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revision 1.57, Tue Sep 16 18:43:45 2008 UTC revision 1.58, Tue Sep 30 15:23:55 2008 UTC
# Line 18  Line 18 
18                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
19                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
20                  </Field>                  </Field>
21                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string" default="">
22                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
23                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
24                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
# Line 27  Line 27 
27                      <Notes>version string for this genome, generally consisting of the genome ID followed                      <Notes>version string for this genome, generally consisting of the genome ID followed
28                      by a period and a string of digits.</Notes>                      by a period and a string of digits.</Notes>
29                  </Field>                  </Field>
                 <Field name="access-code" type="key-string">  
                     <Notes>The access code field is deprecated. Its function has been replaced by  
                     the account management system developed for the [[RapidAnnotationServer]].</Notes>  
                 </Field>  
30                  <Field name="complete" type="boolean">                  <Field name="complete" type="boolean">
31                      <Notes>TRUE if the genome is complete, else FALSE</Notes>                      <Notes>TRUE if the genome is complete, else FALSE</Notes>
32                  </Field>                  </Field>
# Line 61  Line 57 
57              <Indexes>              <Indexes>
58                  <Index>                  <Index>
59                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
                     a specific access code, so that a complete list of the genomes users can view  
                     may be generated.</Notes>  
                     <IndexFields>  
                         <IndexField name="access-code" order="ascending" />  
                         <IndexField name="genus" order="ascending" />  
                         <IndexField name="species" order="ascending" />  
                         <IndexField name="unique-characterization" order="ascending" />  
                     </IndexFields>  
                 </Index>  
                 <Index>  
                     <Notes>This index allows the applications to find all genomes associated with  
60                      a specific primary (NMPDR) group.</Notes>                      a specific primary (NMPDR) group.</Notes>
61                      <IndexFields>                      <IndexFields>
62                          <IndexField name="primary-group" order="ascending" />                          <IndexField name="primary-group" order="ascending" />
# Line 94  Line 79 
79          <Entity name="CDD" keyType="key-string">          <Entity name="CDD" keyType="key-string">
80              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
81              on a feature's protein. The ID is six-digit string assigned by the public              on a feature's protein. The ID is six-digit string assigned by the public
82              Conserved Domain Database. A CDD              Conserved Domain Database. A CDD can occur on multiple features and a feature
83              can occur on multiple features and a feature generally has multiple CDDs.</Notes>              generally has multiple CDDs.</Notes>
84          </Entity>          </Entity>
85          <Entity name="Source" keyType="medium-string">          <Entity name="Source" keyType="medium-string">
86              <Notes>A source describes a place from which genome data was taken. This can be an organization              <Notes>A source describes a place from which genome data was taken. This can be an organization
# Line 148  Line 133 
133                      <Notes>The stem of a keyword is a normalized form that is independent of parts                      <Notes>The stem of a keyword is a normalized form that is independent of parts
134                      of speech. The actual keywords stored in the database search index are stems.</Notes>                      of speech. The actual keywords stored in the database search index are stems.</Notes>
135                  </Field>                  </Field>
                 <Field name="count" type="counter">  
                     <Notes>Number of features that can be found by searching for the specified  
                     keyword.</Notes>  
                 </Field>  
136                  <Field name="phonex" type="name-string">                  <Field name="phonex" type="name-string">
137                      <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the                      <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
138                      word stem. This can be used to find alternative spellings if an matching word is not                      word stem. This can be used to find alternative spellings if an matching word is not
# Line 169  Line 150 
150                      <Notes>This index allows the user to find words by phonex.</Notes>                      <Notes>This index allows the user to find words by phonex.</Notes>
151                      <IndexFields>                      <IndexFields>
152                          <IndexField name="phonex" order="ascending" />                          <IndexField name="phonex" order="ascending" />
                         <IndexField name="count" order="descending" />  
153                      </IndexFields>                      </IndexFields>
154                  </Index>                  </Index>
155              </Indexes>              </Indexes>
# Line 206  Line 186 
186                  <Field name="assignment" type="text">                  <Field name="assignment" type="text">
187                      <Notes>Default functional assignment for this feature.</Notes>                      <Notes>Default functional assignment for this feature.</Notes>
188                  </Field>                  </Field>
                 <Field name="active" type="boolean">  
                     <Notes>(This field is deprecated.) TRUE if this feature is still considered valid,  
                     FALSE if it has been logically deleted.</Notes>  
                 </Field>  
189                  <Field name="assignment-maker" type="name-string">                  <Field name="assignment-maker" type="name-string">
190                      <Notes>name of the user who made the functional assignment</Notes>                      <Notes>name of the user who made the functional assignment</Notes>
191                  </Field>                  </Field>
# Line 467  Line 443 
443                  </Field>                  </Field>
444              </Fields>              </Fields>
445          </Entity>          </Entity>
         <Entity name="Family" keyType="id-string">  
             <DisplayInfo theme="seed" col="5" row="5" />  
             <Notes>A family (also called a FigFam) is a group of homologous features believed to have  
             the same function. Families provide a mechanism for verifying the accuracy of functional  
             assignments and are also used in Rapid Annotation and in determining phylogenetic trees.</Notes>  
             <Fields>  
                 <Field name="function" type="text">  
                     <Notes>The functional assignment expected for all PEGs in this family.</Notes>  
                 </Field>  
                 <Field name="size" type="int">  
                     <Notes>The number of proteins in this family. This may be larger than the  
                     number of PEGs included in the family, since the family may also contain external  
                     IDs.</Notes>  
                 </Field>  
             </Fields>  
         </Entity>  
446          <Entity name="PDB" keyType="id-string">          <Entity name="PDB" keyType="id-string">
447              <DisplayInfo theme="web" col="3" row="5" />              <DisplayInfo theme="web" col="3" row="5" />
448              <Notes>A PDB is a protein data bank entry containing information that can be used              <Notes>A PDB is a protein data bank entry containing information that can be used
# Line 705  Line 665 
665                  </Index>                  </Index>
666              </Indexes>              </Indexes>
667          </Relationship>          </Relationship>
         <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">  
             <DisplayInfo caption="Belongs To" theme="seed" />  
             <Notes>This relationship connects a protein family to all of its PEGs and connects  
             each PEG to all of its protein families.</Notes>  
         </Relationship>  
668          <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">          <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
669              <Notes>This relation connects a synonym group to the features that make it              <Notes>This relation connects a synonym group to the features that make it
670              up.</Notes>              up.</Notes>

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