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revision 1.12, Tue Sep 13 03:50:59 2005 UTC revision 1.18, Thu Oct 20 09:33:25 2005 UTC
# 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 163  Line 163 
163              <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.
164              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>
165              <Fields>              <Fields>
166                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
167                      <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>  
168                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
169                  </Field>                  </Field>
170                    <Field name="abbr" type="name-string">
171                        <Notes>Abbreviated name for the role, generally non-unique, but useful
172                        in column headings for HTML tables.</Notes>
173                    </Field>
174              </Fields>              </Fields>
175                <Indexes>
176                    <Index>
177                        <Notes>This index allows the user to find the role corresponding to
178                        an EC number.</Notes>
179                        <IndexFields>
180                            <IndexField name="EC" order="ascending" />
181                        </IndexFields>
182                    </Index>
183                </Indexes>
184          </Entity>          </Entity>
185          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
186              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
# Line 185  Line 197 
197                  </Field>                  </Field>
198              </Fields>              </Fields>
199          </Entity>          </Entity>
200            <Entity name="Reaction" keyType="key-string">
201                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
202                is generally a small number preceded by a letter.</Notes>
203                <Fields>
204                    <Field name="url" type="string" relation="ReactionURL">
205                        <Notes>HTML string containing a link to a web location that describes the
206                        reaction. This field is optional.</Notes>
207                    </Field>
208                    <Field name="rev" type="boolean">
209                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
210                    </Field>
211                </Fields>
212            </Entity>
213            <Entity name="Compound" keyType="name-string">
214                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
215                All compounds have a unique ID and may also have one or more names.</Notes>
216                <Fields>
217                    <Field name="name-priority" type="int" relation="CompoundName">
218                        <Notes>Priority of a compound name. The name with the loweset
219                        priority is the main name of this compound.</Notes>
220                    </Field>
221                    <Field name="name" type="name-string" relation="CompoundName">
222                        <Notes>Descriptive name for the compound. A compound may
223                        have several names.</Notes>
224                    </Field>
225                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
226                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
227                    </Field>
228                </Fields>
229                <Indexes>
230                    <Index>
231                        <Notes>This index allows the user to find the compound corresponding to
232                        the specified name.</Notes>
233                        <IndexFields>
234                            <IndexField name="name" order="ascending" />
235                        </IndexFields>
236                    </Index>
237                    <Index>
238                        <Notes>This index allows the user to find the compound corresponding to
239                        the specified CAS ID.</Notes>
240                        <IndexFields>
241                            <IndexField name="cas-id" order="ascending" />
242                        </IndexFields>
243                    </Index>
244                    <Index>
245                        <Notes>This index allows the user to access the compound names in
246                        priority order.</Notes>
247                        <IndexFields>
248                            <IndexField name="id" order="ascending" />
249                            <IndexField name="name-priority" order="ascending" />
250                        </IndexFields>
251                    </Index>
252                </Indexes>
253            </Entity>
254          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
255              <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
256              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>
257                <Fields>
258                    <Field name="curator" type="string">
259                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
260                    </Field>
261                    <Field name="notes" type="text">
262                        <Notes>Descriptive notes about the subsystem.</Notes>
263                    </Field>
264                </Fields>
265            </Entity>
266            <Entity name="RoleSubset" keyType="string">
267                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
268                subset names are generally very short, non-unique strings. The ID of the parent
269                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
270          </Entity>          </Entity>
271          <Entity name="SSCell" keyType="name-string">          <Entity name="GenomeSubset" keyType="string">
272                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
273                in a particular subsystem. The subset names are generally very short, non-unique
274                strings. The ID of the parent subsystem is prefixed to the subset ID in order
275                to make it unique.</Notes>
276            </Entity>
277            <Entity name="SSCell" keyType="medium-string">
278              <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
279              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
280              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 398  Line 483 
483              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
484              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
485              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
486                <Fields>
487                    <Field name="variant-code" type="key-string">
488                        <Notes>Numeric code indicating the subsystem variant to which this
489                        genome belongs. Each subsystem can have multiple variants. A variant
490                        code of [b]-1[/b] indicates that the genome's roles apply to all
491                        variants. A variant code of [b]0[/b] indicates that the genome's
492                        participation is considered iffy.</Notes>
493                    </Field>
494                </Fields>
495                <ToIndex>
496                    <Notes>This index enables the application to find all of the genomes using
497                    a subsystem in order by variant code, which is how we wish to display them
498                    in the spreadsheets.</Notes>
499                    <IndexFields>
500                        <IndexField name="variant-code" order="ascending" />
501                    </IndexFields>
502                </ToIndex>
503          </Relationship>          </Relationship>
504          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
505              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
506                <Fields>
507                    <Field name="column-number" type="int">
