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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 :     <Field name="taxonomy" type="text">
29 :     <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
30 :     separated by semi-colons (and optional white space), starting with the domain and ending with
31 :     the disambiguated genus and species (which is the organism's scientific name plus an
32 :     identifying string).</Notes>
33 :     <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
34 :     ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
35 :     </Field>
36 :     <Field name="group-name" type="name-string" relation="GenomeGroups">
37 :     <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
38 :     page or of particular interest to a research group or web site. A single genome can belong to multiple
39 :     such groups or none at all.</Notes>
40 :     </Field>
41 : parrello 1.1 </Fields>
42 :     <Indexes>
43 :     <Index>
44 :     <Notes>This index allows the applications to find all genomes associated with
45 :     a specific access code, so that a complete list of the genomes users can view
46 :     may be generated.</Notes>
47 :     <IndexFields>
48 :     <IndexField name="access-code" order="ascending" />
49 :     <IndexField name="genus" order="ascending" />
50 :     <IndexField name="species" order="ascending" />
51 :     <IndexField name="unique-characterization" order="ascending" />
52 :     </IndexFields>
53 :     </Index>
54 :     <Index Unique="false">
55 :     <Notes>This index allows the applications to find all genomes for a particular
56 :     species.</Notes>
57 :     <IndexFields>
58 :     <IndexField name="genus" order="ascending" />
59 :     <IndexField name="species" order="ascending" />
60 :     <IndexField name="unique-characterization" order="ascending" />
61 :     </IndexFields>
62 :     </Index>
63 :     </Indexes>
64 :     </Entity>
65 :     <Entity name="Source" keyType="medium-string">
66 :     <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
67 :     or a paper citation.</Notes>
68 :     <Fields>
69 :     <Field name="URL" type="string" relation="SourceURL">
70 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
71 :     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>
72 :     </Field>
73 : parrello 1.1 <Field name="description" type="text">
74 : parrello 1.8 <Notes>Description the source. The description can be a street address or a citation.</Notes>
75 :     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>
76 :     </Field>
77 : parrello 1.1 </Fields>
78 :     </Entity>
79 :     <Entity name="Contig" keyType="name-string">
80 :     <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the
81 :     genome ID followed by a name that identifies which contig this is for the parent genome. As
82 :     is the case with all keys in this database, the individual components are separated by a
83 :     period.
84 :     [p]A contig can contain over a million residues. For performance reasons, therefore,
85 :     the contig is split into multiple pieces called [i]sequences[/i]. The sequences
86 :     contain the characters that represent the residues as well as data on the quality of
87 :     the residue identification.</Notes>
88 :     </Entity>
89 :     <Entity name="Sequence" keyType="name-string">
90 :     <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into
91 :     sequences so that we don't have to have the entire contig in memory when we are
92 :     manipulating it. The key of the sequence is the contig ID followed by the index of
93 :     the begin point.</Notes>
94 :     <Fields>
95 :     <Field name="sequence" type="text">
96 : parrello 1.8 <Notes>String consisting of the residues. Each residue is described by a single
97 :     character in the string.</Notes>
98 :     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
99 :     </Field>
100 : parrello 1.1 <Field name="quality-vector" type="text">
101 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
102 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
103 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
104 :     10^-30. A higher quality number a better chance of a correct match. It is possible
105 : parrello 1.9 that the quality data is not known for a sequence. If that is the case, the quality
106 : parrello 1.8 vector will contain the [b]unknown[/b].</Notes>
107 :     <DataGen>unknown</DataGen>
108 :     </Field>
109 : parrello 1.1 </Fields>
110 :     </Entity>
111 :     <Entity name="Feature" keyType="name-string">
112 :     <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
113 :     may be spread across multiple contigs of a genome, but never across more than
114 :     one genome. Features can be assigned to roles via spreadsheet cells,
115 :     and are the targets of annotation.</Notes>
116 :     <Fields>
117 :     <Field name="feature-type" type="string">
118 : parrello 1.8 <Notes>Code indicating the type of this feature.</Notes>
119 :     <DataGen>RandParam('peg','rna')</DataGen>
120 :     </Field>
121 : parrello 1.1 <Field name="alias" type="name-string" relation="FeatureAlias">
122 : parrello 1.9 <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
123 : parrello 1.8 <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
124 :     </Field>
125 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
126 : parrello 1.8 <Notes>[i](optional)[/i] A translation of this feature's residues into character
127 :     codes, formed by concatenating the pieces of the feature together. For a
