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revision 1.30, Sun Jul 9 21:16:47 2006 UTC revision 1.35, Wed Sep 13 04:27:57 2006 UTC
# Line 408  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="int">
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="IsFamilyForFeature" 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 678  Line 697 
697                  </IndexFields>                  </IndexFields>
698              </ToIndex>              </ToIndex>
699          </Relationship>          </Relationship>
         <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">  
             <Notes>This relationship is one of two that relate features to each other. It  
             connects features that are very similar but on separate genomes. A  
             bidirectional best hit relationship exists between two features [b]A[/b]  
             and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome  
             and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>  
             <Fields>  
                 <Field name="genome" type="name-string">  
                     <Notes>ID of the genome containing the target (to) feature.</Notes>  
                 </Field>  
                 <Field name="sc" type="float">  
                     <Notes>score for this relationship</Notes>  
                 </Field>  
             </Fields>  
             <FromIndex>  
                 <Notes>This index allows the application to find a feature's best hit for  
                 a specific target genome.</Notes>  
                 <IndexFields>  
                     <IndexField name="genome" order="ascending" />  
                 </IndexFields>  
             </FromIndex>  
         </Relationship>  
700          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
701              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
702              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization

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