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revision 1.16, Sat Oct 15 07:10:46 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>
169              <Fields>              <Fields>
170                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
171                      <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>EC code for this role.</Notes>
                     that are encoded as EC numbers.</Notes>  
172                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
173                  </Field>                  </Field>
174                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="name-string">
# Line 173  Line 176 
176                      in column headings for HTML tables.</Notes>                      in column headings for HTML tables.</Notes>
177                  </Field>                  </Field>
178              </Fields>              </Fields>
179                <Indexes>
180                    <Index>
181                        <Notes>This index allows the user to find the role corresponding to
182                        an EC number.</Notes>
183                        <IndexFields>
184                            <IndexField name="EC" order="ascending" />
185                        </IndexFields>
186                    </Index>
187                </Indexes>
188          </Entity>          </Entity>
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 188  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 217  Line 235 
235                  <Field name="cas-id" type="name-string" relation="CompoundCAS">                  <Field name="cas-id" type="name-string" relation="CompoundCAS">
236                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
237                  </Field>                  </Field>
238                    <Field name="label" type="name-string">
239                        <Notes>Name used in reaction display strings.
240                        It is the same as the name possessing a priority of 1, but it is placed
241                        here to speed up the query used to create the display strings.</Notes>
242                    </Field>
243              </Fields>              </Fields>
244              <Indexes>              <Indexes>
245                  <Index>                  <Index>
# Line 227  Line 250 
250                      </IndexFields>                      </IndexFields>
251                  </Index>                  </Index>
252                  <Index>                  <Index>
253                        <Notes>This index allows the user to find the compound corresponding to
254                        the specified CAS ID.</Notes>
255                        <IndexFields>
256                            <IndexField name="cas-id" order="ascending" />
257                        </IndexFields>
258                    </Index>
259                    <Index>
260                      <Notes>This index allows the user to access the compound names in                      <Notes>This index allows the user to access the compound names in
261                      priority order.</Notes>                      priority order.</Notes>
262                      <IndexFields>                      <IndexFields>
# Line 246  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 259  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 340  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 356  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 364  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 398  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 470  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>
# Line 536  Line 591 
591                      compound left of the arrow and a value of TRUE still puts it to the                      compound left of the arrow and a value of TRUE still puts it to the
592                      right.</Notes>                      right.</Notes>
593                  </Field>                  </Field>
594                  <Field name="stoichometry" type="key-string">                  <Field name="stoichiometry" type="key-string">
595                      <Notes>Number of molecules of the compound that participate in a                      <Notes>Number of molecules of the compound that participate in a
596                      single instance of the reaction. For example, if a reaction                      single instance of the reaction. For example, if a reaction
597                      produces two water molecules, the stoichometry of water for the                      produces two water molecules, the stoichiometry of water for the
598                      reaction would be two. When a reaction is written on paper in                      reaction would be two. When a reaction is written on paper in
599                      chemical notation, the stoichometry is the number next to the                      chemical notation, the stoichiometry is the number next to the
600                      chemical formula of the compound.</Notes>                      chemical formula of the compound.</Notes>
601                  </Field>                  </Field>
602                  <Field name="main" type="boolean">                  <Field name="main" type="boolean">
# Line 561  Line 616 
616                      sorts first, so if this field is used, it should probably be                      sorts first, so if this field is used, it should probably be
617                      used for every compound in the reaction.</Notes>                      used for every compound in the reaction.</Notes>
618                  </Field>                  </Field>
619                    <Field name="discriminator" type="int">
620                        <Notes>A unique ID for this record. The discriminator does not
621                        provide any useful data, but it prevents identical records from
622                        being collapsed by the SELECT DISTINCT command used by ERDB to
623                        retrieve data.</Notes>
624                    </Field>
625              </Fields>              </Fields>
626              <ToIndex>              <ToIndex>
627                  <Notes>This index presents the compounds in the reaction in the                  <Notes>This index presents the compounds in the reaction in the
628                  order they should be displayed when writing it in chemical notation.                  order they should be displayed when writing it in chemical notation.
629                  All the substrates appear before all the products, and within that                  All the substrates appear before all the products, and within that
630                  ordering, the main compounds appear first.</Notes>                  ordering, the main compounds appear first.</Notes>
631                    <IndexFields>
632                  <IndexField name="product" order="ascending" />                  <IndexField name="product" order="ascending" />
633                  <IndexField name="loc" order="ascending" />                  <IndexField name="loc" order="ascending" />
634                  <IndexField name="main" order="descending" />                  <IndexField name="main" order="descending" />
635                    </IndexFields>
636              </ToIndex>              </ToIndex>
637          </Relationship>          </Relationship>
638          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">

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