128 :     protein encoding group, this is the protein characters. For other types
129 :     it is the DNA characters.</Notes>
130 :     <DataGen testCount="0"></DataGen>
131 :     </Field>
132 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
133 : parrello 1.8 <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
134 :     the feature's initial residues.</Notes>
135 :     <DataGen testCount="0"></DataGen>
136 :     </Field>
137 : parrello 1.1 <Field name="active" type="boolean">
138 : parrello 1.11 <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
139 : parrello 1.8 <DataGen>1</DataGen>
140 :     </Field>
141 :     <Field name="link" type="text" relation="FeatureLink">
142 :     <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
143 :     links are to other websites that have useful about the gene that the feature represents, and
144 :     are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
145 :     <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
146 :     "&amp;Number=" . IntGen(1,99)</DataGen>
147 :     </Field>
148 : parrello 1.1 </Fields>
149 : parrello 1.8 <Indexes>
150 :     <Index>
151 :     <Notes>This index allows the user to find the feature corresponding to
152 :     the specified alias name.</Notes>
153 :     <IndexFields>
154 :     <IndexField name="alias" order="ascending" />
155 :     </IndexFields>
156 :     </Index>
157 :     </Indexes>
158 : parrello 1.1 </Entity>
159 :     <Entity name="Role" keyType="string">
160 :     <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
161 :     One of the main goals of the database is to record the roles of the various features.</Notes>
162 : parrello 1.8 <Fields>
163 :     <Field name="name" type="string" relation="RoleName">
164 :     <Notes>Expanded name of the role. This value is generally only available for roles
165 :     that are encoded as EC numbers.</Notes>
166 :     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
167 :     </Field>
168 :     </Fields>
169 : parrello 1.1 </Entity>
170 :     <Entity name="Annotation" keyType="name-string">
171 :     <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
172 : parrello 1.8 are currently the only objects that may be inserted directly into the database. All other
173 :     information is loaded from data exported by the SEED.
174 :     [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation
175 :     is the target feature ID followed by a timestamp.</Notes>
176 :     <Fields>
177 :     <Field name="time" type="date">
178 :     <Notes>Date and time of the annotation.</Notes>
179 :     </Field>
180 :     <Field name="annotation" type="text">
181 :     <Notes>Text of the annotation.</Notes>
182 :     </Field>
183 : parrello 1.1 </Fields>
184 :     </Entity>
185 : parrello 1.5 <Entity name="Subsystem" keyType="string">
186 : parrello 1.1 <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
187 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
188 :     </Entity>
189 :     <Entity name="SSCell" keyType="name-string">
190 :     <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
191 :     genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
192 :     of the positions on the spreadsheet.</Notes>
193 :     </Entity>
194 :     <Entity name="SproutUser" keyType="name-string">
195 :     <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The
196 :     user object is keyed on the user's login name.</Notes>
197 :     <Fields>
198 : parrello 1.8 <Field name="description" type="string">
199 :     <Notes>Full name or description of this user.</Notes>
200 :     </Field>
201 : parrello 1.1 <Field name="access-code" type="key-string" relation="UserAccess">
202 : parrello 1.8 <Notes>Access code possessed by this
203 : parrello 1.1 user. A user can have many access codes; a genome is accessible to the user if its
204 :     access code matches any one of the user's access codes.</Notes>
205 : parrello 1.8 <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>
206 :     </Field>
207 : parrello 1.1 </Fields>
208 :     </Entity>
209 : parrello 1.8 <Entity name="Property" keyType="int">
210 :     <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of
211 :     a particular feature. Each property instance is a key/value pair and can be associated
212 :     with many different features. Conversely, a feature can be associated with many key/value
213 :     pairs, even some that notionally contradict each other. For example, there can be evidence
214 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
215 :     <Fields>
216 :     <Field name="property-name" type="name-string">
217 :     <Notes>Name of this property.</Notes>
218 :     </Field>
219 :     <Field name="property-value" type="string">
220 :     <Notes>Value associated with this property. For each property
221 :     name, there must by a property record for all of its possible
222 :     values.</Notes>
223 :     </Field>
224 :     </Fields>
225 :     <Indexes>
226 :     <Index>
227 :     <Notes>This index enables the application to find all values for a specified property
228 :     name, or any given name/value pair.</Notes>
229 :     <IndexFields>
230 :     <IndexField name="property-name" order="ascending" />
231 :     <IndexField name="property-value" order="ascending" />
232 :     </IndexFields>
233 :     </Index>
234 :     </Indexes>
235 :     </Entity>
236 :     <Entity name="Diagram" keyType="name-string">
237 :     <Notes>A functional diagram describes the chemical reactions, often comprising a single
238 :     subsystem. A diagram is identified by a short name and contains a longer descriptive name.
