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revision 1.23, Wed Apr 19 03:36:29 2006 UTC revision 1.47, Mon Jan 22 20:24:53 2007 UTC
# Line 7  Line 7 
7              <Fields>              <Fields>
8                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
9                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
                     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>  
10                  </Field>                  </Field>
11                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
12                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
13                  </Field>                  </Field>
14                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
15                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
16                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
17                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
                     <DataGen>StringGen('PKVKVK999')</DataGen>  
18                  </Field>                  </Field>
19                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
20                      <Notes>The access code determines which users can look at the data relating to this genome.                      <Notes>The access code determines which users can look at the data relating to this genome.
21                      Each user is associated with a set of access codes. In order to view a genome, one of                      Each user is associated with a set of access codes. In order to view a genome, one of
22                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
                     <DataGen>RandParam('low','medium','high')</DataGen>  
23                  </Field>                  </Field>
24                  <Field name="complete" type="boolean">                  <Field name="complete" type="boolean">
25                      <Notes>TRUE if the genome is complete, else FALSE</Notes>                      <Notes>TRUE if the genome is complete, else FALSE</Notes>
# Line 33  Line 29 
29                      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
30                      the disambiguated genus and species (which is the organism's scientific name plus an                      the disambiguated genus and species (which is the organism's scientific name plus an
31                      identifying string).</Notes>                      identifying string).</Notes>
32                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                  </Field>
33                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                  <Field name="primary-group" type="name-string">
34                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
35                        (either based on the organism name or the default value "Supporting"), whereas there can be
36                        multiple named groups or even none.</Notes>
37                  </Field>                  </Field>
38                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="group-name" type="name-string" relation="GenomeGroups">
39                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
# Line 54  Line 53 
53                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
54                      </IndexFields>                      </IndexFields>
55                  </Index>                  </Index>
56                  <Index Unique="false">                  <Index>
57                        <Notes>This index allows the applications to find all genomes associated with
58                        a specific primary (NMPDR) group.</Notes>
59                        <IndexFields>
60                            <IndexField name="primary-group" order="ascending" />
61                            <IndexField name="genus" order="ascending" />
62                            <IndexField name="species" order="ascending" />
63                            <IndexField name="unique-characterization" order="ascending" />
64                        </IndexFields>
65                    </Index>
66                    <Index>
67                      <Notes>This index allows the applications to find all genomes for a particular                      <Notes>This index allows the applications to find all genomes for a particular
68                      species.</Notes>                      species.</Notes>
69                      <IndexFields>                      <IndexFields>
# Line 71  Line 80 
80              <Fields>              <Fields>
81                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
82                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>  
83                  </Field>                  </Field>
84                  <Field name="description" type="text">                  <Field name="description" type="text">
85                      <Notes>Description the source. The description can be a street address or a citation.</Notes>                      <Notes>Description the source. The description can be a street address or a citation.</Notes>
                     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
86                  </Field>                  </Field>
87              </Fields>              </Fields>
88          </Entity>          </Entity>
# Line 98  Line 105 
105                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
106                      <Notes>String consisting of the residues. Each residue is described by a single                      <Notes>String consisting of the residues. Each residue is described by a single
107                      character in the string.</Notes>                      character in the string.</Notes>
                     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
108                  </Field>                  </Field>
109                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
110                      <Notes>String describing the quality data for each base pair. Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
# Line 107  Line 113 
113                      10^-30. A higher quality number a better chance of a correct match. It is possible                      10^-30. A higher quality number a better chance of a correct match. It is possible
114                      that the quality data is not known for a sequence. If that is the case, the quality                      that the quality data is not known for a sequence. If that is the case, the quality
115                      vector will contain the [b]unknown[/b].</Notes>                      vector will contain the [b]unknown[/b].</Notes>
                     <DataGen>unknown</DataGen>  
116                  </Field>                  </Field>
117              </Fields>              </Fields>
118          </Entity>          </Entity>
119          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
120              <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
121              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
122              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# Line 119  Line 124 
124              <Fields>              <Fields>
125                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="string">
126                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
                     <DataGen>RandParam('peg','rna')</DataGen>  
127                  </Field>                  </Field>
128                  <Field name="alias" type="medium-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
129                      <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>
                     <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
130                  </Field>                  </Field>
131                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
132                      <Notes>[i](optional)[/i] A translation of this feature's residues into character                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
