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1 : parrello 1.1 <?xml version="1.0" encoding="utf-8" ?>
2 :     <Database>
3 :     <Title>Sprout Genome and Subsystem Database</Title>
4 :     <Entities>
5 :     <Entity name="Genome" keyType="name-string">
6 :     <Notes>A [i]genome[/i] contains the sequence data for a particular individual organism.</Notes>
7 :     <Fields>
8 :     <Field name="genus" type="name-string">
9 :     <Notes>Genus of the relevant organism.</Notes>
10 :     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>
11 :     </Field>
12 :     <Field name="species" type="name-string">
13 : parrello 1.8 <Notes>Species of the relevant organism.</Notes>
14 : parrello 1.1 <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>
15 : parrello 1.8 </Field>
16 : parrello 1.1 <Field name="unique-characterization" type="medium-string">
17 : parrello 1.8 <Notes>The unique characterization identifies the particular organism instance from which the
18 :     genome is taken. It is possible to have in the database more than one genome for a
19 : parrello 1.1 particular species, and every individual organism has variations in its DNA.</Notes>
20 : parrello 1.8 <DataGen>StringGen('PKVKVK999')</DataGen>
21 : parrello 1.1 </Field>
22 :     <Field name="access-code" type="key-string">
23 : parrello 1.8 <Notes>The access code determines which users can look at the data relating to this genome.
24 :     Each user is associated with a set of access codes. In order to view a genome, one of
25 :     the user's access codes must match this value.</Notes>
26 :     <DataGen>RandParam('low','medium','high')</DataGen>
27 :     </Field>
28 : parrello 1.15 <Field name="complete" type="boolean">
29 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
30 :     </Field>
31 : parrello 1.8 <Field name="taxonomy" type="text">
32 :     <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
34 :     the disambiguated genus and species (which is the organism's scientific name plus an
35 :     identifying string).</Notes>
36 :     <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
37 :     ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
38 :     </Field>
39 : parrello 1.37 <Field name="primary-group" type="name-string">
40 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
41 :     (either based on the organism name or the default value "Supporting"), whereas there can be
42 :     multiple named groups or even none.</Notes>
43 :     </Field>
44 : parrello 1.8 <Field name="group-name" type="name-string" relation="GenomeGroups">
45 :     <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
46 :     page or of particular interest to a research group or web site. A single genome can belong to multiple
47 :     such groups or none at all.</Notes>
48 :     </Field>
49 : parrello 1.1 </Fields>
50 :     <Indexes>
51 : parrello 1.37 <Index Unique="false">
52 : parrello 1.1 <Notes>This index allows the applications to find all genomes associated with
53 :     a specific access code, so that a complete list of the genomes users can view
54 :     may be generated.</Notes>
55 :     <IndexFields>
56 :     <IndexField name="access-code" order="ascending" />
57 :     <IndexField name="genus" order="ascending" />
58 :     <IndexField name="species" order="ascending" />
59 :     <IndexField name="unique-characterization" order="ascending" />
60 :     </IndexFields>
61 :     </Index>
62 :     <Index Unique="false">
63 : parrello 1.37 <Notes>This index allows the applications to find all genomes associated with
64 :     a specific primary (NMPDR) group.</Notes>
65 :     <IndexFields>
66 :     <IndexField name="primary-group" order="ascending" />
67 :     <IndexField name="genus" order="ascending" />
68 :     <IndexField name="species" order="ascending" />
69 :     <IndexField name="unique-characterization" order="ascending" />
70 :     </IndexFields>
71 :     </Index>
72 :     <Index Unique="false">
73 : parrello 1.1 <Notes>This index allows the applications to find all genomes for a particular
74 :     species.</Notes>
75 :     <IndexFields>
76 :     <IndexField name="genus" order="ascending" />
77 :     <IndexField name="species" order="ascending" />
78 :     <IndexField name="unique-characterization" order="ascending" />
79 :     </IndexFields>
80 :     </Index>
81 :     </Indexes>
82 :     </Entity>
83 :     <Entity name="Source" keyType="medium-string">
84 :     <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
85 :     or a paper citation.</Notes>
86 :     <Fields>
87 :     <Field name="URL" type="string" relation="SourceURL">
88 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
89 :     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>
90 :     </Field>
91 : parrello 1.1 <Field name="description" type="text">
92 : parrello 1.8 <Notes>Description the source. The description can be a street address or a citation.</Notes>
93 :     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>
94 :     </Field>
95 : parrello 1.1 </Fields>
96 :     </Entity>
97 :     <Entity name="Contig" keyType="name-string">
98 :     <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the
99 :     genome ID followed by a name that identifies which contig this is for the parent genome. As
100 :     is the case with all keys in this database, the individual components are separated by a
101 :     period.
