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revision 1.23, Wed Apr 19 03:36:29 2006 UTC revision 1.26, Tue Jun 6 05:07:42 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 185  Line 185 
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 196  Line 194 
194                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
195                  </Field>                  </Field>
196              </Fields>              </Fields>
197                <Indexes>
198                    <Index>
199                        <Notes>This index allows the user to find recent annotations.</Notes>
200                        <IndexFields>
201                            <IndexField name="time" order="descending" />
202                        </IndexFields>
203                    </Index>
204                </Indexes>
205          </Entity>          </Entity>
206          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
207              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
# Line 279  Line 285 
285              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
286              to make it unique.</Notes>              to make it unique.</Notes>
287          </Entity>          </Entity>
288          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="hash-string">
289              <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
290              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
291              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 360  Line 366 
366                      </Field>                      </Field>
367                  </Fields>                  </Fields>
368          </Entity>          </Entity>
369          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="hash-string">
370              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
371              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
372              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 376  Line 382 
382                  </Field>                  </Field>
383              </Fields>              </Fields>
384          </Entity>          </Entity>
385          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="hash-string">
386              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
387              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
388              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 418  Line 424 
424                  </IndexFields>                  </IndexFields>
425              </ToIndex>              </ToIndex>
426          </Relationship>          </Relationship>
427            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
428                <Notes>This relationship connects a genome to all of its features. This
429                relationship is redundant in a sense, because the genome ID is part
430                of the feature ID; however, it makes the creation of certain queries more
431                convenient because you can drag in filtering information for a feature's
432                genome.</Notes>
433                <Fields>
434                    <Field name="type" type="key-string">
435                        <Notes>Feature type (eg. peg, rna)</Notes>
436                    </Field>
437                </Fields>
438                <ToIndex>
439                    <Notes>This index enables the application to view the features of a
440                    Genome sorted by type.</Notes>
441                    <IndexFields>
442                        <IndexField name="type" order="ascending" />
443                    </IndexFields>
444                </ToIndex>
445            </Relationship>
446          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
447              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
448              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>

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