133                      codes, formed by concatenating the pieces of the feature together. For a                      codes, formed by concatenating the pieces of the feature together. For a
134                      protein encoding group, this is the protein characters. For other types                      protein encoding group, this is the protein characters. For other types
135                      it is the DNA characters.</Notes>                      it is the DNA characters.</Notes>
                     <DataGen testCount="0"></DataGen>  
136                  </Field>                  </Field>
137                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
138                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
139                      the feature's initial residues.</Notes>                      the feature's initial residues.</Notes>
140                      <DataGen testCount="0"></DataGen>                  </Field>
141                    <Field name="assignment" type="text">
142                        <Notes>Default functional assignment for this feature.</Notes>
143                  </Field>                  </Field>
144                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
145                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
146                      <DataGen>1</DataGen>                  </Field>
147                    <Field name="keywords" type="text" searchable="1">
148                        <Notes>This is a list of search keywords for the feature. It includes the
149                        functional assignment, subsystem roles, and special properties.</Notes>
150                  </Field>                  </Field>
151                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
152                      <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
153                      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
154                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
155                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
156                      "&amp;Number=" . IntGen(1,99)</DataGen>                  <Field name="conservation" type="float" relation="FeatureConservation">
157                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
158                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
159                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
160                        between the feature and its close relatives.</Notes>
161                    </Field>
162                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
163                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
164                        cases, this will be a word describing whether the essentiality is confirmed (essential)
165                        or potential (potential-essential), hyperlinked to the document from which the
166                        essentiality was curated. If a feature is not essential, this field will have no
167                        values; otherwise, it may have multiple values.</Notes>
168                    </Field>
169                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
170                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
171                        cases, this will be a phrase or SA number hyperlinked to the document from which
172                        the virulence information was curated. If the feature is not virulent, this field
173                        will have no values; otherwise, it may have multiple values.</Notes>
174                    </Field>
175                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
176                        <Notes>A value indicating whether or not the feature can be found in the
177                        Immune Epitope Database. If the feature has not been matched to that database,
178                        this field will have no values. Otherwise, it will have an epitope name and/or
179                        sequence, hyperlinked to the database.</Notes>
180                  </Field>                  </Field>
181              </Fields>              </Fields>
182              <Indexes>              <Indexes>
# Line 159  Line 189 
189                  </Index>                  </Index>
190              </Indexes>              </Indexes>
191          </Entity>          </Entity>
192            <Entity name="SynonymGroup" keyType="id-string">
193                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
194                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
195            </Entity>
196          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
197              <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.
198              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>
199              <Fields>              <Fields>
200                  <Field name="EC" type="string" relation="RoleEC">                  <Field name="EC" type="string" relation="RoleEC">
201                      <Notes>EC code for this role.</Notes>                      <Notes>EC code for this role.</Notes>
                     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>  
202                  </Field>                  </Field>
203                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="name-string">
204                      <Notes>Abbreviated name for the role, generally non-unique, but useful                      <Notes>Abbreviated name for the role, generally non-unique, but useful
# Line 185  Line 218 
218          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
219              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
220              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
221              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>  
222              <Fields>              <Fields>
223                  <Field name="time" type="date">                  <Field name="time" type="date">
224                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 196  Line 227 
227                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
228                  </Field>                  </Field>
229              </Fields>              </Fields>
230                <Indexes>
231                    <Index>
232                        <Notes>This index allows the user to find recent annotations.</Notes>
233                        <IndexFields>
234                            <IndexField name="time" order="descending" />
235                        </IndexFields>
236                    </Index>
237                </Indexes>
238          </Entity>          </Entity>
239          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
240              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
# Line 266  Line 305 
305                  <Field name="notes" type="text">                  <Field name="notes" type="text">
306                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
307                  </Field>                  </Field>
308                    <Field name="classification" type="string" relation="SubsystemClass">
309                        <Notes>Classification string, colon-delimited. This string organizes the
310                        subsystems into a hierarchy.</Notes>
311                    </Field>
312              </Fields>              </Fields>
313          </Entity>          </Entity>
314          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 279  Line 322 
322              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
323              to make it unique.</Notes>              to make it unique.</Notes>
324          </Entity>          </Entity>
325          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="hash-string">
326              <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
327              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
328              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 295  Line 338 
338                      <Notes>Access code possessed by this                      <Notes>Access code possessed by this
