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revision 1.19, Wed Nov 2 21:47:45 2005 UTC revision 1.30, Sun Jul 9 21:16:47 2006 UTC
# Line 111  Line 111 
111                  </Field>                  </Field>
112              </Fields>              </Fields>
113          </Entity>          </Entity>
114          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
115              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
116              may be spread across multiple contigs of a genome, but never across more than              may be spread across multiple contigs of a genome, but never across more than
117              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# Line 159  Line 159 
159                  </Index>                  </Index>
160              </Indexes>              </Indexes>
161          </Entity>          </Entity>
162            <Entity name="SynonymGroup" keyType="id-string">
163                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
164                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
165            </Entity>
166          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
167              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
168              One of the main goals of the database is to record the roles of the various features.</Notes>              One of the main goals of the database is to record the roles of the various features.</Notes>
# Line 185  Line 189 
189          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
190              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
191              are currently the only objects that may be inserted directly into the database. All other              are currently the only objects that may be inserted directly into the database. All other
192              information is loaded from data exported by the SEED.              information is loaded from data exported by the SEED.</Notes>
             [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation  
             is the target feature ID followed by a timestamp.</Notes>  
193              <Fields>              <Fields>
194                  <Field name="time" type="date">                  <Field name="time" type="date">
195                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 196  Line 198 
198                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
199                  </Field>                  </Field>
200              </Fields>              </Fields>
201                <Indexes>
202                    <Index>
203                        <Notes>This index allows the user to find recent annotations.</Notes>
204                        <IndexFields>
205                            <IndexField name="time" order="descending" />
206                        </IndexFields>
207                    </Index>
208                </Indexes>
209          </Entity>          </Entity>
210          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
211              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
# Line 266  Line 276 
276                  <Field name="notes" type="text">                  <Field name="notes" type="text">
277                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
278                  </Field>                  </Field>
279                    <Field name="classification" type="string" relation="SubsystemClass">
280                        <Notes>General classification data about the subsystem.</Notes>
281                    </Field>
282              </Fields>              </Fields>
283          </Entity>          </Entity>
284          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 279  Line 292 
292              strings. The ID of the parent subsystem is prefixed to the subset ID in order              strings. The ID of the parent subsystem is prefixed to the subset ID in order
293              to make it unique.</Notes>              to make it unique.</Notes>
294          </Entity>          </Entity>
295          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="hash-string">
296              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
297              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
298              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 360  Line 373 
373                      </Field>                      </Field>
374                  </Fields>                  </Fields>
375          </Entity>          </Entity>
376          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
377              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
378              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
379              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 376  Line 389 
389                  </Field>                  </Field>
390              </Fields>              </Fields>
391          </Entity>          </Entity>
392          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
393              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
394              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
395              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 384  Line 397 
397              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
398              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
399              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
400              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
401              <Fields>              <Fields>
402                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
403                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 418  Line 430 
430                  </IndexFields>                  </IndexFields>
431              </ToIndex>              </ToIndex>
432          </Relationship>          </Relationship>
433            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
434                <Notes>This relation connects a synonym group to the features that make it
435                up.</Notes>
436            </Relationship>
437            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
438                <Notes>This relationship connects a genome to all of its features. This
439                relationship is redundant in a sense, because the genome ID is part
440                of the feature ID; however, it makes the creation of certain queries more
441                convenient because you can drag in filtering information for a feature's
442                genome.</Notes>
443                <Fields>
444                    <Field name="type" type="key-string">
445                        <Notes>Feature type (eg. peg, rna)</Notes>
446                    </Field>
447                </Fields>
448                <ToIndex>
449                    <Notes>This index enables the application to view the features of a
450                    Genome sorted by type.</Notes>
451                    <IndexFields>
452                        <IndexField name="type" order="ascending" />
453                    </IndexFields>
454                </ToIndex>
455            </Relationship>
456          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
457              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
458              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 490  Line 525 
525              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
526              <Fields>              <Fields>
527                  <Field name="variant-code" type="key-string">                  <Field name="variant-code" type="key-string">
528                      <Notes>Numeric code indicating the subsystem variant to which this                      <Notes>Code indicating the subsystem variant to which this
529                      genome belongs. Each subsystem can have multiple variants. A variant                      genome belongs. Each subsystem can have multiple variants. A variant
530                      code of [b]-1[/b] indicates that the genome's roles apply to all                      code of [b]-1[/b] indicates that the genome does not have a functional
531                      variants. A variant code of [b]0[/b] indicates that the genome's                      variant of the subsystem. A variant code of [b]0[/b] indicates that
532                      participation is considered iffy.</Notes>                      the genome's participation is considered iffy.</Notes>
533                  </Field>                  </Field>
534              </Fields>              </Fields>
535              <ToIndex>              <ToIndex>

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