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revision 1.30, Sun Jul 9 21:16:47 2006 UTC revision 1.40, Wed Sep 27 12:58:18 2006 UTC
# Line 36  Line 36 
36                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
37                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
38                  </Field>                  </Field>
39                    <Field name="primary-group" type="name-string">
40                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
41                        (either based on the organism name or the default value "Supporting"), whereas there can be
42                        multiple named groups or even none.</Notes>
43                    </Field>
44                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="group-name" type="name-string" relation="GenomeGroups">
45                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
46                      page or of particular interest to a research group or web site. A single genome can belong to multiple                      page or of particular interest to a research group or web site. A single genome can belong to multiple
# Line 43  Line 48 
48                  </Field>                  </Field>
49              </Fields>              </Fields>
50              <Indexes>              <Indexes>
51                  <Index>                  <Index Unique="false">
52                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
53                      a specific access code, so that a complete list of the genomes users can view                      a specific access code, so that a complete list of the genomes users can view
54                      may be generated.</Notes>                      may be generated.</Notes>
# Line 55  Line 60 
60                      </IndexFields>                      </IndexFields>
61                  </Index>                  </Index>
62                  <Index Unique="false">                  <Index Unique="false">
63                        <Notes>This index allows the applications to find all genomes associated with
64                        a specific primary (NMPDR) group.</Notes>
65                        <IndexFields>
66                            <IndexField name="primary-group" order="ascending" />
67                            <IndexField name="genus" order="ascending" />
68                            <IndexField name="species" order="ascending" />
69                            <IndexField name="unique-characterization" order="ascending" />
70                        </IndexFields>
71                    </Index>
72                    <Index Unique="false">
73                      <Notes>This index allows the applications to find all genomes for a particular                      <Notes>This index allows the applications to find all genomes for a particular
74                      species.</Notes>                      species.</Notes>
75                      <IndexFields>                      <IndexFields>
# Line 141  Line 156 
156                      <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>
157                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
158                  </Field>                  </Field>
159                    <Field name="assignment" type="text">
160                        <Notes>This is the primary functional assignment for the feature.</Notes>
161                    </Field>
162                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
163                      <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
164                      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 426 
426                  </Field>                  </Field>
427              </Fields>              </Fields>
428          </Entity>          </Entity>
429            <Entity name="Family" keyType="id-string">
430                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
431                families provide a mechanism for verifying the accuracy of functional assignments
432                and are also used in determining phylogenetic trees.</Notes>
433                <Fields>
434                    <Field name="function" type="text">
435                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
436                    </Field>
437                    <Field name="size" type="int">
438                        <Notes>The number of proteins in this family. This may be larger than the
439                        number of PEGs included in the family, since the family may also contain external
440                        IDs.</Notes>
441                    </Field>
442                </Fields>
443            </Entity>
444      </Entities>      </Entities>
445      <Relationships>      <Relationships>
446            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
447                <Notes>This relationship connects a protein family to all of its PEGs and connects
448                each PEG to all of its protein families.</Notes>
449            </Relationship>
450          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
451              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
452              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 445  Line 482 
482                      <Notes>Feature type (eg. peg, rna)</Notes>                      <Notes>Feature type (eg. peg, rna)</Notes>
483                  </Field>                  </Field>
484              </Fields>              </Fields>
485              <ToIndex>              <FromIndex>
486                  <Notes>This index enables the application to view the features of a                  <Notes>This index enables the application to view the features of a
487                  Genome sorted by type.</Notes>                  Genome sorted by type.</Notes>
488                  <IndexFields>                  <IndexFields>
489                      <IndexField name="type" order="ascending" />                      <IndexField name="type" order="ascending" />
490                  </IndexFields>                  </IndexFields>
491              </ToIndex>              </FromIndex>
492          </Relationship>          </Relationship>
493          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
494              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
# Line 678  Line 715 
715                  </IndexFields>                  </IndexFields>
716              </ToIndex>              </ToIndex>
717          </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>  
718          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
719              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
720              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 765  Line 780 
780              chemical reactions. A single reaction can be triggered by many roles,              chemical reactions. A single reaction can be triggered by many roles,
781              and a role can trigger many reactions.</Notes>              and a role can trigger many reactions.</Notes>
782          </Relationship>          </Relationship>
783            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
784                <Notes>This relationship connects a feature to the subsystems in which it
785                participates. This is technically redundant information, but it is used
786                so often that it deserves its own table.</Notes>
787                <Fields>
788                    <Field name="genome" type="name-string">
789                        <Notes>ID of the genome containing the feature</Notes>
790                    </Field>
791                    <Field name="type" type="key-string">
792                        <Notes>Feature type (eg. peg, rna)</Notes>
793                    </Field>
794                </Fields>
795                <ToIndex>
796                    <Notes>This index enables the application to view the features of a
797                    subsystem sorted by genome and feature type.</Notes>
798                    <IndexFields>
799                        <IndexField name="genome" order="ascending" />
800                        <IndexField name="type" order="ascending" />
801                    </IndexFields>
802                </ToIndex>
803            </Relationship>
804      </Relationships>      </Relationships>
805  </Database>  </Database>

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