102 :     [p]A contig can contain over a million residues. For performance reasons, therefore,
103 :     the contig is split into multiple pieces called [i]sequences[/i]. The sequences
104 :     contain the characters that represent the residues as well as data on the quality of
105 :     the residue identification.</Notes>
106 :     </Entity>
107 :     <Entity name="Sequence" keyType="name-string">
108 :     <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into
109 :     sequences so that we don't have to have the entire contig in memory when we are
110 :     manipulating it. The key of the sequence is the contig ID followed by the index of
111 :     the begin point.</Notes>
112 :     <Fields>
113 :     <Field name="sequence" type="text">
114 : parrello 1.8 <Notes>String consisting of the residues. Each residue is described by a single
115 :     character in the string.</Notes>
116 :     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
117 :     </Field>
118 : parrello 1.1 <Field name="quality-vector" type="text">
119 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
120 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
121 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
122 :     10^-30. A higher quality number a better chance of a correct match. It is possible
123 : parrello 1.9 that the quality data is not known for a sequence. If that is the case, the quality
124 : parrello 1.8 vector will contain the [b]unknown[/b].</Notes>
125 :     <DataGen>unknown</DataGen>
126 :     </Field>
127 : parrello 1.1 </Fields>
128 :     </Entity>
129 : parrello 1.25 <Entity name="Feature" keyType="id-string">
130 : parrello 1.1 <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
131 :     may be spread across multiple contigs of a genome, but never across more than
132 :     one genome. Features can be assigned to roles via spreadsheet cells,
133 :     and are the targets of annotation.</Notes>
134 :     <Fields>
135 :     <Field name="feature-type" type="string">
136 : parrello 1.8 <Notes>Code indicating the type of this feature.</Notes>
137 :     <DataGen>RandParam('peg','rna')</DataGen>
138 :     </Field>
139 : parrello 1.14 <Field name="alias" type="medium-string" relation="FeatureAlias">
140 : parrello 1.9 <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
141 : parrello 1.8 <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
142 :     </Field>
143 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
144 : parrello 1.8 <Notes>[i](optional)[/i] A translation of this feature's residues into character
145 :     codes, formed by concatenating the pieces of the feature together. For a
146 :     protein encoding group, this is the protein characters. For other types
147 :     it is the DNA characters.</Notes>
148 :     <DataGen testCount="0"></DataGen>
149 :     </Field>
150 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
151 : parrello 1.8 <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
152 :     the feature's initial residues.</Notes>
153 :     <DataGen testCount="0"></DataGen>
154 :     </Field>
155 : parrello 1.1 <Field name="active" type="boolean">
156 : parrello 1.11 <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
157 : parrello 1.8 <DataGen>1</DataGen>
158 :     </Field>
159 : parrello 1.41 <Field name="keywords" type="text" searchable="1">
160 :     <Notes>This is a list of search keywords for the feature. It includes the
161 :     functional assignment, subsystem roles, and special properties.</Notes>
162 : parrello 1.36 </Field>
163 : parrello 1.8 <Field name="link" type="text" relation="FeatureLink">
164 :     <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
165 :     links are to other websites that have useful about the gene that the feature represents, and
166 :     are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
167 :     <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
168 :     "&amp;Number=" . IntGen(1,99)</DataGen>
169 :     </Field>
170 : parrello 1.41 <Field name="conservation" type="float" relation="FeatureConservation">
171 :     <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
172 :     conserved in related genomes. A value of 1 indicates perfect conservation. A value less
173 :     than 1 is a reflect of the degree to which gap characters interfere in the alignment
174 :     between the feature and its close relatives.</Notes>
175 :     </Field>
176 : parrello 1.1 </Fields>
177 : parrello 1.8 <Indexes>
178 :     <Index>
179 :     <Notes>This index allows the user to find the feature corresponding to
180 :     the specified alias name.</Notes>
181 :     <IndexFields>
182 :     <IndexField name="alias" order="ascending" />
183 :     </IndexFields>
184 :     </Index>
185 :     </Indexes>
186 : parrello 1.1 </Entity>
187 : parrello 1.27 <Entity name="SynonymGroup" keyType="id-string">
188 :     <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
189 :     are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
190 :     </Entity>
191 : parrello 1.1 <Entity name="Role" keyType="string">
192 :     <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
193 :     One of the main goals of the database is to record the roles of the various features.</Notes>
194 : parrello 1.8 <Fields>
195 : parrello 1.18 <Field name="EC" type="string" relation="RoleEC">
196 :     <Notes>EC code for this role.</Notes>
197 : parrello 1.8 <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
198 :     </Field>
199 : parrello 1.15 <Field name="abbr" type="name-string">
200 :     <Notes>Abbreviated name for the role, generally non-unique, but useful
201 :     in column headings for HTML tables.</Notes>
202 :     </Field>
203 : parrello 1.8 </Fields>
204 : parrello 1.18 <Indexes>
205 :     <Index>
206 :     <Notes>This index allows the user to find the role corresponding to
207 :     an EC number.</Notes>
208 :     <IndexFields>
209 :     <IndexField name="EC" order="ascending" />
210 :     </IndexFields>
211 :     </Index>
212 :     </Indexes>
213 : parrello 1.1 </Entity>
214 :     <Entity name="Annotation" keyType="name-string">
215 :     <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
216 : parrello 1.8 are currently the only objects that may be inserted directly into the database. All other
217 : parrello 1.24 information is loaded from data exported by the SEED.</Notes>
218 : parrello 1.8 <Fields>
219 :     <Field name="time" type="date">
220 :     <Notes>Date and time of the annotation.</Notes>
221 :     </Field>
222 :     <Field name="annotation" type="text">
223 :     <Notes>Text of the annotation.</Notes>
224 :     </Field>
225 : parrello 1.1 </Fields>
226 : parrello 1.26 <Indexes>
227 :     <Index>
228 :     <Notes>This index allows the user to find recent annotations.</Notes>
229 :     <IndexFields>
230 :     <IndexField name="time" order="descending" />
231 :     </IndexFields>
232 :     </Index>
233 :     </Indexes>
234 : parrello 1.1 </Entity>
235 : parrello 1.15 <Entity name="Reaction" keyType="key-string">
236 :     <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
237 :     is generally a small number preceded by a letter.</Notes>
238 :     <Fields>
239 :     <Field name="url" type="string" relation="ReactionURL">
240 :     <Notes>HTML string containing a link to a web location that describes the
241 :     reaction. This field is optional.</Notes>
242 :     </Field>
243 :     <Field name="rev" type="boolean">
244 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
245 :     </Field>
246 :     </Fields>
247 :     </Entity>
248 :     <Entity name="Compound" keyType="name-string">
249 :     <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
250 :     All compounds have a unique ID and may also have one or more names.</Notes>
251 :     <Fields>
252 :     <Field name="name-priority" type="int" relation="CompoundName">
253 :     <Notes>Priority of a compound name. The name with the loweset
254 :     priority is the main name of this compound.</Notes>
255 :     </Field>
256 :     <Field name="name" type="name-string" relation="CompoundName">
257 :     <Notes>Descriptive name for the compound. A compound may
258 :     have several names.</Notes>
259 :     </Field>
260 :     <Field name="cas-id" type="name-string" relation="CompoundCAS">
261 :     <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
262 :     </Field>
263 : parrello 1.19 <Field name="label" type="name-string">
264 :     <Notes>Name used in reaction display strings.
