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revision 1.12, Tue Sep 13 03:50:59 2005 UTC revision 1.34, Wed Aug 2 23:51:19 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 121  Line 121 
121                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
122                      <DataGen>RandParam('peg','rna')</DataGen>                      <DataGen>RandParam('peg','rna')</DataGen>
123                  </Field>                  </Field>
124                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
125                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
126                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                      <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
127                  </Field>                  </Field>
# 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">
175                        <Notes>Abbreviated name for the role, generally non-unique, but useful
176                        in column headings for HTML tables.</Notes>
177                    </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 184  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>
210            <Entity name="Reaction" keyType="key-string">
211                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
212                is generally a small number preceded by a letter.</Notes>
213                <Fields>
214                    <Field name="url" type="string" relation="ReactionURL">
215                        <Notes>HTML string containing a link to a web location that describes the
216                        reaction. This field is optional.</Notes>
217                    </Field>
218                    <Field name="rev" type="boolean">
219                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
220                    </Field>
221                </Fields>
222            </Entity>
223            <Entity name="Compound" keyType="name-string">
224                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
225                All compounds have a unique ID and may also have one or more names.</Notes>
226                <Fields>
227                    <Field name="name-priority" type="int" relation="CompoundName">
228                        <Notes>Priority of a compound name. The name with the loweset
229                        priority is the main name of this compound.</Notes>
230                    </Field>
231                    <Field name="name" type="name-string" relation="CompoundName">
232                        <Notes>Descriptive name for the compound. A compound may
233                        have several names.</Notes>
234                    </Field>
235                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
236                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
237                    </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>
244                <Indexes>
245                    <Index>
246                        <Notes>This index allows the user to find the compound corresponding to
247                        the specified name.</Notes>
248                        <IndexFields>
249                            <IndexField name="name" order="ascending" />
250                        </IndexFields>
251                    </Index>
252                    <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
261                        priority order.</Notes>
262                        <IndexFields>
263                            <IndexField name="id" order="ascending" />
264                            <IndexField name="name-priority" order="ascending" />
265                        </IndexFields>
266                    </Index>
267                </Indexes>
268          </Entity>          </Entity>
269          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
270              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
271              is an important tool for recognizing parallel genetic features in different organisms.</Notes>              is an important tool for recognizing parallel genetic features in different organisms.</Notes>
272                <Fields>
273                    <Field name="curator" type="string">
274                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
275                    </Field>
276                    <Field name="notes" type="text">
277                        <Notes>Descriptive notes about the subsystem.</Notes>
278                    </Field>
279                    <Field name="classification" type="string" relation="SubsystemClass">
280                        <Notes>General classification data about the subsystem.</Notes>
281                    </Field>
282                </Fields>
283          </Entity>          </Entity>
284          <Entity name="SSCell" keyType="name-string">          <Entity name="RoleSubset" keyType="string">
285                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
286                subset names are generally very short, non-unique strings. The ID of the parent
287                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
288            </Entity>
289            <Entity name="GenomeSubset" keyType="string">
290                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
291                in a particular subsystem. The subset names are generally very short, non-unique
292                strings. The ID of the parent subsystem is prefixed to the subset ID in order
293                to make it unique.</Notes>
294            </Entity>
295            <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 270  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 286  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 294  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 306  Line 408 
408                  </Field>                  </Field>
409              </Fields>              </Fields>
410          </Entity>          </Entity>
411            <Entity name="Family" keyType="id-string">
412                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
413                families provide a mechanism for verifying the accuracy of functional assignments
414                and are also used in determining phylogenetic trees.</Notes>
415                <Fields>
416                    <Field name="function" type="text">
417                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
418                    </Field>
419                    <Field name="size" type="int">
420                        <Notes>The number of proteins in this family. This may be larger than the
421                        number of PEGs included in the family, since the family may also contain external
422                        IDs.</Notes>
423                    </Field>
424                </Fields>
425            </Entity>
426      </Entities>      </Entities>
427      <Relationships>      <Relationships>
428            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
429                <Notes>This relationship connects a protein family to all of its PEGs and connects
430                each PEG to all of its protein families.</Notes>
431            </Relationship>
432          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
433              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
434              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 328  Line 449 
449                  </IndexFields>                  </IndexFields>
450              </ToIndex>              </ToIndex>
451          </Relationship>          </Relationship>
452            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
453                <Notes>This relation connects a synonym group to the features that make it
454                up.</Notes>
455            </Relationship>
456            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
457                <Notes>This relationship connects a genome to all of its features. This
458                relationship is redundant in a sense, because the genome ID is part
459                of the feature ID; however, it makes the creation of certain queries more
460                convenient because you can drag in filtering information for a feature's
461                genome.</Notes>
462                <Fields>
463                    <Field name="type" type="key-string">
464                        <Notes>Feature type (eg. peg, rna)</Notes>
465                    </Field>
466                </Fields>
467                <ToIndex>
468                    <Notes>This index enables the application to view the features of a
469                    Genome sorted by type.</Notes>
470                    <IndexFields>
471                        <IndexField name="type" order="ascending" />
472                    </IndexFields>
473                </ToIndex>
474            </Relationship>
475          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
476              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
477              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 398  Line 542 
542              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
543              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
544              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
545                <Fields>
546                    <Field name="variant-code" type="key-string">
547                        <Notes>Code indicating the subsystem variant to which this
548                        genome belongs. Each subsystem can have multiple variants. A variant
549                        code of [b]-1[/b] indicates that the genome does not have a functional
