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revision 1.23, Wed Apr 19 03:36:29 2006 UTC revision 1.38, Wed Sep 27 11:07:32 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 111  Line 126 
126                  </Field>                  </Field>
127              </Fields>              </Fields>
128          </Entity>          </Entity>
129          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
130              <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
131              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
132              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# 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 159  Line 177 
177                  </Index>                  </Index>
178              </Indexes>              </Indexes>
179          </Entity>          </Entity>
180            <Entity name="SynonymGroup" keyType="id-string">
181                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
182                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
183            </Entity>
184          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
185              <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.
186              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 207 
207          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
208              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
209              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
210              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>  
211              <Fields>              <Fields>
212                  <Field name="time" type="date">                  <Field name="time" type="date">
213                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 196  Line 216 
216                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
217                  </Field>                  </Field>
218              </Fields>              </Fields>
219                <Indexes>
220                    <Index>
221                        <Notes>This index allows the user to find recent annotations.</Notes>
222                        <IndexFields>
223                            <IndexField name="time" order="descending" />
224                        </IndexFields>
225                    </Index>
226                </Indexes>
227          </Entity>          </Entity>
228          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
229              <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 294 
294                  <Field name="notes" type="text">                  <Field name="notes" type="text">
295                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
296                  </Field>                  </Field>
297                    <Field name="classification" type="string" relation="SubsystemClass">
298                        <Notes>General classification data about the subsystem.</Notes>
299                    </Field>
300              </Fields>              </Fields>
301          </Entity>          </Entity>
302          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 279  Line 310 
310              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
311              to make it unique.</Notes>              to make it unique.</Notes>
312          </Entity>          </Entity>
313          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="hash-string">
314              <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
315              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
316              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 360  Line 391 
391                      </Field>                      </Field>
392                  </Fields>                  </Fields>
393          </Entity>          </Entity>
394          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
395              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
396              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
397              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 407 
407                  </Field>                  </Field>
408              </Fields>              </Fields>
409          </Entity>          </Entity>
410          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
411              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
412              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
413              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 415 
415              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
416              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
417              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
418              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>  
419              <Fields>              <Fields>
420                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
421                      <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 396  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 418  Line 467 
467                  </IndexFields>                  </IndexFields>
468              </ToIndex>              </ToIndex>
469          </Relationship>          </Relationship>
470            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
471                <Notes>This relation connects a synonym group to the features that make it
472                up.</Notes>
473            </Relationship>
474            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
475                <Notes>This relationship connects a genome to all of its features. This
476                relationship is redundant in a sense, because the genome ID is part
477                of the feature ID; however, it makes the creation of certain queries more
478                convenient because you can drag in filtering information for a feature's
479                genome.</Notes>
480                <Fields>
481                    <Field name="type" type="key-string">
482                        <Notes>Feature type (eg. peg, rna)</Notes>
483                    </Field>
484                </Fields>
485                <FromIndex>
486                    <Notes>This index enables the application to view the features of a
487                    Genome sorted by type.</Notes>
488                    <IndexFields>
489                        <IndexField name="type" order="ascending" />
490                    </IndexFields>
491                </FromIndex>
492            </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
495              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 643  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

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