relationship is redundant in a sense, because the genome ID is part
422                of the feature ID; however, it makes the creation of certain queries more
423                convenient because you can drag in filtering information for a feature's
424                genome.</Notes>
425                <Fields>
426                    <Field name="type" type="key-string">
427                        <Notes>Feature type (eg. peg, rna)</Notes>
428                    </Field>
429                </Fields>
430                <ToIndex>
431                    <Notes>This index enables the application to view the features of a
432                    Genome sorted by type.</Notes>
433                    <IndexFields>
434                        <IndexField name="type" order="ascending" />
435                    </IndexFields>
436                </ToIndex>
437            </Relationship>
438          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
439              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
440              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 398  Line 505 
505              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
506              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
507              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
508                <Fields>
509                    <Field name="variant-code" type="key-string">
510                        <Notes>Code indicating the subsystem variant to which this
511                        genome belongs. Each subsystem can have multiple variants. A variant
512                        code of [b]-1[/b] indicates that the genome does not have a functional
513                        variant of the subsystem. A variant code of [b]0[/b] indicates that
514                        the genome's participation is considered iffy.</Notes>
515                    </Field>
516                </Fields>
517                <ToIndex>
518                    <Notes>This index enables the application to find all of the genomes using
519                    a subsystem in order by variant code, which is how we wish to display them
520                    in the spreadsheets.</Notes>
521                    <IndexFields>
522                        <IndexField name="variant-code" order="ascending" />
523                    </IndexFields>
524                </ToIndex>
525          </Relationship>          </Relationship>
526          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
527              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
528                <Fields>
529                    <Field name="column-number" type="int">
530                        <Notes>Column number for this role in the specified subsystem's
531                        spreadsheet.</Notes>
532                    </Field>
533                </Fields>
534                <ToIndex>
535                    <Notes>This index enables the application to see the subsystem roles
536                    in column order. The ordering of the roles is usually significant,
537                    so it is important to preserve it.</Notes>
538                    <IndexFields>
539                        <IndexField name="column-number" order="ascending" />
540                    </IndexFields>
541                </ToIndex>
542          </Relationship>          </Relationship>
543          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
544              <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 551 
551          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
552              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
553              features assigned to it.</Notes>              features assigned to it.</Notes>
554                <Fields>
555                    <Field name="cluster-number" type="int">
556                        <Notes>ID of this feature's cluster. Clusters represent families of
557                        related proteins participating in a subsystem.</Notes>
558                    </Field>
559                </Fields>
560            </Relationship>
561            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
562                <Notes>This relationship connects a reaction to the compounds that participate
563                in it.</Notes>
564                <Fields>
565                    <Field name="product" type="boolean">
566                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
567                        it is a substrate. When a reaction is written on paper in
568                        chemical notation, the substrates are left of the arrow and the
569                        products are to the right. Sorting on this field will cause
570                        the substrates to appear first, followed by the products. If the
571                        reaction is reversible, then the notion of substrates and products
572                        is not at intuitive; however, a value here of FALSE still puts the
573                        compound left of the arrow and a value of TRUE still puts it to the
574                        right.</Notes>
575                    </Field>
576                    <Field name="stoichiometry" type="key-string">
577                        <Notes>Number of molecules of the compound that participate in a
578                        single instance of the reaction. For example, if a reaction
579                        produces two water molecules, the stoichiometry of water for the
580                        reaction would be two. When a reaction is written on paper in
581                        chemical notation, the stoichiometry is the number next to the
582                        chemical formula of the compound.</Notes>
583                    </Field>
584                    <Field name="main" type="boolean">
585                        <Notes>TRUE if this compound is one of the main participants in
586                        the reaction, else FALSE. It is permissible for none of the
587                        compounds in the reaction to be considered main, in which
588                        case this value would be FALSE for all of the relevant
589                        compounds.</Notes>
590                    </Field>
591                    <Field name="loc" type="key-string">
592                        <Notes>An optional character string that indicates the relative
593                        position of this compound in the reaction's chemical formula. The
594                        location affects the way the compounds present as we cross the
595                        relationship from the reaction side. The product/substrate flag
596                        comes first, then the value of this field, then the main flag.
597                        The default value is an empty string; however, the empty string
598                        sorts first, so if this field is used, it should probably be
599                        used for every compound in the reaction.</Notes>
600                    </Field>
601                    <Field name="discriminator" type="int">
602                        <Notes>A unique ID for this record. The discriminator does not
603                        provide any useful data, but it prevents identical records from
604                        being collapsed by the SELECT DISTINCT command used by ERDB to
605                        retrieve data.</Notes>
606                    </Field>
607                </Fields>
608                <ToIndex>
609                    <Notes>This index presents the compounds in the reaction in the
610                    order they should be displayed when writing it in chemical notation.
611                    All the substrates appear before all the products, and within that
612                    ordering, the main compounds appear first.</Notes>
613                    <IndexFields>
614                        <IndexField name="product" order="ascending" />
615                        <IndexField name="loc" order="ascending" />
616                        <IndexField name="main" order="descending" />
617                    </IndexFields>
618                </ToIndex>
619          </Relationship>          </Relationship>
620          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
621              <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 715 
715              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
716              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
717          </Relationship>          </Relationship>
718            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
719                <Notes>This relationship connects a role subset to the roles that it covers.
720                A subset is, essentially, a named group of roles belonging to a specific
721                subsystem, and this relationship effects that. Note that will a role
722                may belong to many subsystems, a subset belongs to only one subsystem,
723                and all roles in the subset must have that subsystem in common.</Notes>
724            </Relationship>
725            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
726                <Notes>This relationship connects a subset to the genomes that it covers.
727                A subset is, essentially, a named group of genomes participating in a specific
728                subsystem, and this relationship effects that. Note that while a genome
729                may belong to many subsystems, a subset belongs to only one subsystem,
730                and all genomes in the subset must have that subsystem in common.</Notes>
731            </Relationship>
732            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
733                <Notes>This relationship connects a subsystem to its constituent
734                role subsets. Note that some roles in a subsystem may not belong to a
735                subset, so the relationship between roles and subsystems cannot be
736                derived from the relationships going through the subset.</Notes>
737            </Relationship>
738            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
739                <Notes>This relationship connects a subsystem to its constituent
740                genome subsets. Note that some genomes in a subsystem may not belong to a
741                subset, so the relationship between genomes and subsystems cannot be
742                derived from the relationships going through the subset.</Notes>
743            </Relationship>
744            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
745                <Notes>This relationship connects a role to the reactions it catalyzes.
746                The purpose of a role is to create proteins that trigger certain
747                chemical reactions. A single reaction can be triggered by many roles,
748                and a role can trigger many reactions.</Notes>
749            </Relationship>
750      </Relationships>      </Relationships>
751  </Database>  </Database>

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