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

Diff of /Sprout/SproutDBD.xml

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

revision 1.9, Sun Aug 14 23:59:03 2005 UTC revision 1.36, Tue Sep 19 00:11:12 2006 UTC
# Line 25  Line 25 
25                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
26                      <DataGen>RandParam('low','medium','high')</DataGen>                      <DataGen>RandParam('low','medium','high')</DataGen>
27                  </Field>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                  <Field name="taxonomy" type="text">                  <Field name="taxonomy" type="text">
32                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
33                      separated by semi-colons (and optional white space), starting with the domain and ending with                      separated by semi-colons (and optional white space), starting with the domain and ending with
# Line 38  Line 41 
41                      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
42                      such groups or none at all.</Notes>                      such groups or none at all.</Notes>
43                  </Field>                  </Field>
                 <Field name="complete" type="boolean">  
                     <Notes>This field is TRUE if the genome is believed to be complete, else  
                     FALSE.</Notes>  
                 </Field>  
44              </Fields>              </Fields>
45              <Indexes>              <Indexes>
46                  <Index>                  <Index>
# Line 112  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 122  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 139  Line 138 
138                      <DataGen testCount="0"></DataGen>                      <DataGen testCount="0"></DataGen>
139                  </Field>                  </Field>
140                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
141                      <Notes>TRUE if this feature is still considered valid, if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
142                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
143                  </Field>                  </Field>
144                    <Field name="assignment" type="text">
145                        <Notes>This is the primary functional assignment for the feature.</Notes>
146                    </Field>
147                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
148                      <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
149                      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 160  Line 162 
162                  </Index>                  </Index>
163              </Indexes>              </Indexes>
164          </Entity>          </Entity>
165            <Entity name="SynonymGroup" keyType="id-string">
166                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
167                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
168            </Entity>
169          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
170              <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.
171              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>
172              <Fields>              <Fields>
173                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
174                      <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>  
175                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
176                  </Field>                  </Field>
177                    <Field name="abbr" type="name-string">
178                        <Notes>Abbreviated name for the role, generally non-unique, but useful
179                        in column headings for HTML tables.</Notes>
180                    </Field>
181              </Fields>              </Fields>
182                <Indexes>
183                    <Index>
184                        <Notes>This index allows the user to find the role corresponding to
185                        an EC number.</Notes>
186                        <IndexFields>
187                            <IndexField name="EC" order="ascending" />
188                        </IndexFields>
189                    </Index>
190                </Indexes>
191          </Entity>          </Entity>
192          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
193              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
194              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
195              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>  
196              <Fields>              <Fields>
197                  <Field name="time" type="date">                  <Field name="time" type="date">
198                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 185  Line 201 
201                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
202                  </Field>                  </Field>
203              </Fields>              </Fields>
204                <Indexes>
205                    <Index>
206                        <Notes>This index allows the user to find recent annotations.</Notes>
207                        <IndexFields>
208                            <IndexField name="time" order="descending" />
209                        </IndexFields>
210                    </Index>
211                </Indexes>
212            </Entity>
213            <Entity name="Reaction" keyType="key-string">
214                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
215                is generally a small number preceded by a letter.</Notes>
216                <Fields>
217                    <Field name="url" type="string" relation="ReactionURL">
218                        <Notes>HTML string containing a link to a web location that describes the
219                        reaction. This field is optional.</Notes>
220                    </Field>
221                    <Field name="rev" type="boolean">
222                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
223                    </Field>
224                </Fields>
225            </Entity>
226            <Entity name="Compound" keyType="name-string">
227                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
228                All compounds have a unique ID and may also have one or more names.</Notes>
229                <Fields>
230                    <Field name="name-priority" type="int" relation="CompoundName">
231                        <Notes>Priority of a compound name. The name with the loweset
232                        priority is the main name of this compound.</Notes>
233                    </Field>
234                    <Field name="name" type="name-string" relation="CompoundName">
235                        <Notes>Descriptive name for the compound. A compound may
236                        have several names.</Notes>
237                    </Field>
238                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
239                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
240                    </Field>
241                    <Field name="label" type="name-string">
242                        <Notes>Name used in reaction display strings.
243                        It is the same as the name possessing a priority of 1, but it is placed
244                        here to speed up the query used to create the display strings.</Notes>
245                    </Field>
246                </Fields>
247                <Indexes>
248                    <Index>
249                        <Notes>This index allows the user to find the compound corresponding to
250                        the specified name.</Notes>
251                        <IndexFields>
252                            <IndexField name="name" order="ascending" />
253                        </IndexFields>
254                    </Index>
255                    <Index>
256                        <Notes>This index allows the user to find the compound corresponding to
257                        the specified CAS ID.</Notes>
258                        <IndexFields>
259                            <IndexField name="cas-id" order="ascending" />
260                        </IndexFields>
261                    </Index>
262                    <Index>
263                        <Notes>This index allows the user to access the compound names in
264                        priority order.</Notes>
265                        <IndexFields>
266                            <IndexField name="id" order="ascending" />
