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revision 1.22, Wed Apr 19 03:34:15 2006 UTC revision 1.23, Wed Apr 19 03:36:29 2006 UTC
# 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.</Notes>              information is loaded from data exported by the SEED.
189                [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation
190                is the target feature ID followed by a timestamp.</Notes>
191              <Fields>              <Fields>
192                  <Field name="time" type="date">                  <Field name="time" type="date">
193                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 277  Line 279 
279              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
280              to make it unique.</Notes>              to make it unique.</Notes>
281          </Entity>          </Entity>
282          <Entity name="SSCell" keyType="hash-string">          <Entity name="SSCell" keyType="medium-string">
283              <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
284              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
285              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 358  Line 360 
360                      </Field>                      </Field>
361                  </Fields>                  </Fields>
362          </Entity>          </Entity>
363          <Entity name="Coupling" keyType="hash-string">          <Entity name="Coupling" keyType="medium-string">
364              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
365              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
366              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 374  Line 376 
376                  </Field>                  </Field>
377              </Fields>              </Fields>
378          </Entity>          </Entity>
379          <Entity name="PCH" keyType="hash-string">          <Entity name="PCH" keyType="string">
380              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
381              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
382              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 416  Line 418 
418                  </IndexFields>                  </IndexFields>
419              </ToIndex>              </ToIndex>
420          </Relationship>          </Relationship>
         <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">  
             <Notes>This relationship connects a genome to all of its features. This  
             relationship is redundant in a sense, because the genome ID is part  
             of the feature ID; however, it makes the creation of certain queries more  
             convenient because you can drag in filtering information for a feature's  
             genome.</Notes>  
             <Fields>  
                 <Field name="type" type="key-string">  
                     <Notes>Feature type (eg. peg, rna)</Notes>  
                 </Field>  
             </Fields>  
             <ToIndex>  
                 <Notes>This index enables the application to view the features of a  
                 Genome sorted by type.</Notes>  
                 <IndexFields>  
                     <IndexField name="type" order="ascending" />  
                 </IndexFields>  
             </ToIndex>  
         </Relationship>  
421          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
422              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
423              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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