550                        variant of the subsystem. A variant code of [b]0[/b] indicates that
551                        the genome's participation is considered iffy.</Notes>
552                    </Field>
553                </Fields>
554                <ToIndex>
555                    <Notes>This index enables the application to find all of the genomes using
556                    a subsystem in order by variant code, which is how we wish to display them
557                    in the spreadsheets.</Notes>
558                    <IndexFields>
559                        <IndexField name="variant-code" order="ascending" />
560                    </IndexFields>
561                </ToIndex>
562          </Relationship>          </Relationship>
563          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
564              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
565                <Fields>
566                    <Field name="column-number" type="int">
567                        <Notes>Column number for this role in the specified subsystem's
568                        spreadsheet.</Notes>
569                    </Field>
570                </Fields>
571                <ToIndex>
572                    <Notes>This index enables the application to see the subsystem roles
573                    in column order. The ordering of the roles is usually significant,
574                    so it is important to preserve it.</Notes>
575                    <IndexFields>
576                        <IndexField name="column-number" order="ascending" />
577                    </IndexFields>
578                </ToIndex>
579          </Relationship>          </Relationship>
580          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
581              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 413  Line 588 
588          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
589              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
590              features assigned to it.</Notes>              features assigned to it.</Notes>
591                <Fields>
592                    <Field name="cluster-number" type="int">
593                        <Notes>ID of this feature's cluster. Clusters represent families of
594                        related proteins participating in a subsystem.</Notes>
595                    </Field>
596                </Fields>
597            </Relationship>
598            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
599                <Notes>This relationship connects a reaction to the compounds that participate
600                in it.</Notes>
601                <Fields>
602                    <Field name="product" type="boolean">
603                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
604                        it is a substrate. When a reaction is written on paper in
605                        chemical notation, the substrates are left of the arrow and the
606                        products are to the right. Sorting on this field will cause
607                        the substrates to appear first, followed by the products. If the
608                        reaction is reversible, then the notion of substrates and products
609                        is not at intuitive; however, a value here of FALSE still puts the
610                        compound left of the arrow and a value of TRUE still puts it to the
611                        right.</Notes>
612                    </Field>
613                    <Field name="stoichiometry" type="key-string">
614                        <Notes>Number of molecules of the compound that participate in a
615                        single instance of the reaction. For example, if a reaction
616                        produces two water molecules, the stoichiometry of water for the
617                        reaction would be two. When a reaction is written on paper in
618                        chemical notation, the stoichiometry is the number next to the
619                        chemical formula of the compound.</Notes>
620                    </Field>
621                    <Field name="main" type="boolean">
622                        <Notes>TRUE if this compound is one of the main participants in
623                        the reaction, else FALSE. It is permissible for none of the
624                        compounds in the reaction to be considered main, in which
625                        case this value would be FALSE for all of the relevant
626                        compounds.</Notes>
627                    </Field>
628                    <Field name="loc" type="key-string">
629                        <Notes>An optional character string that indicates the relative
630                        position of this compound in the reaction's chemical formula. The
631                        location affects the way the compounds present as we cross the
632                        relationship from the reaction side. The product/substrate flag
633                        comes first, then the value of this field, then the main flag.
634                        The default value is an empty string; however, the empty string
635                        sorts first, so if this field is used, it should probably be
636                        used for every compound in the reaction.</Notes>
637                    </Field>
638                    <Field name="discriminator" type="int">
639                        <Notes>A unique ID for this record. The discriminator does not
640                        provide any useful data, but it prevents identical records from
641                        being collapsed by the SELECT DISTINCT command used by ERDB to
642                        retrieve data.</Notes>
643                    </Field>
644                </Fields>
645                <ToIndex>
646                    <Notes>This index presents the compounds in the reaction in the
647                    order they should be displayed when writing it in chemical notation.
648                    All the substrates appear before all the products, and within that
649                    ordering, the main compounds appear first.</Notes>
650                    <IndexFields>
651                        <IndexField name="product" order="ascending" />
652                        <IndexField name="loc" order="ascending" />
653                        <IndexField name="main" order="descending" />
654                    </IndexFields>
655                </ToIndex>
656          </Relationship>          </Relationship>
657          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
658              <Notes>This relationship connects a feature to the contig segments that work together              <Notes>This relationship connects a feature to the contig segments that work together
# Line 512  Line 752 
752              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
753              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
754          </Relationship>          </Relationship>
755            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
756                <Notes>This relationship connects a role subset to the roles that it covers.
757                A subset is, essentially, a named group of roles belonging to a specific
758                subsystem, and this relationship effects that. Note that will a role
759                may belong to many subsystems, a subset belongs to only one subsystem,
760                and all roles in the subset must have that subsystem in common.</Notes>
761            </Relationship>
762            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
763                <Notes>This relationship connects a subset to the genomes that it covers.
764                A subset is, essentially, a named group of genomes participating in a specific
765                subsystem, and this relationship effects that. Note that while a genome
766                may belong to many subsystems, a subset belongs to only one subsystem,
767                and all genomes in the subset must have that subsystem in common.</Notes>
768            </Relationship>
769            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
770                <Notes>This relationship connects a subsystem to its constituent
771                role subsets. Note that some roles in a subsystem may not belong to a
772                subset, so the relationship between roles and subsystems cannot be
773                derived from the relationships going through the subset.</Notes>
774            </Relationship>
775            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
776                <Notes>This relationship connects a subsystem to its constituent
777                genome subsets. Note that some genomes in a subsystem may not belong to a
778                subset, so the relationship between genomes and subsystems cannot be
779                derived from the relationships going through the subset.</Notes>
780            </Relationship>
781            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
782                <Notes>This relationship connects a role to the reactions it catalyzes.
783                The purpose of a role is to create proteins that trigger certain
784                chemical reactions. A single reaction can be triggered by many roles,
785                and a role can trigger many reactions.</Notes>
786            </Relationship>
787      </Relationships>      </Relationships>
788  </Database>  </Database>

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