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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 1.12 <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 :     <Field name="group-name" type="name-string" relation="GenomeGroups">
40 :     <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
41 :     page or of particular interest to a research group or web site. A single genome can belong to multiple
42 :     such groups or none at all.</Notes>
43 :     </Field>
44 : parrello 1.1 </Fields>
45 :     <Indexes>
46 :     <Index>
47 :     <Notes>This index allows the applications to find all genomes associated with
48 :     a specific access code, so that a complete list of the genomes users can view
49 :     may be generated.</Notes>
50 :     <IndexFields>
51 :     <IndexField name="access-code" order="ascending" />
52 :     <IndexField name="genus" order="ascending" />
53 :     <IndexField name="species" order="ascending" />
54 :     <IndexField name="unique-characterization" order="ascending" />
55 :     </IndexFields>
56 :     </Index>
57 :     <Index Unique="false">
58 :     <Notes>This index allows the applications to find all genomes for a particular
59 :     species.</Notes>
60 :     <IndexFields>
61 :     <IndexField name="genus" order="ascending" />
62 :     <IndexField name="species" order="ascending" />
63 :     <IndexField name="unique-characterization" order="ascending" />
64 :     </IndexFields>
65 :     </Index>
66 :     </Indexes>
67 :     </Entity>
68 :     <Entity name="Source" keyType="medium-string">
69 :     <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
70 :     or a paper citation.</Notes>
71 :     <Fields>
72 :     <Field name="URL" type="string" relation="SourceURL">
73 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
74 :     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>
75 :     </Field>
76 : parrello 1.1 <Field name="description" type="text">
77 : parrello 1.8 <Notes>Description the source. The description can be a street address or a citation.</Notes>
78 :     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>
79 :     </Field>
80 : parrello 1.1 </Fields>
81 :     </Entity>
82 :     <Entity name="Contig" keyType="name-string">
83 :     <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the
84 :     genome ID followed by a name that identifies which contig this is for the parent genome. As
85 :     is the case with all keys in this database, the individual components are separated by a
86 :     period.
87 :     [p]A contig can contain over a million residues. For performance reasons, therefore,
88 :     the contig is split into multiple pieces called [i]sequences[/i]. The sequences
89 :     contain the characters that represent the residues as well as data on the quality of
90 :     the residue identification.</Notes>
91 :     </Entity>
92 :     <Entity name="Sequence" keyType="name-string">
93 :     <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into
94 :     sequences so that we don't have to have the entire contig in memory when we are
95 :     manipulating it. The key of the sequence is the contig ID followed by the index of
96 :     the begin point.</Notes>
97 :     <Fields>
98 :     <Field name="sequence" type="text">
99 : parrello 1.8 <Notes>String consisting of the residues. Each residue is described by a single
100 :     character in the string.</Notes>
101 :     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
102 :     </Field>
103 : parrello 1.1 <Field name="quality-vector" type="text">
104 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
105 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
106 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
107 :     10^-30. A higher quality number a better chance of a correct match. It is possible
108 : parrello 1.9 that the quality data is not known for a sequence. If that is the case, the quality
109 : parrello 1.8 vector will contain the [b]unknown[/b].</Notes>
110 :     <DataGen>unknown</DataGen>
111 :     </Field>
112 : parrello 1.1 </Fields>
113 :     </Entity>
114 :     <Entity name="Feature" keyType="name-string">
115 :     <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
116 :     may be spread across multiple contigs of a genome, but never across more than
117 :     one genome. Features can be assigned to roles via spreadsheet cells,
118 :     and are the targets of annotation.</Notes>
119 :     <Fields>
120 :     <Field name="feature-type" type="string">
121 : parrello 1.8 <Notes>Code indicating the type of this feature.</Notes>
122 :     <DataGen>RandParam('peg','rna')</DataGen>
123 :     </Field>
124 : parrello 1.14 <Field name="alias" type="medium-string" relation="FeatureAlias">
125 : parrello 1.9 <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
126 : parrello 1.8 <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
127 :     </Field>
128 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
129 : parrello 1.8 <Notes>[i](optional)[/i] A translation of this feature's residues into character
130 :     codes, formed by concatenating the pieces of the feature together. For a
131 :     protein encoding group, this is the protein characters. For other types
132 :     it is the DNA characters.</Notes>
133 :     <DataGen testCount="0"></DataGen>
134 :     </Field>
135 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