267                            <IndexField name="name-priority" order="ascending" />
268                        </IndexFields>
269                    </Index>
270                </Indexes>
271          </Entity>          </Entity>
272          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
273              <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
274              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>
275                <Fields>
276                    <Field name="curator" type="string">
277                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
278                    </Field>
279                    <Field name="notes" type="text">
280                        <Notes>Descriptive notes about the subsystem.</Notes>
281                    </Field>
282                    <Field name="classification" type="string" relation="SubsystemClass">
283                        <Notes>General classification data about the subsystem.</Notes>
284                    </Field>
285                </Fields>
286            </Entity>
287            <Entity name="RoleSubset" keyType="string">
288                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
289                subset names are generally very short, non-unique strings. The ID of the parent
290                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
291          </Entity>          </Entity>
292          <Entity name="SSCell" keyType="name-string">          <Entity name="GenomeSubset" keyType="string">
293                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
294                in a particular subsystem. The subset names are generally very short, non-unique
295                strings. The ID of the parent subsystem is prefixed to the subset ID in order
296                to make it unique.</Notes>
297            </Entity>
298            <Entity name="SSCell" keyType="hash-string">
299              <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
300              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
301              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 271  Line 376 
376                      </Field>                      </Field>
377                  </Fields>                  </Fields>
378          </Entity>          </Entity>
379          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
380              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
381              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
382              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 287  Line 392 
392                  </Field>                  </Field>
393              </Fields>              </Fields>
394          </Entity>          </Entity>
395          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
396              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
397              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
398              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 295  Line 400 
400              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
401              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
402              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
403              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>  
404              <Fields>              <Fields>
405                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
406                      <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 307  Line 411 
411                  </Field>                  </Field>
412              </Fields>              </Fields>
413          </Entity>          </Entity>
414            <Entity name="Family" keyType="id-string">
415                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
416                families provide a mechanism for verifying the accuracy of functional assignments
417                and are also used in determining phylogenetic trees.</Notes>
418                <Fields>
419                    <Field name="function" type="text">
420                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
421                    </Field>
422                    <Field name="size" type="int">
423                        <Notes>The number of proteins in this family. This may be larger than the
424                        number of PEGs included in the family, since the family may also contain external
425                        IDs.</Notes>
426                    </Field>
427                </Fields>
428            </Entity>
429      </Entities>      </Entities>
430      <Relationships>      <Relationships>
431            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
432                <Notes>This relationship connects a protein family to all of its PEGs and connects
433                each PEG to all of its protein families.</Notes>
434            </Relationship>
435          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
436              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
437              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 329  Line 452 
452                  </IndexFields>                  </IndexFields>
453              </ToIndex>              </ToIndex>
454          </Relationship>          </Relationship>
455            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
456                <Notes>This relation connects a synonym group to the features that make it
457                up.</Notes>
458            </Relationship>
459            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
460                <Notes>This relationship connects a genome to all of its features. This
461                relationship is redundant in a sense, because the genome ID is part
462                of the feature ID; however, it makes the creation of certain queries more
463                convenient because you can drag in filtering information for a feature's
464                genome.</Notes>
465                <Fields>
466                    <Field name="type" type="key-string">
467                        <Notes>Feature type (eg. peg, rna)</Notes>
468                    </Field>
469                </Fields>
470                <ToIndex>
471                    <Notes>This index enables the application to view the features of a
472                    Genome sorted by type.</Notes>
473                    <IndexFields>
474                        <IndexField name="type" order="ascending" />
475                    </IndexFields>
476                </ToIndex>
477            </Relationship>
478          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
479              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
480              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 399  Line 545 
545              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
546              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
547              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
548                <Fields>
549                    <Field name="variant-code" type="key-string">
550                        <Notes>Code indicating the subsystem variant to which this
551                        genome belongs. Each subsystem can have multiple variants. A variant
552                        code of [b]-1[/b] indicates that the genome does not have a functional
553                        variant of the subsystem. A variant code of [b]0[/b] indicates that
554                        the genome's participation is considered iffy.</Notes>
555                    </Field>
556                </Fields>
557                <ToIndex>
558                    <Notes>This index enables the application to find all of the genomes using
559                    a subsystem in order by variant code, which is how we wish to display them
560                    in the spreadsheets.</Notes>
561                    <IndexFields>
562                        <IndexField name="variant-code" order="ascending" />
563                    </IndexFields>
564                </ToIndex>
565          </Relationship>          </Relationship>
566          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
567              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
568                <Fields>
569                    <Field name="column-number" type="int">
570                        <Notes>Column number for this role in the specified subsystem's
571                        spreadsheet.</Notes>
572                    </Field>
573                </Fields>
574                <ToIndex>
575                    <Notes>This index enables the application to see the subsystem roles
