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revision 1.22, Wed Apr 19 03:34:15 2006 UTC revision 1.28, Mon Jun 26 19:13:16 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 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 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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