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revision 1.21, Sun Mar 26 12:35:21 2006 UTC revision 1.22, Wed Apr 19 03:34:15 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.              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 279  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 360  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 376  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

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