265 :     It is the same as the name possessing a priority of 1, but it is placed
266 :     here to speed up the query used to create the display strings.</Notes>
267 :     </Field>
268 : parrello 1.15 </Fields>
269 :     <Indexes>
270 :     <Index>
271 :     <Notes>This index allows the user to find the compound corresponding to
272 :     the specified name.</Notes>
273 :     <IndexFields>
274 :     <IndexField name="name" order="ascending" />
275 :     </IndexFields>
276 :     </Index>
277 :     <Index>
278 : parrello 1.17 <Notes>This index allows the user to find the compound corresponding to
279 :     the specified CAS ID.</Notes>
280 :     <IndexFields>
281 :     <IndexField name="cas-id" order="ascending" />
282 :     </IndexFields>
283 :     </Index>
284 :     <Index>
285 : parrello 1.15 <Notes>This index allows the user to access the compound names in
286 :     priority order.</Notes>
287 :     <IndexFields>
288 :     <IndexField name="id" order="ascending" />
289 :     <IndexField name="name-priority" order="ascending" />
290 :     </IndexFields>
291 :     </Index>
292 :     </Indexes>
293 :     </Entity>
294 : parrello 1.5 <Entity name="Subsystem" keyType="string">
295 : parrello 1.1 <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
296 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
297 : parrello 1.15 <Fields>
298 :     <Field name="curator" type="string">
299 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
300 :     </Field>
301 :     <Field name="notes" type="text">
302 :     <Notes>Descriptive notes about the subsystem.</Notes>
303 :     </Field>
304 : parrello 1.28 <Field name="classification" type="string" relation="SubsystemClass">
305 :     <Notes>General classification data about the subsystem.</Notes>
306 :     </Field>
307 : parrello 1.15 </Fields>
308 :     </Entity>
309 :     <Entity name="RoleSubset" keyType="string">
310 :     <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
311 :     subset names are generally very short, non-unique strings. The ID of the parent
312 :     subsystem is prefixed to the subset ID in order to make it unique.</Notes>
313 :     </Entity>
314 :     <Entity name="GenomeSubset" keyType="string">
315 :     <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
316 :     in a particular subsystem. The subset names are generally very short, non-unique
317 :     strings. The ID of the parent subsystem is prefixed to the subset ID in order
318 :     to make it unique.</Notes>
319 : parrello 1.1 </Entity>
320 : parrello 1.24 <Entity name="SSCell" keyType="hash-string">
321 : parrello 1.1 <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
322 :     genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
323 :     of the positions on the spreadsheet.</Notes>
324 :     </Entity>
325 :     <Entity name="SproutUser" keyType="name-string">
326 :     <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The
327 :     user object is keyed on the user's login name.</Notes>
328 :     <Fields>
329 : parrello 1.8 <Field name="description" type="string">
330 :     <Notes>Full name or description of this user.</Notes>
331 :     </Field>
332 : parrello 1.1 <Field name="access-code" type="key-string" relation="UserAccess">
333 : parrello 1.8 <Notes>Access code possessed by this
334 : parrello 1.1 user. A user can have many access codes; a genome is accessible to the user if its
335 :     access code matches any one of the user's access codes.</Notes>
336 : parrello 1.8 <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>
337 :     </Field>
338 : parrello 1.1 </Fields>
339 :     </Entity>
340 : parrello 1.8 <Entity name="Property" keyType="int">
341 :     <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of
342 :     a particular feature. Each property instance is a key/value pair and can be associated
343 :     with many different features. Conversely, a feature can be associated with many key/value
344 :     pairs, even some that notionally contradict each other. For example, there can be evidence
345 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
346 :     <Fields>
347 :     <Field name="property-name" type="name-string">
348 :     <Notes>Name of this property.</Notes>
349 :     </Field>
350 :     <Field name="property-value" type="string">
351 :     <Notes>Value associated with this property. For each property
352 :     name, there must by a property record for all of its possible
353 :     values.</Notes>
354 :     </Field>
355 :     </Fields>
356 :     <Indexes>
357 :     <Index>
358 :     <Notes>This index enables the application to find all values for a specified property
359 :     name, or any given name/value pair.</Notes>
360 :     <IndexFields>
361 :     <IndexField name="property-name" order="ascending" />
362 :     <IndexField name="property-value" order="ascending" />
363 :     </IndexFields>
364 :     </Index>
365 :     </Indexes>
366 :     </Entity>
367 :     <Entity name="Diagram" keyType="name-string">
368 :     <Notes>A functional diagram describes the chemical reactions, often comprising a single
369 :     subsystem. A diagram is identified by a short name and contains a longer descriptive name.
