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revision 1.22, Wed Apr 19 03:34:15 2006 UTC revision 1.32, Sun Jul 30 01:41:34 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 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 374  Line 389 
389                  </Field>                  </Field>
390              </Fields>              </Fields>
391          </Entity>          </Entity>
392          <Entity name="PCH" keyType="hash-string">          <Entity name="PCH" keyType="counter">
393              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
394              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
395              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 382  Line 397 
397              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
398              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
399              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
400              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
401              <Fields>              <Fields>
402                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
403                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 394  Line 408 
408                  </Field>                  </Field>
409              </Fields>              </Fields>
410          </Entity>          </Entity>
411            <Entity name="Family" keyType="id-string">
412                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
413                families provide a mechanism for verifying the accuracy of functional assignments
414                and are also used in determining phylogenetic trees.</Notes>
415                <Fields>
416                    <Field name="function" type="text">
417                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
418                    </Field>
419                    <Field name="size" type="integer">
420                        <Notes>The number of proteins in this family. This may be larger than the
421                        number of PEGs included in the family, since the family may also contain external
422                        IDs.</Notes>
423                    </Field>
424                </Fields>
425            </Entity>
426      </Entities>      </Entities>
427      <Relationships>      <Relationships>
428            <Relationship name="ContainsFeature" from="Family" to="Feature" arity="MM">
429                <Notes>This relationship connects a protein family to all of its PEGs and connects
430                each PEG to all of its protein families.</Notes>
431            </Relationship>
432          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
433              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
434              in which it participates. A functional coupling is a recognition of the fact              in which it participates. A functional coupling is a recognition of the fact
# Line 416  Line 449 
449                  </IndexFields>                  </IndexFields>
450              </ToIndex>              </ToIndex>
451          </Relationship>          </Relationship>
452            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
453                <Notes>This relation connects a synonym group to the features that make it
454                up.</Notes>
455            </Relationship>
456          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
457              <Notes>This relationship connects a genome to all of its features. This              <Notes>This relationship connects a genome to all of its features. This
458              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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