239 :     The actual diagram shows which functional roles guide the reactions along with the inputs
240 :     and outputs; the database, however, only indicate which roles belong to a particular
241 :     map.</Notes>
242 :     <Fields>
243 :     <Field name="name" type="text">
244 :     <Notes>Descriptive name of this diagram.</Notes>
245 :     </Field>
246 :     </Fields>
247 :     </Entity>
248 :     <Entity name="ExternalAliasOrg" keyType="name-string">
249 :     <Notes>An external alias is a feature name for a functional assignment that is not a
250 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
251 :     the database. This table contains a description of the relevant organism for an
252 :     external alias functional assignment.</Notes>
253 :     <Fields>
254 :     <Field name="org" type="text">
255 :     <Notes>Descriptive name of the target organism for this external alias.</Notes>
256 :     </Field>
257 :     </Fields>
258 :     </Entity>
259 :     <Entity name="ExternalAliasFunc" keyType="name-string">
260 :     <Notes>An external alias is a feature name for a functional assignment that is not a
261 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
262 :     the database. This table contains the functional role for the external alias functional
263 :     assignment.</Notes>
264 :     <Fields>
265 :     <Field name="func" type="text">
266 :     <Notes>Functional role for this external alias.</Notes>
267 :     </Field>
268 :     </Fields>
269 :     </Entity>
270 : parrello 1.6 <Entity name="Coupling" keyType="medium-string">
271 :     <Notes>A coupling is a relationship between two features. The features are
272 :     physically close on the contig, and there is evidence that they generally
273 :     belong together. The key of this entity is formed by combining the coupled
274 : parrello 1.8 feature IDs with a space.</Notes>
275 : parrello 1.6 <Fields>
276 :     <Field name="score" type="int">
277 :     <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH
278 :     indicates that two genes near each other on one genome are very similar to
279 :     genes near each other on another genome. The score only counts PCHs for which
280 :     the genomes are very different. (In other words, we have a pairing that persists
281 :     between different organisms.) A higher score implies a stronger meaning to the
282 :     clustering.</Notes>
283 :     </Field>
284 :     </Fields>
285 :     </Entity>
286 :     <Entity name="PCH" keyType="string">
287 :     <Notes>A PCH (physically close homolog) connects a clustering (which is a
288 :     pair of physically close features on a contig) to a second pair of physically
289 :     close features that are similar to the first. Essentially, the PCH is a
290 :     relationship between two clusterings in which the first clustering's features
291 :     are similar to the second clustering's features. The simplest model for
292 :     this would be to simply relate clusterings to each other; however, not all
293 :     physically close pairs qualify as clusterings, so we relate a clustering to
294 :     a pair of features. The key is the clustering key followed by the IDs
295 :     of the features in the second pair.</Notes>
296 :     <Fields>
297 :     <Field name="used" type="boolean">
298 :     <Notes>TRUE if this PCH is used in scoring the attached clustering,
299 :     else FALSE. If a clustering has a PCH for a particular genome and many
300 :     similar genomes are present, then a PCH will probably exist for the
301 :     similar genomes as well. When this happens, only one of the PCHs will
302 :     be scored: the others are considered duplicates of the same evidence.</Notes>
303 :     </Field>
304 :     </Fields>
305 :     </Entity>
306 : parrello 1.1 </Entities>
307 :     <Relationships>
308 : parrello 1.6 <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
309 :     <Notes>This relationship connects a feature to all the functional couplings
310 :     in which it participates. A functional coupling is a recognition of the fact
311 :     that the features are close to each other on a chromosome, and similar
312 :     features in other genomes also tend to be close.</Notes>
313 :     <Fields>
314 :     <Field name="pos" type="int">
315 :     <Notes>Ordinal position of the feature in the coupling. Currently,
316 :     this is either "1" or "2".</Notes>
317 :     </Field>
318 :     </Fields>
319 :     <ToIndex>
320 :     <Notes>This index enables the application to view the features of
321 :     a coupling in the proper order. The order influences the way the
322 :     PCHs are examined.</Notes>
323 :     <IndexFields>
324 :     <IndexField name="pos" order="ascending" />
325 :     </IndexFields>
326 :     </ToIndex>
327 :     </Relationship>
328 :     <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