370 :     The actual diagram shows which functional roles guide the reactions along with the inputs
371 :     and outputs; the database, however, only indicate which roles belong to a particular
372 :     map.</Notes>
373 :     <Fields>
374 :     <Field name="name" type="text">
375 :     <Notes>Descriptive name of this diagram.</Notes>
376 :     </Field>
377 :     </Fields>
378 :     </Entity>
379 :     <Entity name="ExternalAliasOrg" keyType="name-string">
380 :     <Notes>An external alias is a feature name for a functional assignment that is not a
381 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
382 :     the database. This table contains a description of the relevant organism for an
383 :     external alias functional assignment.</Notes>
384 :     <Fields>
385 :     <Field name="org" type="text">
386 :     <Notes>Descriptive name of the target organism for this external alias.</Notes>
387 :     </Field>
388 :     </Fields>
389 :     </Entity>
390 :     <Entity name="ExternalAliasFunc" keyType="name-string">
391 :     <Notes>An external alias is a feature name for a functional assignment that is not a
392 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
393 :     the database. This table contains the functional role for the external alias functional
394 :     assignment.</Notes>
395 :     <Fields>
396 :     <Field name="func" type="text">
397 :     <Notes>Functional role for this external alias.</Notes>
398 :     </Field>
399 :     </Fields>
400 :     </Entity>
401 : parrello 1.29 <Entity name="Coupling" keyType="id-string">
402 : parrello 1.6 <Notes>A coupling is a relationship between two features. The features are
403 :     physically close on the contig, and there is evidence that they generally
404 :     belong together. The key of this entity is formed by combining the coupled
405 : parrello 1.8 feature IDs with a space.</Notes>
406 : parrello 1.6 <Fields>
407 :     <Field name="score" type="int">
408 :     <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH
409 :     indicates that two genes near each other on one genome are very similar to
410 :     genes near each other on another genome. The score only counts PCHs for which
411 :     the genomes are very different. (In other words, we have a pairing that persists
412 :     between different organisms.) A higher score implies a stronger meaning to the
413 :     clustering.</Notes>
414 :     </Field>
415 :     </Fields>
416 :     </Entity>
417 : parrello 1.30 <Entity name="PCH" keyType="counter">
418 : parrello 1.6 <Notes>A PCH (physically close homolog) connects a clustering (which is a
419 :     pair of physically close features on a contig) to a second pair of physically
420 :     close features that are similar to the first. Essentially, the PCH is a
421 :     relationship between two clusterings in which the first clustering's features
422 :     are similar to the second clustering's features. The simplest model for
423 :     this would be to simply relate clusterings to each other; however, not all
424 :     physically close pairs qualify as clusterings, so we relate a clustering to
425 : parrello 1.30 a pair of features. The key a unique ID number.</Notes>
426 : parrello 1.6 <Fields>
427 :     <Field name="used" type="boolean">
428 :     <Notes>TRUE if this PCH is used in scoring the attached clustering,
429 :     else FALSE. If a clustering has a PCH for a particular genome and many
430 :     similar genomes are present, then a PCH will probably exist for the
431 :     similar genomes as well. When this happens, only one of the PCHs will
432 :     be scored: the others are considered duplicates of the same evidence.</Notes>
433 :     </Field>
434 :     </Fields>
435 :     </Entity>
436 : parrello 1.31 <Entity name="Family" keyType="id-string">
437 :     <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
438 :     families provide a mechanism for verifying the accuracy of functional assignments
439 :     and are also used in determining phylogenetic trees.</Notes>
440 :     <Fields>
441 : parrello 1.32 <Field name="function" type="text">
442 : parrello 1.31 <Notes>The functional assignment expected for all PEGs in this family.</Notes>
443 :     </Field>
444 : parrello 1.33 <Field name="size" type="int">
445 : parrello 1.31 <Notes>The number of proteins in this family. This may be larger than the
446 :     number of PEGs included in the family, since the family may also contain external
447 :     IDs.</Notes>
448 :     </Field>
449 :     </Fields>
450 :     </Entity>
451 : parrello 1.41 <Entity name="DrugProject" keyType="name-string">
452 :     <Notes>A drug project is a coherent sent of drug target data that came through the
453 :     pipeline. In other words, data is put into the database one drug project at a time.
