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revision 1.15, Wed Oct 12 03:14:27 2005 UTC revision 1.25, Sat May 27 02:02:47 2006 UTC
# Line 111  Line 111 
111                  </Field>                  </Field>
112              </Fields>              </Fields>
113          </Entity>          </Entity>
114          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
115              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
116              may be spread across multiple contigs of a genome, but never across more than              may be spread across multiple contigs of a genome, but never across more than
117              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# 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">                  <Field name="abbr" type="name-string">
# Line 173  Line 172 
172                      in column headings for HTML tables.</Notes>                      in column headings for HTML tables.</Notes>
173                  </Field>                  </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 217  Line 223 
223                  <Field name="cas-id" type="name-string" relation="CompoundCAS">                  <Field name="cas-id" type="name-string" relation="CompoundCAS">
224                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
225                  </Field>                  </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>              </Fields>
232              <Indexes>              <Indexes>
233                  <Index>                  <Index>
# Line 227  Line 238 
238                      </IndexFields>                      </IndexFields>
239                  </Index>                  </Index>
240                  <Index>                  <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                      <Notes>This index allows the user to access the compound names in
249                      priority order.</Notes>                      priority order.</Notes>
250                      <IndexFields>                      <IndexFields>
# Line 259  Line 277 
277              strings. The ID of the parent subsystem is prefixed to the subset ID in order              strings. The ID of the parent subsystem is prefixed to the subset ID in order
278              to make it unique.</Notes>              to make it unique.</Notes>
279          </Entity>          </Entity>
280          <Entity name="SSCell" keyType="medium-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 340  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 356  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 398  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 470  Line 507 
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>              <Fields>
509                  <Field name="variant-code" type="key-string">                  <Field name="variant-code" type="key-string">
510                      <Notes>Numeric code indicating the subsystem variant to which this                      <Notes>Code indicating the subsystem variant to which this
511                      genome belongs. Each subsystem can have multiple variants. A variant                      genome belongs. Each subsystem can have multiple variants. A variant
512                      code of [b]-1[/b] indicates that the genome's roles apply to all                      code of [b]-1[/b] indicates that the genome does not have a functional
513                      variants. A variant code of [b]0[/b] indicates that the genome's                      variant of the subsystem. A variant code of [b]0[/b] indicates that
514                      participation is considered iffy.</Notes>                      the genome's participation is considered iffy.</Notes>
515                  </Field>                  </Field>
516              </Fields>              </Fields>
517              <ToIndex>              <ToIndex>
# Line 536  Line 573 
573                      compound left of the arrow and a value of TRUE still puts it to the                      compound left of the arrow and a value of TRUE still puts it to the
574                      right.</Notes>                      right.</Notes>
575                  </Field>                  </Field>
576                  <Field name="stoichometry" type="int">                  <Field name="stoichiometry" type="key-string">
577                      <Notes>Number of molecules of the compound that participate in a                      <Notes>Number of molecules of the compound that participate in a
578                      single instance of the reaction. For example, if a reaction                      single instance of the reaction. For example, if a reaction
579                      produces two water molecules, the stoichometry of water for the                      produces two water molecules, the stoichiometry of water for the
580                      reaction would be two. When a reaction is written on paper in                      reaction would be two. When a reaction is written on paper in
581                      chemical notation, the stoichometry is the number next to the                      chemical notation, the stoichiometry is the number next to the
582                      chemical formula of the compound.</Notes>                      chemical formula of the compound.</Notes>
583                  </Field>                  </Field>
584                  <Field name="main" type="boolean">                  <Field name="main" type="boolean">
# Line 561  Line 598 
598                      sorts first, so if this field is used, it should probably be                      sorts first, so if this field is used, it should probably be
599                      used for every compound in the reaction.</Notes>                      used for every compound in the reaction.</Notes>
600                  </Field>                  </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>              </Fields>
608              <ToIndex>              <ToIndex>
609                  <Notes>This index presents the compounds in the reaction in the                  <Notes>This index presents the compounds in the reaction in the
610                  order they should be displayed when writing it in chemical notation.                  order they should be displayed when writing it in chemical notation.
611                  All the substrates appear before all the products, and within that                  All the substrates appear before all the products, and within that
612                  ordering, the main compounds appear first.</Notes>                  ordering, the main compounds appear first.</Notes>
613                    <IndexFields>
614                  <IndexField name="product" order="ascending" />                  <IndexField name="product" order="ascending" />
615                  <IndexField name="loc" order="ascending" />                  <IndexField name="loc" order="ascending" />
616                  <IndexField name="main" order="descending" />                  <IndexField name="main" order="descending" />
617                    </IndexFields>
618              </ToIndex>              </ToIndex>
619          </Relationship>          </Relationship>
620          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">

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