136 : parrello 1.8 <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
137 :     the feature's initial residues.</Notes>
138 :     <DataGen testCount="0"></DataGen>
139 :     </Field>
140 : parrello 1.1 <Field name="active" type="boolean">
141 : parrello 1.11 <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
142 : parrello 1.8 <DataGen>1</DataGen>
143 :     </Field>
144 :     <Field name="link" type="text" relation="FeatureLink">
145 :     <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
146 :     links are to other websites that have useful about the gene that the feature represents, and
147 :     are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
148 :     <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
149 :     "&amp;Number=" . IntGen(1,99)</DataGen>
150 :     </Field>
151 : parrello 1.1 </Fields>
152 : parrello 1.8 <Indexes>
153 :     <Index>
154 :     <Notes>This index allows the user to find the feature corresponding to
155 :     the specified alias name.</Notes>
156 :     <IndexFields>
157 :     <IndexField name="alias" order="ascending" />
158 :     </IndexFields>
159 :     </Index>
160 :     </Indexes>
161 : parrello 1.1 </Entity>
162 :     <Entity name="Role" keyType="string">
163 :     <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
164 :     One of the main goals of the database is to record the roles of the various features.</Notes>
165 : parrello 1.8 <Fields>
166 :     <Field name="name" type="string" relation="RoleName">
167 :     <Notes>Expanded name of the role. This value is generally only available for roles
168 :     that are encoded as EC numbers.</Notes>
169 :     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
170 :     </Field>
171 :     </Fields>
172 : parrello 1.1 </Entity>
173 :     <Entity name="Annotation" keyType="name-string">
174 :     <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
175 : parrello 1.8 are currently the only objects that may be inserted directly into the database. All other
176 :     information is loaded from data exported by the SEED.
177 :     [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation
178 :     is the target feature ID followed by a timestamp.</Notes>
179 :     <Fields>
180 :     <Field name="time" type="date">
181 :     <Notes>Date and time of the annotation.</Notes>
182 :     </Field>
183 :     <Field name="annotation" type="text">
184 :     <Notes>Text of the annotation.</Notes>
185 :     </Field>
186 : parrello 1.1 </Fields>
187 :     </Entity>
188 : parrello 1.5 <Entity name="Subsystem" keyType="string">
189 : parrello 1.1 <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
190 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
191 :     </Entity>
192 : parrello 1.13 <Entity name="SSCell" keyType="medium-string">
193 : parrello 1.1 <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
194 :     genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
195 :     of the positions on the spreadsheet.</Notes>
196 :     </Entity>
197 :     <Entity name="SproutUser" keyType="name-string">
198 :     <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The
199 :     user object is keyed on the user's login name.</Notes>
200 :     <Fields>
201 : parrello 1.8 <Field name="description" type="string">
202 :     <Notes>Full name or description of this user.</Notes>
203 :     </Field>
204 : parrello 1.1 <Field name="access-code" type="key-string" relation="UserAccess">
205 : parrello 1.8 <Notes>Access code possessed by this
206 : parrello 1.1 user. A user can have many access codes; a genome is accessible to the user if its
207 :     access code matches any one of the user's access codes.</Notes>
208 : parrello 1.8 <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>
209 :     </Field>
210 : parrello 1.1 </Fields>
211 :     </Entity>
212 : parrello 1.8 <Entity name="Property" keyType="int">
213 :     <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of
214 :     a particular feature. Each property instance is a key/value pair and can be associated
215 :     with many different features. Conversely, a feature can be associated with many key/value
216 :     pairs, even some that notionally contradict each other. For example, there can be evidence
217 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
218 :     <Fields>
219 :     <Field name="property-name" type="name-string">
220 :     <Notes>Name of this property.</Notes>
221 :     </Field>
222 :     <Field name="property-value" type="string">
223 :     <Notes>Value associated with this property. For each property
224 :     name, there must by a property record for all of its possible
225 :     values.</Notes>
226 :     </Field>
227 :     </Fields>
228 :     <Indexes>
229 :     <Index>
230 :     <Notes>This index enables the application to find all values for a specified property
231 :     name, or any given name/value pair.</Notes>
232 :     <IndexFields>
233 :     <IndexField name="property-name" order="ascending" />
234 :     <IndexField name="property-value" order="ascending" />
235 :     </IndexFields>
236 :     </Index>
237 :     </Indexes>
238 :     </Entity>
239 :     <Entity name="Diagram" keyType="name-string">
240 :     <Notes>A functional diagram describes the chemical reactions, often comprising a single
241 :     subsystem. A diagram is identified by a short name and contains a longer descriptive name.