339                      user. A user can have many access codes; a genome is accessible to the user if its                      user. A user can have many access codes; a genome is accessible to the user if its
340                      access code matches any one of the user's access codes.</Notes>                      access code matches any one of the user's access codes.</Notes>
                     <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>  
341                  </Field>                  </Field>
342              </Fields>              </Fields>
343          </Entity>          </Entity>
# Line 360  Line 402 
402                      </Field>                      </Field>
403                  </Fields>                  </Fields>
404          </Entity>          </Entity>
405          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
406              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
407              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
408              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 376  Line 418 
418                  </Field>                  </Field>
419              </Fields>              </Fields>
420          </Entity>          </Entity>
421          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
422              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
423              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
424              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 384  Line 426 
426              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
427              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
428              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
429              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>  
430              <Fields>              <Fields>
431                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
432                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 396  Line 437 
437                  </Field>                  </Field>
438              </Fields>              </Fields>
439          </Entity>          </Entity>
440            <Entity name="Family" keyType="id-string">
441                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
442                families provide a mechanism for verifying the accuracy of functional assignments
443                and are also used in determining phylogenetic trees.</Notes>
444                <Fields>
445                    <Field name="function" type="text">
446                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
447                    </Field>
448                    <Field name="size" type="int">
449                        <Notes>The number of proteins in this family. This may be larger than the
450                        number of PEGs included in the family, since the family may also contain external
451                        IDs.</Notes>
452                    </Field>
453                </Fields>
454            </Entity>
455      </Entities>      </Entities>
456      <Relationships>      <Relationships>
457            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
458                <Notes>This relationship connects a protein family to all of its PEGs and connects
459                each PEG to all of its protein families.</Notes>
460            </Relationship>
461          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
462              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
463              in which it participates. A functional coupling is a recognition of the fact              in which it participates. A functional coupling is a recognition of the fact
# Line 418  Line 478 
478                  </IndexFields>                  </IndexFields>
479              </ToIndex>              </ToIndex>
480          </Relationship>          </Relationship>
481            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
482                <Notes>This relation connects a synonym group to the features that make it
483                up.</Notes>
484            </Relationship>
485            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
486                <Notes>This relationship connects a genome to all of its features. This
487                relationship is redundant in a sense, because the genome ID is part
488                of the feature ID; however, it makes the creation of certain queries more
489                convenient because you can drag in filtering information for a feature's
490                genome.</Notes>
491                <Fields>
492                    <Field name="type" type="key-string">
493                        <Notes>Feature type (eg. peg, rna)</Notes>
494                    </Field>
495                </Fields>
496                <FromIndex>
497                    <Notes>This index enables the application to view the features of a
498                    Genome sorted by type.</Notes>
499                    <IndexFields>
500                        <IndexField name="type" order="ascending" />
501                    </IndexFields>
502                </FromIndex>
503            </Relationship>
504          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
505              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
506              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 628  Line 711 
711                      [b]-[/b] if it is backward.</Notes>                      [b]-[/b] if it is backward.</Notes>
712                  </Field>                  </Field>
713              </Fields>              </Fields>
714              <FromIndex Unique="false">              <FromIndex>
715                  <Notes>This index allows the application to find all the segments of a feature in                  <Notes>This index allows the application to find all the segments of a feature in
716                  the proper order.</Notes>                  the proper order.</Notes>
717                  <IndexFields>                  <IndexFields>
# Line 643  Line 726 
726                  </IndexFields>                  </IndexFields>
727              </ToIndex>              </ToIndex>
728          </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>  
729          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
730              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
731              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 730  Line 791 
791              chemical reactions. A single reaction can be triggered by many roles,              chemical reactions. A single reaction can be triggered by many roles,
792              and a role can trigger many reactions.</Notes>              and a role can trigger many reactions.</Notes>
793          </Relationship>          </Relationship>
794            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
795                <Notes>This relationship connects a feature to the subsystems in which it
796                participates. This is technically redundant information, but it is used
797                so often that it deserves its own table.</Notes>
798                <Fields>
799                    <Field name="genome" type="name-string">
800                        <Notes>ID of the genome containing the feature</Notes>
801                    </Field>
802                    <Field name="type" type="key-string">
803                        <Notes>Feature type (eg. peg, rna)</Notes>
804                    </Field>
805                </Fields>
806                <ToIndex>
807                    <Notes>This index enables the application to view the features of a
808                    subsystem sorted by genome and feature type.</Notes>
809                    <IndexFields>
810                        <IndexField name="genome" order="ascending" />
811                        <IndexField name="type" order="ascending" />
812                    </IndexFields>
813                </ToIndex>
814            </Relationship>
815      </Relationships>      </Relationships>
816  </Database>  </Database>

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