[Bio] / Sprout / SproutDBD.xml Repository:
ViewVC logotype

Diff of /Sprout/SproutDBD.xml

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.30, Sun Jul 9 21:16:47 2006 UTC revision 1.36, Tue Sep 19 00:11:12 2006 UTC
# Line 141  Line 141 
141                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
142                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
143                  </Field>                  </Field>
144                    <Field name="assignment" type="text">
145                        <Notes>This is the primary functional assignment for the feature.</Notes>
146                    </Field>
147                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
148                      <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The                      <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
149                      links are to other websites that have useful about the gene that the feature represents, and                      links are to other websites that have useful about the gene that the feature represents, and
# Line 408  Line 411 
411                  </Field>                  </Field>
412              </Fields>              </Fields>
413          </Entity>          </Entity>
414            <Entity name="Family" keyType="id-string">
415                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
416                families provide a mechanism for verifying the accuracy of functional assignments
417                and are also used in determining phylogenetic trees.</Notes>
418                <Fields>
419                    <Field name="function" type="text">
420                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
421                    </Field>
422                    <Field name="size" type="int">
423                        <Notes>The number of proteins in this family. This may be larger than the
424                        number of PEGs included in the family, since the family may also contain external
425                        IDs.</Notes>
426                    </Field>
427                </Fields>
428            </Entity>
429      </Entities>      </Entities>
430      <Relationships>      <Relationships>
431            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
432                <Notes>This relationship connects a protein family to all of its PEGs and connects
433                each PEG to all of its protein families.</Notes>
434            </Relationship>
435          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
436              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
437              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 700 
700                  </IndexFields>                  </IndexFields>
701              </ToIndex>              </ToIndex>
702          </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>  
703          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
704              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
705              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization

Legend:
Removed from v.1.30  
changed lines
  Added in v.1.36

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3