242 :     The actual diagram shows which functional roles guide the reactions along with the inputs
243 :     and outputs; the database, however, only indicate which roles belong to a particular
244 :     map.</Notes>
245 :     <Fields>
246 :     <Field name="name" type="text">
247 :     <Notes>Descriptive name of this diagram.</Notes>
248 :     </Field>
249 :     </Fields>
250 :     </Entity>
251 :     <Entity name="ExternalAliasOrg" keyType="name-string">
252 :     <Notes>An external alias is a feature name for a functional assignment that is not a
253 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
254 :     the database. This table contains a description of the relevant organism for an
255 :     external alias functional assignment.</Notes>
256 :     <Fields>
257 :     <Field name="org" type="text">
258 :     <Notes>Descriptive name of the target organism for this external alias.</Notes>
259 :     </Field>
260 :     </Fields>
261 :     </Entity>
262 :     <Entity name="ExternalAliasFunc" keyType="name-string">
263 :     <Notes>An external alias is a feature name for a functional assignment that is not a
264 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
265 :     the database. This table contains the functional role for the external alias functional
266 :     assignment.</Notes>
267 :     <Fields>
268 :     <Field name="func" type="text">
269 :     <Notes>Functional role for this external alias.</Notes>
270 :     </Field>
271 :     </Fields>
272 :     </Entity>
273 : parrello 1.6 <Entity name="Coupling" keyType="medium-string">
274 :     <Notes>A coupling is a relationship between two features. The features are
275 :     physically close on the contig, and there is evidence that they generally
276 :     belong together. The key of this entity is formed by combining the coupled
277 : parrello 1.8 feature IDs with a space.</Notes>
278 : parrello 1.6 <Fields>
279 :     <Field name="score" type="int">
280 :     <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH
281 :     indicates that two genes near each other on one genome are very similar to
282 :     genes near each other on another genome. The score only counts PCHs for which
283 :     the genomes are very different. (In other words, we have a pairing that persists
284 :     between different organisms.) A higher score implies a stronger meaning to the
285 :     clustering.</Notes>
286 :     </Field>
287 :     </Fields>
288 :     </Entity>
289 :     <Entity name="PCH" keyType="string">
290 :     <Notes>A PCH (physically close homolog) connects a clustering (which is a
291 :     pair of physically close features on a contig) to a second pair of physically
292 :     close features that are similar to the first. Essentially, the PCH is a
293 :     relationship between two clusterings in which the first clustering's features
294 :     are similar to the second clustering's features. The simplest model for
295 :     this would be to simply relate clusterings to each other; however, not all
296 :     physically close pairs qualify as clusterings, so we relate a clustering to
297 :     a pair of features. The key is the clustering key followed by the IDs
298 :     of the features in the second pair.</Notes>
299 :     <Fields>
300 :     <Field name="used" type="boolean">
301 :     <Notes>TRUE if this PCH is used in scoring the attached clustering,
302 :     else FALSE. If a clustering has a PCH for a particular genome and many
303 :     similar genomes are present, then a PCH will probably exist for the
304 :     similar genomes as well. When this happens, only one of the PCHs will
305 :     be scored: the others are considered duplicates of the same evidence.</Notes>
306 :     </Field>
307 :     </Fields>
308 :     </Entity>
309 : parrello 1.1 </Entities>
310 :     <Relationships>
311 : parrello 1.6 <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
312 :     <Notes>This relationship connects a feature to all the functional couplings
313 :     in which it participates. A functional coupling is a recognition of the fact
314 :     that the features are close to each other on a chromosome, and similar
315 :     features in other genomes also tend to be close.</Notes>
316 :     <Fields>
317 :     <Field name="pos" type="int">
318 :     <Notes>Ordinal position of the feature in the coupling. Currently,
319 :     this is either "1" or "2".</Notes>
320 :     </Field>
321 :     </Fields>
322 :     <ToIndex>
323 :     <Notes>This index enables the application to view the features of
324 :     a coupling in the proper order. The order influences the way the
325 :     PCHs are examined.</Notes>
326 :     <IndexFields>
327 :     <IndexField name="pos" order="ascending" />
328 :     </IndexFields>
329 :     </ToIndex>
330 :     </Relationship>
331 :     <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