508                        <Notes>Column number for this role in the specified subsystem's
509                        spreadsheet.</Notes>
510                    </Field>
511                </Fields>
512                <ToIndex>
513                    <Notes>This index enables the application to see the subsystem roles
514                    in column order. The ordering of the roles is usually significant,
515                    so it is important to preserve it.</Notes>
516                    <IndexFields>
517                        <IndexField name="column-number" order="ascending" />
518                    </IndexFields>
519                </ToIndex>
520          </Relationship>          </Relationship>
521          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
522              <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 529 
529          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
530              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
531              features assigned to it.</Notes>              features assigned to it.</Notes>
532                <Fields>
533                    <Field name="cluster-number" type="int">
534                        <Notes>ID of this feature's cluster. Clusters represent families of
535                        related proteins participating in a subsystem.</Notes>
536                    </Field>
537                </Fields>
538            </Relationship>
539            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
540                <Notes>This relationship connects a reaction to the compounds that participate
541                in it.</Notes>
542                <Fields>
543                    <Field name="product" type="boolean">
544                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
545                        it is a substrate. When a reaction is written on paper in
546                        chemical notation, the substrates are left of the arrow and the
547                        products are to the right. Sorting on this field will cause
548                        the substrates to appear first, followed by the products. If the
549                        reaction is reversible, then the notion of substrates and products
550                        is not at intuitive; however, a value here of FALSE still puts the
551                        compound left of the arrow and a value of TRUE still puts it to the
552                        right.</Notes>
553                    </Field>
554                    <Field name="stoichometry" type="key-string">
555                        <Notes>Number of molecules of the compound that participate in a
556                        single instance of the reaction. For example, if a reaction
557                        produces two water molecules, the stoichometry of water for the
558                        reaction would be two. When a reaction is written on paper in
559                        chemical notation, the stoichometry is the number next to the
560                        chemical formula of the compound.</Notes>
561                    </Field>
562                    <Field name="main" type="boolean">
563                        <Notes>TRUE if this compound is one of the main participants in
564                        the reaction, else FALSE. It is permissible for none of the
565                        compounds in the reaction to be considered main, in which
566                        case this value would be FALSE for all of the relevant
567                        compounds.</Notes>
568                    </Field>
569                    <Field name="loc" type="key-string">
570                        <Notes>An optional character string that indicates the relative
571                        position of this compound in the reaction's chemical formula. The
572                        location affects the way the compounds present as we cross the
573                        relationship from the reaction side. The product/substrate flag
574                        comes first, then the value of this field, then the main flag.
575                        The default value is an empty string; however, the empty string
576                        sorts first, so if this field is used, it should probably be
577                        used for every compound in the reaction.</Notes>
578                    </Field>
579                </Fields>
580                <ToIndex>
581                    <Notes>This index presents the compounds in the reaction in the
582                    order they should be displayed when writing it in chemical notation.
583                    All the substrates appear before all the products, and within that
584                    ordering, the main compounds appear first.</Notes>
585                    <IndexField name="product" order="ascending" />
586                    <IndexField name="loc" order="ascending" />
587                    <IndexField name="main" order="descending" />
588                </ToIndex>
589          </Relationship>          </Relationship>
590          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
591              <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 685 
685              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
686              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
687          </Relationship>          </Relationship>
688            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
689                <Notes>This relationship connects a role subset to the roles that it covers.
690                A subset is, essentially, a named group of roles belonging to a specific
691                subsystem, and this relationship effects that. Note that will a role
692                may belong to many subsystems, a subset belongs to only one subsystem,
693                and all roles in the subset must have that subsystem in common.</Notes>
694            </Relationship>
695            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
696                <Notes>This relationship connects a subset to the genomes that it covers.
697                A subset is, essentially, a named group of genomes participating in a specific
698                subsystem, and this relationship effects that. Note that while a genome
699                may belong to many subsystems, a subset belongs to only one subsystem,
700                and all genomes in the subset must have that subsystem in common.</Notes>
701            </Relationship>
702            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
703                <Notes>This relationship connects a subsystem to its constituent
704                role subsets. Note that some roles in a subsystem may not belong to a
705                subset, so the relationship between roles and subsystems cannot be
706                derived from the relationships going through the subset.</Notes>
707            </Relationship>
708            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
709                <Notes>This relationship connects a subsystem to its constituent
710                genome subsets. Note that some genomes in a subsystem may not belong to a
711                subset, so the relationship between genomes and subsystems cannot be
712                derived from the relationships going through the subset.</Notes>
713            </Relationship>
714            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
715                <Notes>This relationship connects a role to the reactions it catalyzes.
716                The purpose of a role is to create proteins that trigger certain
717                chemical reactions. A single reaction can be triggered by many roles,
718                and a role can trigger many reactions.</Notes>
719            </Relationship>
720      </Relationships>      </Relationships>
721  </Database>  </Database>

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