454 :     This makes it easier to manage the incoming data and to track where a particular
455 :     piece of data originated.</Notes>
456 :     </Entity>
457 :     <Entity name="DrugTopic" keyType="int">
458 :     <Notes>A drug topic organizes the data in a project relating to a single organism
459 :     group's features as they apply to a specific category of activity. Categories include
460 :     features essential to the organism's survival, those that are targets or inhibitors
461 :     of anti-biotics, and those associated with virulence. Thus, a drug topic consists
462 :     of data from a single project for features that make good drug targets for the same
463 :     reason. Drug topics have an artificial, internally-generated key.</Notes>
464 :     <Fields>
465 :     <Field name="identifier" type="name-string">
466 :     <Notes>The topic identifier, consisting usually of a generalized organism name
467 :     (e.g. Staphylococcus) and the last name of the project's author. More than
468 :     one topic may have the same identifier, which is why this isn't the key.</Notes>
469 :     </Field>
470 :     <Field name="function" type="name-string">
471 :     <Notes>A short phrase describing the topic.</Notes>
472 :     </Field>
473 :     <Field name="URL" type="string">
474 :     <Notes>A URL for the paper from which the topic was gathered.</Notes>
475 :     </Field>
476 :     <Field name="category" type="key-string">
477 :     <Notes>The code for this topic's activity category.</Notes>
478 :     </Field>
479 :     </Fields>
480 :     <Indexes>
481 :     <Index>
482 :     <Notes>This index enables the application to find all topics with a specified
483 :     category, ordered by function.</Notes>
484 :     <IndexFields>
485 :     <IndexField name="category" order="ascending" />
486 :     <IndexField name="function" order="ascending" />
487 :     </IndexFields>
488 :     </Index>
489 :     <Index>
490 :     <Notes>This index enables the application to find all topics with a specified
491 :     identifier, ordered by category.</Notes>
492 :     <IndexFields>
493 :     <IndexField name="identifier" order="ascending" />
494 :     <IndexField name="category" order="ascending" />
495 :     </IndexFields>
496 :     </Index>
497 :     </Indexes>
498 :     </Entity>
499 :     <Entity name="PDB" keyType="key-string">
500 :     <Notes>A PDB is a database of protein structure and related information of use
501 :     in drug targeting. The purpose of drug targeting is to analyze the ability
502 :     of drug molecules, or ligands, to bond to proteins. A PDB for a protein already
503 :     attached to a ligand is called a bound PDB. A PDB for the protein by itself is
504 :     called a free PDB. The key of the PDB is its code name on the Protein Data
505 :     Bank web site.</Notes>
506 :     <Fields>
507 :     <Field name="type" type="id-string">
508 :     <Notes>The type of PDB: "bound" or "free".</Notes>
509 :     </Field>
510 :     <Field name="title" type="string">
511 :     <Notes>The descriptive title of this PDB.</Notes>
512 :     </Field>
513 :     </Fields>
514 :     </Entity>
515 :     <Entity name="Ligand" keyType="string">
516 :     <Notes>A ligand is a molecule that can bind to a PDB. The CLIBE analysis
517 :     for a PDB is an attribute of the relationship between a PDB and a ligand.</Notes>
518 :     </Entity>
519 : parrello 1.1 </Entities>
520 :     <Relationships>
521 : parrello 1.41 <Relationship name="BindsWith" from="PDB" to="Ligand" arity="MM">
522 :     <Notes>This relationship describes the energy required for a ligand to bind
523 :     to the protein described by a PDB. The total energy required to bind
524 :     the ligand to the protein is described in this relationship by four
525 :     quantities. A negative value is energy released; a positive value is
526 :     energy required.</Notes>
527 :     <Fields>
528 :     <Field name="URL" type="string">
529 :     <Notes>URL for viewing the CLIBE data for this binding relationship.</Notes>
530 :     </Field>
531 :     <Field name="vanderwaals-energy" type="float">
532 :     <Notes>kCal/mol of energy due to Van der Waals force.</Notes>
533 :     </Field>
534 :     <Field name="hbond-energy" type="float">
535 :     <Notes>kCal/mol of energy due to hydrogen bonding.</Notes>
536 :     </Field>
537 :     <Field name="ionic-energy" type="float">
538 :     <Notes>kCal/mol of energy due to ionic bonding.</Notes>
539 :     </Field>
540 :     <Field name="solvation-energy" type="float">
541 :     <Notes>kCal/mol of energy due to attraction to the solvent in which
542 :     the ligand is immersed.</Notes>
543 :     </Field>
544 :     </Fields>
545 :     </Relationship>
546 :     <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="1M">
547 :     <Notes>This relationship describes the analysis of a free PDB as produced from a
548 :     particular topic.</Notes>
549 :     <Fields>
550 :     <Field name="pass-asp-info" type="int">
551 :     <Notes>The number of Active Site Points at which ligands can bind to
552 :     the protein.</Notes>
553 :     </Field>
554 :     <Field name="ramsol-file" type="string">
555 :     <Notes>The URL of a file that can be downloaded by the user and
556 :     passed to the Ramsol program for viewing the protein.</Notes>
557 :     </Field>
558 :     <Field name="pass-weight" type="float">
559 :     <Notes>A score for the largest pocket into which a ligand can bind. A
560 :     higher score makes for a better target.</Notes>
561 :     </Field>
562 :     <Field name="pass-file" type="string">
563 :     <Notes>The URL for a GIF file that shows the active sites on the protein.</Notes>
564 :     </Field>
565 :     </Fields>
566 :     </Relationship>
567 :     <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="1M">
568 :     <Note>This relationship connects a free PDB to its bound counterparts.</Note>
569 :     </Relationship>
570 :     <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
571 :     <Notes>This relationship connects a feature to a protein database (PDB) that
572 :     is relevant for determining drugs that target the feature.</Notes>
573 :     <Fields>
574 :     <Field name="score" type="float">
575 :     <Notes>The BLAST score for the feature as it relates to the PDB's
576 :     protein, expressed as a small positive number. Generally only a
577 :     very low BLAST score (1e-15 or less) indicates a good match.</Notes>
578 :     </Field>
579 :     <Field name="distance" type="float">
580 :     <Notes>A distance value indicating how far the PDB's protein is
581 :     from the feature's protein. A distance of 0 indicates a perfect