332 :     <Notes>This relationship connects a functional coupling to the physically
333 :     close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
334 :     </Relationship>
335 :     <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">
336 :     <Notes>This relationship connects a PCH to the features that represent its
337 :     evidence. Each PCH is connected to a parent coupling that relates two features
338 :     on a specific genome. The PCH's evidence that the parent coupling is functional
339 :     is the existence of two physically close features on a different genome that
340 :     correspond to the features in the coupling. Those features are found on the
341 :     far side of this relationship.</Notes>
342 :     <Fields>
343 :     <Field name="pos" type="int">
344 :     <Notes>Ordinal position of the feature in the coupling that corresponds
345 :     to our target feature. There is a one-to-one correspondence between the
346 :     features connected to the PCH by this relationship and the features
347 :     connected to the PCH's parent coupling. The ordinal position is used
348 :     to decode that relationship. Currently, this field is either "1" or
349 :     "2".</Notes>
350 :     </Field>
351 :     </Fields>
352 :     <FromIndex>
353 :     <Notes>This index enables the application to view the features of
354 :     a PCH in the proper order.</Notes>
355 :     <IndexFields>
356 :     <IndexField name="pos" order="ascending" />
357 :     </IndexFields>
358 :     </FromIndex>
359 :     </Relationship>
360 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
361 :     <Notes>This relationship connects a genome to the contigs that contain the actual genetic
362 :     information.</Notes>
363 :     </Relationship>
364 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
365 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
366 :     come from a single source or from a cooperation among multiple sources.</Notes>
367 :     </Relationship>
368 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
369 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
370 :     contig into sequences, we get a performance boost from only needing to keep small portions
371 :     of a contig in memory at any one time. This relationship connects the contig to its
372 :     constituent sequences.</Notes>
373 :     <Fields>
374 :     <Field name="len" type="int">
375 : parrello 1.6 <Notes>Length of the sequence.</Notes>
376 :     </Field>
377 : parrello 1.1 <Field name="start-position" type="int">
378 : parrello 1.6 <Notes>Index (1-based) of the point in the contig where this
379 :     sequence starts.</Notes>
380 :     </Field>
381 : parrello 1.1 </Fields>
382 :     <FromIndex>
383 :     <Notes>This index enables the application to find all of the sequences in
384 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
385 : parrello 1.1 <IndexFields>
386 :     <IndexField name="start-position" order="ascending" />
387 :     <IndexField name="len" order="ascending" />
388 :     </IndexFields>
389 :     </FromIndex>
390 :     </Relationship>
391 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
392 :     <Notes>This relationship connects a feature to its annotations.</Notes>
393 :     </Relationship>
394 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
395 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
396 :     </Relationship>
397 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
398 :     <Notes>This relationship connects subsystems to the genomes that use
399 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
400 :     connected to the genome features through the [b]SSCell[/b] object.</Notes>
401 :     </Relationship>
402 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
403 :     <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
404 :     </Relationship>
405 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
406 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
407 :     genome for the spreadsheet column.</Notes>
408 :     </Relationship>
409 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
410 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
411 :     role for the spreadsheet row.</Notes>
412 :     </Relationship>
413 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
414 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
415 :     features assigned to it.</Notes>
416 :     </Relationship>
417 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
418 :     <Notes>This relationship connects a feature to the contig segments that work together
419 :     to effect it. The segments are numbered sequentially starting from 1. The database is
420 :     required to place an upper limit on the length of each segment. If a segment is longer
421 :     than the maximum, it can be broken into smaller bits.
