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

Diff of /Sprout/SaplingDBD.xml

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

revision 1.2, Wed Sep 3 20:57:52 2008 UTC revision 1.3, Mon Sep 22 20:33:30 2008 UTC
# Line 4  Line 4 
4      Unlike Sprout, which is optimized for searching, Sapling is designed to be structurally      Unlike Sprout, which is optimized for searching, Sapling is designed to be structurally
5      simple without sacrificing the ability to find information quickly.</Notes>      simple without sacrificing the ability to find information quickly.</Notes>
6    <Issues>    <Issues>
7      <Issue>Must add the new "image" data type to ERDB.</Issue>      <Issue>We may want to do some compression on the "dna" data type.</Issue>
     <Issue>Must add the new "dna" data type to ERDB.</Issue>  
8      <Issue>Must add back the ability to index a secondary relation. Note that      <Issue>Must add back the ability to index a secondary relation. Note that
9             such indexes can only have a single field.</Issue>             such indexes can only have a single field.</Issue>
10      <Issue>We probably need some type tables that describe things like Identifier(source)      <Issue>We probably need some type tables that describe things like Identifier(source)
11             or Family(kind).</Issue>             or Family(kind).</Issue>
12      <Issue>The ERDB documentation needs to be updated to include DisplayInfo, Asides,      <Issue>The ERDB documentation needs to be updated to include DisplayInfo, Asides,
13             the "converse" attribute for relationships, and the Shapes section.</Issue>             the "converse" attribute for relationships, and the Shapes section.</Issue>
     <Issue>Similarities and pairings are not hooked in correctly.</Issue>  
14    </Issues>    </Issues>
15    <Entities>    <Entities>
16      <Entity name="Compound" keyType="name-string">      <Entity name="Compound" keyType="name-string">
# Line 520  Line 518 
518        <ToIndex>        <ToIndex>
519          <Notes>This index allows the application to view a scenario's compounds by group.</Notes>          <Notes>This index allows the application to view a scenario's compounds by group.</Notes>
520          <IndexFields>          <IndexFields>
521            <IndexField name="group-number" type="int"/>            <IndexField name="group-number" order="ascending"/>
522          </IndexFields>          </IndexFields>
523        </ToIndex>        </ToIndex>
524      </Relationship>      </Relationship>
# Line 536  Line 534 
534              to implement it. Each variant contains a slightly different subset of the              to implement it. Each variant contains a slightly different subset of the
535              roles in the parent subsystem.</Notes>              roles in the parent subsystem.</Notes>
536      </Relationship>      </Relationship>
537      <Relationship name="Shows" from="Diagram" to="Reaction" arity="MM" converse="IsShowedOn">      <Relationship name="Displays" from="Diagram" to="Reaction" arity="MM" converse="IsDisplayedOn">
538        <DisplayInfo theme="web"/>        <DisplayInfo theme="web"/>
539        <Notes>This relationship connects a diagram to its reactions. A diagram shows multiple        <Notes>This relationship connects a diagram to its reactions. A diagram shows multiple
540              reactions, and a reaction can be on many diagrams.</Notes>              reactions, and a reaction can be on many diagrams.</Notes>
# Line 581  Line 579 
579          </IndexFields>          </IndexFields>
580        </FromIndex>        </FromIndex>
581      </Relationship>      </Relationship>
582      <Relationship name="Implements" from="ProteinSequence" to="Role" arity="MM" converse="IsCatalyzedBy">      <Relationship name="Catalyzes" from="ProteinSequence" to="Role" arity="MM" converse="IsCatalyzedBy">
583        <DisplayInfo theme="web" caption="Is\nImplemented\nBy"/>        <DisplayInfo theme="web" caption="Is\nCatalyzed\nBy"/>
584        <Notes>This relationship connects a protein sequence to the functional roles it        <Notes>This relationship connects a protein sequence to the functional roles it
585              implements in the cell. A protein sequence can implement many roles, and a role can              implements in the cell. A protein sequence can implement many roles, and a role can
586              be implemented by many protein sequences. Roles that perform regulatory or message              be implemented by many protein sequences. Roles that perform regulatory or message
# Line 793  Line 791 
791          </IndexFields>          </IndexFields>
792        </ToIndex>        </ToIndex>
793      </Relationship>      </Relationship>
794      <Relationship name="Contains" from="Diagram" to="Compound" arity="MM" converse="IsContainedIn">      <Relationship name="Shows" from="Diagram" to="Compound" arity="MM" converse="IsShownOn">
795        <DisplayInfo theme="web" fixed="1" caption="Is\nContained\nIn" row="2" col="3.5"/>        <DisplayInfo theme="web" fixed="1" caption="Is\nShown\nOn" row="2" col="3.5"/>
796        <Notes>This relationship indicates that a compound appears on a particular diagram.        <Notes>This relationship indicates that a compound appears on a particular diagram.