582 :     match.</Notes>
583 :     </Field>
584 :     </Fields>
585 :     <FromIndex>
586 :     <Notes>This index yields the Features for a PDB in order from best
587 :     score to worst.</Notes>
588 :     <IndexFields>
589 :     <IndexField name="score" order="ascending" />
590 :     </IndexFields>
591 :     </FromIndex>
592 :     <ToIndex>
593 :     <Notes>This index yields the Features for a PDB in order from best
594 :     score to worst.</Notes>
595 :     <IndexFields>
596 :     <IndexField name="score" order="ascending" />
597 :     </IndexFields>
598 :     </ToIndex>
599 :     </Relationship>
600 :     <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">
601 :     <Notes>This relationship connects a drug target project to all of its
602 :     topics.</Notes>
603 :     </Relationship>
604 : parrello 1.34 <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
605 : parrello 1.31 <Notes>This relationship connects a protein family to all of its PEGs and connects
606 :     each PEG to all of its protein families.</Notes>
607 :     </Relationship>
608 : parrello 1.6 <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
609 :     <Notes>This relationship connects a feature to all the functional couplings
610 :     in which it participates. A functional coupling is a recognition of the fact
611 :     that the features are close to each other on a chromosome, and similar
612 :     features in other genomes also tend to be close.</Notes>
613 :     <Fields>
614 :     <Field name="pos" type="int">
615 :     <Notes>Ordinal position of the feature in the coupling. Currently,
616 :     this is either "1" or "2".</Notes>
617 :     </Field>
618 :     </Fields>
619 :     <ToIndex>
620 :     <Notes>This index enables the application to view the features of
621 :     a coupling in the proper order. The order influences the way the
622 :     PCHs are examined.</Notes>
623 :     <IndexFields>
624 :     <IndexField name="pos" order="ascending" />
625 :     </IndexFields>
626 :     </ToIndex>
627 :     </Relationship>
628 : parrello 1.27 <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
629 :     <Notes>This relation connects a synonym group to the features that make it
630 :     up.</Notes>
631 :     </Relationship>
632 : parrello 1.24 <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
633 :     <Notes>This relationship connects a genome to all of its features. This
634 :     relationship is redundant in a sense, because the genome ID is part
635 :     of the feature ID; however, it makes the creation of certain queries more
636 :     convenient because you can drag in filtering information for a feature's
637 :     genome.</Notes>
638 :     <Fields>
639 :     <Field name="type" type="key-string">
640 :     <Notes>Feature type (eg. peg, rna)</Notes>
641 :     </Field>
642 :     </Fields>
643 : parrello 1.38 <FromIndex>
644 : parrello 1.24 <Notes>This index enables the application to view the features of a
645 :     Genome sorted by type.</Notes>
646 :     <IndexFields>
647 :     <IndexField name="type" order="ascending" />
648 :     </IndexFields>
649 : parrello 1.38 </FromIndex>
650 : parrello 1.24 </Relationship>
651 : parrello 1.6 <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
652 :     <Notes>This relationship connects a functional coupling to the physically
653 :     close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
654 :     </Relationship>
655 :     <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">
656 :     <Notes>This relationship connects a PCH to the features that represent its
657 :     evidence. Each PCH is connected to a parent coupling that relates two features
658 :     on a specific genome. The PCH's evidence that the parent coupling is functional
659 :     is the existence of two physically close features on a different genome that
660 :     correspond to the features in the coupling. Those features are found on the
661 :     far side of this relationship.</Notes>
662 :     <Fields>
663 :     <Field name="pos" type="int">
664 :     <Notes>Ordinal position of the feature in the coupling that corresponds
665 :     to our target feature. There is a one-to-one correspondence between the
666 :     features connected to the PCH by this relationship and the features
667 :     connected to the PCH's parent coupling. The ordinal position is used
668 :     to decode that relationship. Currently, this field is either "1" or
669 :     "2".</Notes>
670 :     </Field>
671 :     </Fields>
672 :     <FromIndex>
673 :     <Notes>This index enables the application to view the features of
674 :     a PCH in the proper order.</Notes>
675 :     <IndexFields>
676 :     <IndexField name="pos" order="ascending" />
677 :     </IndexFields>
678 :     </FromIndex>
679 :     </Relationship>
680 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
681 :     <Notes>This relationship connects a genome to the contigs that contain the actual genetic
682 :     information.</Notes>
683 :     </Relationship>
684 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
685 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
686 :     come from a single source or from a cooperation among multiple sources.</Notes>
687 :     </Relationship>
688 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
689 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
690 :     contig into sequences, we get a performance boost from only needing to keep small portions
691 :     of a contig in memory at any one time. This relationship connects the contig to its
692 :     constituent sequences.</Notes>
693 :     <Fields>
694 :     <Field name="len" type="int">
695 : parrello 1.15 <Notes>Length of the sequence.</Notes>
696 :     </Field>
697 : parrello 1.1 <Field name="start-position" type="int">
698 : parrello 1.15 <Notes>Index (1-based) of the point in the contig where this
699 :     sequence starts.</Notes>
700 :     </Field>
701 : parrello 1.1 </Fields>
702 :     <FromIndex>
703 :     <Notes>This index enables the application to find all of the sequences in
704 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
705 : parrello 1.1 <IndexFields>
706 :     <IndexField name="start-position" order="ascending" />
707 :     <IndexField name="len" order="ascending" />
708 :     </IndexFields>
709 :     </FromIndex>
710 :     </Relationship>
711 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
712 :     <Notes>This relationship connects a feature to its annotations.</Notes>
713 :     </Relationship>
714 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
715 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