422 :     [p]The upper limit enables applications to locate all features that contain a specific
423 :     residue. For example, if the upper limit is 100 and we are looking for a feature that
424 :     contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point
425 :     between 135 and 333. The results can then be filtered by direction and length of the
426 :     segment.</Notes>
427 :     <Fields>
428 :     <Field name="locN" type="int">
429 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
430 :     </Field>
431 : parrello 1.1 <Field name="beg" type="int">
432 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
433 :     belongs to the segment.</Notes>
434 :     </Field>
435 : parrello 1.1 <Field name="len" type="int">
436 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
437 :     a specific point between residues. This is the point before the residue if the direction
438 :     is forward and the point after the residue if the direction is backward.</Notes>
439 :     </Field>
440 : parrello 1.1 <Field name="dir" type="char">
441 : parrello 1.8 <Notes>Direction of the segment: [b]+[/b] if it is forward and
442 :     [b]-[/b] if it is backward.</Notes>
443 :     </Field>
444 : parrello 1.1 </Fields>
445 :     <FromIndex Unique="false">
446 :     <Notes>This index allows the application to find all the segments of a feature in
447 : parrello 1.8 the proper order.</Notes>
448 : parrello 1.1 <IndexFields>
449 :     <IndexField name="locN" order="ascending" />
450 :     </IndexFields>
451 :     </FromIndex>
452 :     <ToIndex>
453 :     <Notes>This index is the one used by applications to find all the feature
454 :     segments that contain a specific residue.</Notes>
455 :     <IndexFields>
456 :     <IndexField name="beg" order="ascending" />
457 :     </IndexFields>
458 :     </ToIndex>
459 :     </Relationship>
460 :     <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">
461 :     <Notes>This relationship is one of two that relate features to each other. It
462 :     connects features that are very similar but on separate genomes. A
463 :     bidirectional best hit relationship exists between two features [b]A[/b]
464 :     and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome
465 :     and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>
466 :     <Fields>
467 :     <Field name="genome" type="name-string">
468 : parrello 1.8 <Notes>ID of the genome containing the target (to) feature.</Notes>
469 :     </Field>
470 :     <Field name="sc" type="float">
471 :     <Notes>score for this relationship</Notes>
472 :     </Field>
473 : parrello 1.1 </Fields>
474 :     <FromIndex>
475 :     <Notes>This index allows the application to find a feature's best hit for
476 : parrello 1.8 a specific target genome.</Notes>
477 : parrello 1.1 <IndexFields>
478 :     <IndexField name="genome" order="ascending" />
479 :     </IndexFields>
480 :     </FromIndex>
481 :     </Relationship>
482 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
483 :     <Notes>This relationship connects a feature to its known property values.
484 :     The relationship contains text data that indicates the paper or organization
485 :     that discovered evidence that the feature possesses the property. So, for
486 :     example, if two papers presented evidence that a feature is essential,
487 :     there would be an instance of this relationship for both.</Notes>
488 :     <Fields>
489 :     <Field name="evidence" type="text">
490 :     <Notes>URL or citation of the paper or
491 :     institution that reported evidence of the relevant feature possessing
492 :     the specified property value.</Notes>
493 :     </Field>
494 :     </Fields>
495 :     </Relationship>
496 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
497 :     <Notes>This relationship connects a role to the diagrams on which it
498 :     appears. A role frequently identifies an enzyme, and can appear in many
499 :     diagrams. A diagram generally contains many different roles.</Notes>
500 :     </Relationship>
501 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
502 :     <Notes>This relationship connects a subsystem to the spreadsheet cells
503 :     used to analyze and display it. The cells themselves can be thought of
504 :     as a grid with Roles on one axis and Genomes on the other. The
505 :     various features of the subsystem are then assigned to the cells.</Notes>
506 :     </Relationship>
507 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
508 :     <Notes>This relationship identifies the users trusted by each
509 :     particular user. When viewing functional assignments, the
510 :     assignment displayed is the most recent one by a user trusted
511 :     by the current user. The current user implicitly trusts himself.
512 :     If no trusted users are specified in the database, the user
513 :     also implicitly trusts the user [b]FIG[/b].</Notes>
514 :     </Relationship>
515 : parrello 1.1 </Relationships>
516 :     </Database>

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