329 :     <Notes>This relationship connects a functional coupling to the physically
330 :     close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
331 :     </Relationship>
332 :     <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">
333 :     <Notes>This relationship connects a PCH to the features that represent its
334 :     evidence. Each PCH is connected to a parent coupling that relates two features
335 :     on a specific genome. The PCH's evidence that the parent coupling is functional
336 :     is the existence of two physically close features on a different genome that
337 :     correspond to the features in the coupling. Those features are found on the
338 :     far side of this relationship.</Notes>
339 :     <Fields>
340 :     <Field name="pos" type="int">
341 :     <Notes>Ordinal position of the feature in the coupling that corresponds
342 :     to our target feature. There is a one-to-one correspondence between the
343 :     features connected to the PCH by this relationship and the features
344 :     connected to the PCH's parent coupling. The ordinal position is used
345 :     to decode that relationship. Currently, this field is either "1" or
346 :     "2".</Notes>
347 :     </Field>
348 :     </Fields>
349 :     <FromIndex>
350 :     <Notes>This index enables the application to view the features of
351 :     a PCH in the proper order.</Notes>
352 :     <IndexFields>
353 :     <IndexField name="pos" order="ascending" />
354 :     </IndexFields>
355 :     </FromIndex>
356 :     </Relationship>
357 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
358 :     <Notes>This relationship connects a genome to the contigs that contain the actual genetic
359 :     information.</Notes>
360 :     </Relationship>
361 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
362 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
363 :     come from a single source or from a cooperation among multiple sources.</Notes>
364 :     </Relationship>
365 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
366 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
367 :     contig into sequences, we get a performance boost from only needing to keep small portions
368 :     of a contig in memory at any one time. This relationship connects the contig to its
369 :     constituent sequences.</Notes>
370 :     <Fields>
371 :     <Field name="len" type="int">
372 : parrello 1.6 <Notes>Length of the sequence.</Notes>
373 :     </Field>
374 : parrello 1.1 <Field name="start-position" type="int">
375 : parrello 1.6 <Notes>Index (1-based) of the point in the contig where this
376 :     sequence starts.</Notes>
377 :     </Field>
378 : parrello 1.1 </Fields>
379 :     <FromIndex>
380 :     <Notes>This index enables the application to find all of the sequences in
381 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
382 : parrello 1.1 <IndexFields>
383 :     <IndexField name="start-position" order="ascending" />
384 :     <IndexField name="len" order="ascending" />
385 :     </IndexFields>
386 :     </FromIndex>
387 :     </Relationship>
388 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
389 :     <Notes>This relationship connects a feature to its annotations.</Notes>
390 :     </Relationship>
391 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
392 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
393 :     </Relationship>
394 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
395 :     <Notes>This relationship connects subsystems to the genomes that use
396 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
397 :     connected to the genome features through the [b]SSCell[/b] object.</Notes>
398 :     </Relationship>
399 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
400 :     <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
401 :     </Relationship>
402 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
403 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
404 :     genome for the spreadsheet column.</Notes>
405 :     </Relationship>
406 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
407 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
408 :     role for the spreadsheet row.</Notes>
409 :     </Relationship>
410 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
411 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
412 :     features assigned to it.</Notes>
413 :     </Relationship>
414 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
415 :     <Notes>This relationship connects a feature to the contig segments that work together
416 :     to effect it. The segments are numbered sequentially starting from 1. The database is
417 :     required to place an upper limit on the length of each segment. If a segment is longer
418 :     than the maximum, it can be broken into smaller bits.