716 :     </Relationship>
717 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
718 :     <Notes>This relationship connects subsystems to the genomes that use
719 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
720 :     connected to the genome features through the [b]SSCell[/b] object.</Notes>
721 : parrello 1.15 <Fields>
722 :     <Field name="variant-code" type="key-string">
723 : parrello 1.20 <Notes>Code indicating the subsystem variant to which this
724 : parrello 1.15 genome belongs. Each subsystem can have multiple variants. A variant
725 : parrello 1.20 code of [b]-1[/b] indicates that the genome does not have a functional
726 :     variant of the subsystem. A variant code of [b]0[/b] indicates that
727 :     the genome's participation is considered iffy.</Notes>
728 : parrello 1.15 </Field>
729 :     </Fields>
730 :     <ToIndex>
731 :     <Notes>This index enables the application to find all of the genomes using
732 :     a subsystem in order by variant code, which is how we wish to display them
733 :     in the spreadsheets.</Notes>
734 :     <IndexFields>
735 :     <IndexField name="variant-code" order="ascending" />
736 :     </IndexFields>
737 :     </ToIndex>
738 : parrello 1.1 </Relationship>
739 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
740 :     <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
741 : parrello 1.15 <Fields>
742 :     <Field name="column-number" type="int">
743 :     <Notes>Column number for this role in the specified subsystem's
744 :     spreadsheet.</Notes>
745 :     </Field>
746 :     </Fields>
747 :     <ToIndex>
748 :     <Notes>This index enables the application to see the subsystem roles
749 :     in column order. The ordering of the roles is usually significant,
750 :     so it is important to preserve it.</Notes>
751 :     <IndexFields>
752 :     <IndexField name="column-number" order="ascending" />
753 :     </IndexFields>
754 :     </ToIndex>
755 : parrello 1.1 </Relationship>
756 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
757 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
758 :     genome for the spreadsheet column.</Notes>
759 :     </Relationship>
760 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
761 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
762 :     role for the spreadsheet row.</Notes>
763 :     </Relationship>
764 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
765 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
766 :     features assigned to it.</Notes>
767 : parrello 1.15 <Fields>
768 :     <Field name="cluster-number" type="int">
769 :     <Notes>ID of this feature's cluster. Clusters represent families of
770 :     related proteins participating in a subsystem.</Notes>
771 :     </Field>
772 :     </Fields>
773 :     </Relationship>
774 :     <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
775 :     <Notes>This relationship connects a reaction to the compounds that participate
776 :     in it.</Notes>
777 :     <Fields>
778 :     <Field name="product" type="boolean">
779 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
780 :     it is a substrate. When a reaction is written on paper in
781 :     chemical notation, the substrates are left of the arrow and the
782 :     products are to the right. Sorting on this field will cause
783 :     the substrates to appear first, followed by the products. If the
784 :     reaction is reversible, then the notion of substrates and products
785 :     is not at intuitive; however, a value here of FALSE still puts the
786 :     compound left of the arrow and a value of TRUE still puts it to the
787 :     right.</Notes>
788 :     </Field>
789 : parrello 1.19 <Field name="stoichiometry" type="key-string">
790 : parrello 1.15 <Notes>Number of molecules of the compound that participate in a
791 :     single instance of the reaction. For example, if a reaction
792 : parrello 1.19 produces two water molecules, the stoichiometry of water for the
793 : parrello 1.15 reaction would be two. When a reaction is written on paper in
794 : parrello 1.19 chemical notation, the stoichiometry is the number next to the
795 : parrello 1.15 chemical formula of the compound.</Notes>
796 :     </Field>
797 :     <Field name="main" type="boolean">
798 :     <Notes>TRUE if this compound is one of the main participants in
799 :     the reaction, else FALSE. It is permissible for none of the
800 :     compounds in the reaction to be considered main, in which
801 :     case this value would be FALSE for all of the relevant
802 :     compounds.</Notes>
803 :     </Field>
804 :     <Field name="loc" type="key-string">
805 :     <Notes>An optional character string that indicates the relative
806 :     position of this compound in the reaction's chemical formula. The
807 :     location affects the way the compounds present as we cross the
808 :     relationship from the reaction side. The product/substrate flag
809 :     comes first, then the value of this field, then the main flag.
810 :     The default value is an empty string; however, the empty string
811 :     sorts first, so if this field is used, it should probably be
812 :     used for every compound in the reaction.</Notes>
813 :     </Field>
814 : parrello 1.19 <Field name="discriminator" type="int">
815 :     <Notes>A unique ID for this record. The discriminator does not
816 :     provide any useful data, but it prevents identical records from
817 :     being collapsed by the SELECT DISTINCT command used by ERDB to
818 :     retrieve data.</Notes>
819 :     </Field>
820 : parrello 1.15 </Fields>
821 :     <ToIndex>
822 :     <Notes>This index presents the compounds in the reaction in the
823 :     order they should be displayed when writing it in chemical notation.
824 :     All the substrates appear before all the products, and within that
825 :     ordering, the main compounds appear first.</Notes>
826 : parrello 1.19 <IndexFields>
827 :     <IndexField name="product" order="ascending" />
828 :     <IndexField name="loc" order="ascending" />
829 :     <IndexField name="main" order="descending" />
830 :     </IndexFields>
831 : parrello 1.15 </ToIndex>
832 : parrello 1.1 </Relationship>
833 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
834 :     <Notes>This relationship connects a feature to the contig segments that work together
835 :     to effect it. The segments are numbered sequentially starting from 1. The database is
836 :     required to place an upper limit on the length of each segment. If a segment is longer
837 :     than the maximum, it can be broken into smaller bits.
