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revision 1.25, Sat May 27 02:02:47 2006 UTC revision 1.29, Fri Jun 30 18:31:34 2006 UTC
# Line 159  Line 159 
159                  </Index>                  </Index>
160              </Indexes>              </Indexes>
161          </Entity>          </Entity>
162            <Entity name="SynonymGroup" keyType="id-string">
163                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
164                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
165            </Entity>
166          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
167              <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.
168              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>
# Line 194  Line 198 
198                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
199                  </Field>                  </Field>
200              </Fields>              </Fields>
201                <Indexes>
202                    <Index>
203                        <Notes>This index allows the user to find recent annotations.</Notes>
204                        <IndexFields>
205                            <IndexField name="time" order="descending" />
206                        </IndexFields>
207                    </Index>
208                </Indexes>
209          </Entity>          </Entity>
210          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
211              <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 264  Line 276 
276                  <Field name="notes" type="text">                  <Field name="notes" type="text">
277                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
278                  </Field>                  </Field>
279                    <Field name="classification" type="string" relation="SubsystemClass">
280                        <Notes>General classification data about the subsystem.</Notes>
281                    </Field>
282              </Fields>              </Fields>
283          </Entity>          </Entity>
284          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 358  Line 373 
373                      </Field>                      </Field>
374                  </Fields>                  </Fields>
375          </Entity>          </Entity>
376          <Entity name="Coupling" keyType="hash-string">          <Entity name="Coupling" keyType="id-string">
377              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
378              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
379              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 416  Line 431 
431                  </IndexFields>                  </IndexFields>
432              </ToIndex>              </ToIndex>
433          </Relationship>          </Relationship>
434            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
435                <Notes>This relation connects a synonym group to the features that make it
436                up.</Notes>
437            </Relationship>
438          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
439              <Notes>This relationship connects a genome to all of its features. This              <Notes>This relationship connects a genome to all of its features. This
440              relationship is redundant in a sense, because the genome ID is part              relationship is redundant in a sense, because the genome ID is part

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