419 :     [p]The upper limit enables applications to locate all features that contain a specific
420 :     residue. For example, if the upper limit is 100 and we are looking for a feature that
421 :     contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point
422 :     between 135 and 333. The results can then be filtered by direction and length of the
423 :     segment.</Notes>
424 :     <Fields>
425 :     <Field name="locN" type="int">
426 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
427 :     </Field>
428 : parrello 1.1 <Field name="beg" type="int">
429 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
430 :     belongs to the segment.</Notes>
431 :     </Field>
432 : parrello 1.1 <Field name="len" type="int">
433 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
434 :     a specific point between residues. This is the point before the residue if the direction
435 :     is forward and the point after the residue if the direction is backward.</Notes>
436 :     </Field>
437 : parrello 1.1 <Field name="dir" type="char">
438 : parrello 1.8 <Notes>Direction of the segment: [b]+[/b] if it is forward and
439 :     [b]-[/b] if it is backward.</Notes>
440 :     </Field>
441 : parrello 1.1 </Fields>
442 :     <FromIndex Unique="false">
443 :     <Notes>This index allows the application to find all the segments of a feature in
444 : parrello 1.8 the proper order.</Notes>
445 : parrello 1.1 <IndexFields>
446 :     <IndexField name="locN" order="ascending" />
447 :     </IndexFields>
448 :     </FromIndex>
449 :     <ToIndex>
450 :     <Notes>This index is the one used by applications to find all the feature
451 :     segments that contain a specific residue.</Notes>
452 :     <IndexFields>
453 :     <IndexField name="beg" order="ascending" />
454 :     </IndexFields>
455 :     </ToIndex>
456 :     </Relationship>
457 :     <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">
458 :     <Notes>This relationship is one of two that relate features to each other. It
459 :     connects features that are very similar but on separate genomes. A
460 :     bidirectional best hit relationship exists between two features [b]A[/b]
461 :     and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome
462 :     and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>
463 :     <Fields>
464 :     <Field name="genome" type="name-string">
465 : parrello 1.8 <Notes>ID of the genome containing the target (to) feature.</Notes>
466 :     </Field>
467 :     <Field name="sc" type="float">
468 :     <Notes>score for this relationship</Notes>
469 :     </Field>
470 : parrello 1.1 </Fields>
471 :     <FromIndex>
472 :     <Notes>This index allows the application to find a feature's best hit for
473 : parrello 1.8 a specific target genome.</Notes>
474 : parrello 1.1 <IndexFields>
475 :     <IndexField name="genome" order="ascending" />
476 :     </IndexFields>
477 :     </FromIndex>
478 :     </Relationship>
479 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
480 :     <Notes>This relationship connects a feature to its known property values.
481 :     The relationship contains text data that indicates the paper or organization
482 :     that discovered evidence that the feature possesses the property. So, for
483 :     example, if two papers presented evidence that a feature is essential,
484 :     there would be an instance of this relationship for both.</Notes>
485 :     <Fields>
486 :     <Field name="evidence" type="text">
487 :     <Notes>URL or citation of the paper or
488 :     institution that reported evidence of the relevant feature possessing
489 :     the specified property value.</Notes>
490 :     </Field>
491 :     </Fields>
492 :     </Relationship>
493 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
494 :     <Notes>This relationship connects a role to the diagrams on which it
495 :     appears. A role frequently identifies an enzyme, and can appear in many
496 :     diagrams. A diagram generally contains many different roles.</Notes>
497 :     </Relationship>
498 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
499 :     <Notes>This relationship connects a subsystem to the spreadsheet cells
500 :     used to analyze and display it. The cells themselves can be thought of
501 :     as a grid with Roles on one axis and Genomes on the other. The
502 :     various features of the subsystem are then assigned to the cells.</Notes>
503 :     </Relationship>
504 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
505 :     <Notes>This relationship identifies the users trusted by each
506 :     particular user. When viewing functional assignments, the
507 :     assignment displayed is the most recent one by a user trusted
508 :     by the current user. The current user implicitly trusts himself.
509 :     If no trusted users are specified in the database, the user
510 :     also implicitly trusts the user [b]FIG[/b].</Notes>
511 :     </Relationship>
512 : parrello 1.1 </Relationships>
513 :     </Database>

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