838 :     [p]The upper limit enables applications to locate all features that contain a specific
839 :     residue. For example, if the upper limit is 100 and we are looking for a feature that
840 :     contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point
841 :     between 135 and 333. The results can then be filtered by direction and length of the
842 :     segment.</Notes>
843 :     <Fields>
844 :     <Field name="locN" type="int">
845 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
846 :     </Field>
847 : parrello 1.1 <Field name="beg" type="int">
848 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
849 :     belongs to the segment.</Notes>
850 :     </Field>
851 : parrello 1.1 <Field name="len" type="int">
852 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
853 :     a specific point between residues. This is the point before the residue if the direction
854 :     is forward and the point after the residue if the direction is backward.</Notes>
855 :     </Field>
856 : parrello 1.1 <Field name="dir" type="char">
857 : parrello 1.8 <Notes>Direction of the segment: [b]+[/b] if it is forward and
858 :     [b]-[/b] if it is backward.</Notes>
859 :     </Field>
860 : parrello 1.1 </Fields>
861 :     <FromIndex Unique="false">
862 :     <Notes>This index allows the application to find all the segments of a feature in
863 : parrello 1.8 the proper order.</Notes>
864 : parrello 1.1 <IndexFields>
865 :     <IndexField name="locN" order="ascending" />
866 :     </IndexFields>
867 :     </FromIndex>
868 :     <ToIndex>
869 :     <Notes>This index is the one used by applications to find all the feature
870 :     segments that contain a specific residue.</Notes>
871 :     <IndexFields>
872 :     <IndexField name="beg" order="ascending" />
873 :     </IndexFields>
874 :     </ToIndex>
875 :     </Relationship>
876 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
877 :     <Notes>This relationship connects a feature to its known property values.
878 :     The relationship contains text data that indicates the paper or organization
879 :     that discovered evidence that the feature possesses the property. So, for
880 :     example, if two papers presented evidence that a feature is essential,
881 :     there would be an instance of this relationship for both.</Notes>
882 :     <Fields>
883 :     <Field name="evidence" type="text">
884 :     <Notes>URL or citation of the paper or
885 :     institution that reported evidence of the relevant feature possessing
886 :     the specified property value.</Notes>
887 :     </Field>
888 :     </Fields>
889 :     </Relationship>
890 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
891 :     <Notes>This relationship connects a role to the diagrams on which it
892 :     appears. A role frequently identifies an enzyme, and can appear in many
893 :     diagrams. A diagram generally contains many different roles.</Notes>
894 :     </Relationship>
895 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
896 :     <Notes>This relationship connects a subsystem to the spreadsheet cells
897 :     used to analyze and display it. The cells themselves can be thought of
898 :     as a grid with Roles on one axis and Genomes on the other. The
899 :     various features of the subsystem are then assigned to the cells.</Notes>
900 :     </Relationship>
901 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
902 :     <Notes>This relationship identifies the users trusted by each
903 :     particular user. When viewing functional assignments, the
904 :     assignment displayed is the most recent one by a user trusted
905 :     by the current user. The current user implicitly trusts himself.
906 :     If no trusted users are specified in the database, the user
907 :     also implicitly trusts the user [b]FIG[/b].</Notes>
908 :     </Relationship>
909 : parrello 1.15 <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
910 :     <Notes>This relationship connects a role subset to the roles that it covers.
911 :     A subset is, essentially, a named group of roles belonging to a specific
912 :     subsystem, and this relationship effects that. Note that will a role
913 :     may belong to many subsystems, a subset belongs to only one subsystem,
914 :     and all roles in the subset must have that subsystem in common.</Notes>
915 :     </Relationship>
916 :     <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
917 :     <Notes>This relationship connects a subset to the genomes that it covers.
918 :     A subset is, essentially, a named group of genomes participating in a specific
919 :     subsystem, and this relationship effects that. Note that while a genome
920 :     may belong to many subsystems, a subset belongs to only one subsystem,
921 :     and all genomes in the subset must have that subsystem in common.</Notes>
922 :     </Relationship>
923 :     <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
924 :     <Notes>This relationship connects a subsystem to its constituent
925 :     role subsets. Note that some roles in a subsystem may not belong to a
926 :     subset, so the relationship between roles and subsystems cannot be
927 :     derived from the relationships going through the subset.</Notes>
928 :     </Relationship>
929 :     <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
930 :     <Notes>This relationship connects a subsystem to its constituent
931 :     genome subsets. Note that some genomes in a subsystem may not belong to a
932 :     subset, so the relationship between genomes and subsystems cannot be
933 :     derived from the relationships going through the subset.</Notes>
934 :     </Relationship>
935 :     <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
936 :     <Notes>This relationship connects a role to the reactions it catalyzes.
937 :     The purpose of a role is to create proteins that trigger certain
938 :     chemical reactions. A single reaction can be triggered by many roles,
939 :     and a role can trigger many reactions.</Notes>
940 :     </Relationship>
941 : parrello 1.39 <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
942 :     <Notes>This relationship connects a feature to the subsystems in which it
943 :     participates. This is technically redundant information, but it is used
944 :     so often that it deserves its own table.</Notes>
945 : parrello 1.40 <Fields>
946 :     <Field name="genome" type="name-string">
947 :     <Notes>ID of the genome containing the feature</Notes>
948 :     </Field>
949 :     <Field name="type" type="key-string">
950 :     <Notes>Feature type (eg. peg, rna)</Notes>
951 :     </Field>
952 :     </Fields>
953 :     <ToIndex>
954 :     <Notes>This index enables the application to view the features of a
955 :     subsystem sorted by genome and feature type.</Notes>
956 :     <IndexFields>
957 :     <IndexField name="genome" order="ascending" />
958 :     <IndexField name="type" order="ascending" />
959 :     </IndexFields>
960 :     </ToIndex>
961 : parrello 1.39 </Relationship>
962 : parrello 1.1 </Relationships>
963 :     </Database>

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