797              The same compound can appear on many diagrams, and a diagram always contains many              The same compound can appear on many diagrams, and a diagram always contains many
798              compounds.</Notes>              compounds.</Notes>
# Line 811  Line 809 
809        appearance in a molecular machine. A machine role has exactly one associated role,        appearance in a molecular machine. A machine role has exactly one associated role,
810        but a role may be represented by many machine roles.</Notes>        but a role may be represented by many machine roles.</Notes>
811      </Relationship>      </Relationship>
     <Relationship name="IsTerminusFor" from="Compound" to="Scenario" arity="MM" converse="HasAsTerminus">  
       <DisplayInfo theme="web" caption="Is\nTerminus\nFor"/>  
       <Notes>A terminus for a scenario is a compound that acts as its input or output. A  
             compound can be the terminus for many scenarios, and a scenario will have many termini.  
             The relationship attributes indicate whether the compound is an input to the scenario or  
             an output.</Notes>  
       <Fields>  
         <Field name="group-number" type="int">  
           <Notes>The group number is 0 for an input compound; 1, for an output compound, and 2 for  
                     an auxiliary compound. An ancillary compound is one that is produced by the  
                     scenario, but is not the primary output.</Notes>  
         </Field>  
       </Fields>  
       <ToIndex>  
         <Notes>This index presents the terminal compounds for a scenario in group  
                 order.</Notes>  
         <IndexFields>  
           <IndexField name="group-number" order="ascending"/>  
         </IndexFields>  
       </ToIndex>  
     </Relationship>  
812      <Relationship name="Exposes" from="ProteinSequence" to="Structure" arity="MM" converse="IsExposedBy">      <Relationship name="Exposes" from="ProteinSequence" to="Structure" arity="MM" converse="IsExposedBy">
813        <DisplayInfo theme="web" fixed="1" row="7" col="2" caption="Is\nExposed\nBy"/>        <DisplayInfo theme="web" fixed="1" row="7" col="2" caption="Is\nExposed\nBy"/>
814        <Notes>This relationship connects a protein sequence to its structural representations. It is a        <Notes>This relationship connects a protein sequence to its structural representations. It is a
# Line 868  Line 845 
845          </IndexFields>          </IndexFields>
846        </FromIndex>        </FromIndex>
847      </Relationship>      </Relationship>
848      <Relationship name="IsInPair" from="Feature" to="Pairing" arity="MM" converse="Contains">      <Relationship name="IsInPair" from="Feature" to="Pairing" arity="MM" converse="IsPairOf">
849        <DisplayInfo theme="seed" caption="Is In\nPair"/>        <DisplayInfo theme="seed" caption="Is In\nPair"/>
850        <Notes>A pairing contains exactly two protein sequences. A protein sequence can        <Notes>A pairing contains exactly two protein sequences. A protein sequence can
851               belong to multiple pairings. When going from a protein sequence to its pairings,               belong to multiple pairings. When going from a protein sequence to its pairings,
# Line 885  Line 862 
862    contains many genomes. Some taxonomic groupings do not contain any genomes. These    contains many genomes. Some taxonomic groupings do not contain any genomes. These
863    in fact contain other taxonomic groups.</Notes>    in fact contain other taxonomic groups.</Notes>
864      </Relationship>      </Relationship>
865      <Relationship name="IsMachineOf" from="MolecularMachine" to="MachineRole" arity="1M" converse="IsRoleOf">      <Relationship name="IsMachineOf" from="MolecularMachine" to="MachineRole" arity="1M" converse="IsRoleFor">
866        <DisplayInfo caption="Is\nMachine\nOf" theme="seed"/>        <DisplayInfo caption="Is\nMachine\nOf" theme="seed"/>
867        <Notes>This relationship connects a molecular machine to its various machine roles.        <Notes>This relationship connects a molecular machine to its various machine roles.
868        Each machine has many machine roles, but each machine role belongs to only one machine.</Notes>        Each machine has many machine roles, but each machine role belongs to only one machine.</Notes>
# Line 914  Line 891 
891      <Shape type="diamond" name="IsIdentifiedBy" from="Feature" to="Identifier">      <Shape type="diamond" name="IsIdentifiedBy" from="Feature" to="Identifier">
892        <DisplayInfo theme="neutral" caption="Identifies" connected="1"/>        <DisplayInfo theme="neutral" caption="Identifies" connected="1"/>
893        <Notes>This relationship is not physically implemented in the database. It is        <Notes>This relationship is not physically implemented in the database. It is
894        implicit in the data for an identifier. If the identifiers is a FIG feature        implicit in the data for an identifier. If the identifier is a FIG feature
895        ID, then it identifies that feature, as do all other identifiers in the same        ID, then it identifies that feature, as do all other identifiers in the same
896        identifier set.</Notes>        identifier set.</Notes>
897      </Shape>      </Shape>

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.3

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3