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

Diff of /Sprout/SproutDBD.xml

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

revision 1.27, Sun Jun 25 07:34:46 2006 UTC revision 1.30, Sun Jul 9 21:16:47 2006 UTC
# Line 276  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 370  Line 373 
373                      </Field>                      </Field>
374                  </Fields>                  </Fields>
375          </Entity>          </Entity>
376          <Entity name="Coupling" keyType="hash-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 386  Line 389 
389                  </Field>                  </Field>
390              </Fields>              </Fields>
391          </Entity>          </Entity>
392          <Entity name="PCH" keyType="hash-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 394  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,

Legend:
Removed from v.1.27  
changed lines
  Added in v.1.30

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3