576                    in column order. The ordering of the roles is usually significant,
577                    so it is important to preserve it.</Notes>
578                    <IndexFields>
579                        <IndexField name="column-number" order="ascending" />
580                    </IndexFields>
581                </ToIndex>
582          </Relationship>          </Relationship>
583          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
584              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 414  Line 591 
591          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
592              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
593              features assigned to it.</Notes>              features assigned to it.</Notes>
594                <Fields>
595                    <Field name="cluster-number" type="int">
596                        <Notes>ID of this feature's cluster. Clusters represent families of
597                        related proteins participating in a subsystem.</Notes>
598                    </Field>
599                </Fields>
600            </Relationship>
601            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
602                <Notes>This relationship connects a reaction to the compounds that participate
603                in it.</Notes>
604                <Fields>
605                    <Field name="product" type="boolean">
606                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
607                        it is a substrate. When a reaction is written on paper in
608                        chemical notation, the substrates are left of the arrow and the
609                        products are to the right. Sorting on this field will cause
610                        the substrates to appear first, followed by the products. If the
611                        reaction is reversible, then the notion of substrates and products
612                        is not at intuitive; however, a value here of FALSE still puts the
613                        compound left of the arrow and a value of TRUE still puts it to the
614                        right.</Notes>
615                    </Field>
616                    <Field name="stoichiometry" type="key-string">
617                        <Notes>Number of molecules of the compound that participate in a
618                        single instance of the reaction. For example, if a reaction
619                        produces two water molecules, the stoichiometry of water for the
620                        reaction would be two. When a reaction is written on paper in
621                        chemical notation, the stoichiometry is the number next to the
622                        chemical formula of the compound.</Notes>
623                    </Field>
624                    <Field name="main" type="boolean">
625                        <Notes>TRUE if this compound is one of the main participants in
626                        the reaction, else FALSE. It is permissible for none of the
627                        compounds in the reaction to be considered main, in which
628                        case this value would be FALSE for all of the relevant
629                        compounds.</Notes>
630                    </Field>
631                    <Field name="loc" type="key-string">
632                        <Notes>An optional character string that indicates the relative
633                        position of this compound in the reaction's chemical formula. The
634                        location affects the way the compounds present as we cross the
635                        relationship from the reaction side. The product/substrate flag
636                        comes first, then the value of this field, then the main flag.
637                        The default value is an empty string; however, the empty string
638                        sorts first, so if this field is used, it should probably be
639                        used for every compound in the reaction.</Notes>
640                    </Field>
641                    <Field name="discriminator" type="int">
642                        <Notes>A unique ID for this record. The discriminator does not
643                        provide any useful data, but it prevents identical records from
644                        being collapsed by the SELECT DISTINCT command used by ERDB to
645                        retrieve data.</Notes>
646                    </Field>
647                </Fields>
648                <ToIndex>
649                    <Notes>This index presents the compounds in the reaction in the
650                    order they should be displayed when writing it in chemical notation.
651                    All the substrates appear before all the products, and within that
652                    ordering, the main compounds appear first.</Notes>
653                    <IndexFields>
654                        <IndexField name="product" order="ascending" />
655                        <IndexField name="loc" order="ascending" />
656                        <IndexField name="main" order="descending" />
657                    </IndexFields>
658                </ToIndex>
659          </Relationship>          </Relationship>
660          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
661              <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 458  Line 700 
700                  </IndexFields>                  </IndexFields>
701              </ToIndex>              </ToIndex>
702          </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>  
703          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
704              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
705              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 513  Line 733 
733              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
734              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
735          </Relationship>          </Relationship>
736            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
737                <Notes>This relationship connects a role subset to the roles that it covers.
738                A subset is, essentially, a named group of roles belonging to a specific
739                subsystem, and this relationship effects that. Note that will a role
740                may belong to many subsystems, a subset belongs to only one subsystem,
741                and all roles in the subset must have that subsystem in common.</Notes>
742            </Relationship>
743            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
744                <Notes>This relationship connects a subset to the genomes that it covers.
745                A subset is, essentially, a named group of genomes participating in a specific
746                subsystem, and this relationship effects that. Note that while a genome
747                may belong to many subsystems, a subset belongs to only one subsystem,
748                and all genomes in the subset must have that subsystem in common.</Notes>
749            </Relationship>
750            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
751                <Notes>This relationship connects a subsystem to its constituent
752                role subsets. Note that some roles in a subsystem may not belong to a
753                subset, so the relationship between roles and subsystems cannot be
754                derived from the relationships going through the subset.</Notes>
755            </Relationship>
756            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
757                <Notes>This relationship connects a subsystem to its constituent
758                genome subsets. Note that some genomes in a subsystem may not belong to a
759                subset, so the relationship between genomes and subsystems cannot be
760                derived from the relationships going through the subset.</Notes>
761            </Relationship>
762            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
763                <Notes>This relationship connects a role to the reactions it catalyzes.
764                The purpose of a role is to create proteins that trigger certain
765                chemical reactions. A single reaction can be triggered by many roles,
766                and a role can trigger many reactions.</Notes>
767            </Relationship>
768      </Relationships>      </Relationships>
769  </Database>  </Database>

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.36

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3