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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 : parrello 1.51 <Notes>The Sprout database contains the genetic data for all complete organisms in the SEED.
5 :     The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external
6 :     servers available to the Sprout software. The Sprout database is reloaded approximately once
7 :     per month. There is significant redundancy in the Sprout database because it has been
8 :     optimized for searching. In particular, the Feature table contains an extra copy of the
9 :     feature's functional role and a list of possible search terms.</Notes>
10 : parrello 1.1 <Entities>
11 :     <Entity name="Genome" keyType="name-string">
12 :     <Notes>A [i]genome[/i] contains the sequence data for a particular individual organism.</Notes>
13 :     <Fields>
14 :     <Field name="genus" type="name-string">
15 :     <Notes>Genus of the relevant organism.</Notes>
16 :     </Field>
17 :     <Field name="species" type="name-string">
18 : parrello 1.8 <Notes>Species of the relevant organism.</Notes>
19 :     </Field>
20 : parrello 1.1 <Field name="unique-characterization" type="medium-string">
21 : parrello 1.8 <Notes>The unique characterization identifies the particular organism instance from which the
22 :     genome is taken. It is possible to have in the database more than one genome for a
23 : parrello 1.1 particular species, and every individual organism has variations in its DNA.</Notes>
24 :     </Field>
25 : parrello 1.48 <Field name="version" type="name-string">
26 :     <Notes>version string for this genome, generally consisting of the genome ID followed
27 :     by a period and a string of digits.</Notes>
28 :     </Field>
29 : parrello 1.1 <Field name="access-code" type="key-string">
30 : parrello 1.8 <Notes>The access code determines which users can look at the data relating to this genome.
31 :     Each user is associated with a set of access codes. In order to view a genome, one of
32 :     the user's access codes must match this value.</Notes>
33 :     </Field>
34 : parrello 1.15 <Field name="complete" type="boolean">
35 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
36 :     </Field>
37 : parrello 1.48 <Field name="dna-size" type="counter">
38 :     <Notes>number of base pairs in the genome</Notes>
39 :     </Field>
40 : parrello 1.8 <Field name="taxonomy" type="text">
41 :     <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
42 :     separated by semi-colons (and optional white space), starting with the domain and ending with
43 :     the disambiguated genus and species (which is the organism's scientific name plus an
44 :     identifying string).</Notes>
45 :     </Field>
46 : parrello 1.37 <Field name="primary-group" type="name-string">
47 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
48 :     (either based on the organism name or the default value "Supporting"), whereas there can be
49 :     multiple named groups or even none.</Notes>
50 :     </Field>
51 : parrello 1.1 </Fields>
52 :     <Indexes>
53 : parrello 1.45 <Index>
54 : parrello 1.1 <Notes>This index allows the applications to find all genomes associated with
55 :     a specific access code, so that a complete list of the genomes users can view
56 :     may be generated.</Notes>
57 :     <IndexFields>
58 :     <IndexField name="access-code" order="ascending" />
59 :     <IndexField name="genus" order="ascending" />
60 :     <IndexField name="species" order="ascending" />
61 :     <IndexField name="unique-characterization" order="ascending" />
62 :     </IndexFields>
63 :     </Index>
64 : parrello 1.45 <Index>
65 : parrello 1.37 <Notes>This index allows the applications to find all genomes associated with
66 :     a specific primary (NMPDR) group.</Notes>
67 :     <IndexFields>
68 :     <IndexField name="primary-group" order="ascending" />
69 :     <IndexField name="genus" order="ascending" />
70 :     <IndexField name="species" order="ascending" />
71 :     <IndexField name="unique-characterization" order="ascending" />
72 :     </IndexFields>
73 :     </Index>
74 : parrello 1.45 <Index>
75 : parrello 1.1 <Notes>This index allows the applications to find all genomes for a particular
76 :     species.</Notes>
77 :     <IndexFields>
78 :     <IndexField name="genus" order="ascending" />
79 :     <IndexField name="species" order="ascending" />
80 :     <IndexField name="unique-characterization" order="ascending" />
81 :     </IndexFields>
82 :     </Index>
83 :     </Indexes>
84 :     </Entity>
85 : parrello 1.50 <Entity name="CDD" keyType="key-string">
86 :     <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
87 :     on a feature's protein. The ID is six-digit string assigned by the public Conserved Domain
88 :     Database. A CDD can occur on multiple features and a feature generally has multiple CDDs.</Notes>
89 :     </Entity>
90 : parrello 1.1 <Entity name="Source" keyType="medium-string">
91 :     <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
92 :     or a paper citation.</Notes>
93 :     <Fields>
94 :     <Field name="URL" type="string" relation="SourceURL">
95 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
96 :     </Field>
97 : parrello 1.1 <Field name="description" type="text">
98 : parrello 1.8 <Notes>Description the source. The description can be a street address or a citation.</Notes>
99 :     </Field>
100 : parrello 1.1 </Fields>
101 :     </Entity>
102 :     <Entity name="Contig" keyType="name-string">
103 :     <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the
104 :     genome ID followed by a name that identifies which contig this is for the parent genome. As
105 :     is the case with all keys in this database, the individual components are separated by a
106 :     period.
107 :     [p]A contig can contain over a million residues. For performance reasons, therefore,
108 :     the contig is split into multiple pieces called [i]sequences[/i]. The sequences
109 :     contain the characters that represent the residues as well as data on the quality of
110 :     the residue identification.</Notes>
111 :     </Entity>
112 :     <Entity name="Sequence" keyType="name-string">
113 :     <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into
114 :     sequences so that we don't have to have the entire contig in memory when we are
115 :     manipulating it. The key of the sequence is the contig ID followed by the index of
116 :     the begin point.</Notes>
117 :     <Fields>
118 :     <Field name="sequence" type="text">
119 : parrello 1.8 <Notes>String consisting of the residues. Each residue is described by a single
120 :     character in the string.</Notes>
121 :     </Field>
122 : parrello 1.1 <Field name="quality-vector" type="text">
123 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
124 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
125 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
126 :     10^-30. A higher quality number a better chance of a correct match. It is possible
127 : parrello 1.9 that the quality data is not known for a sequence. If that is the case, the quality
128 : parrello 1.8 vector will contain the [b]unknown[/b].</Notes>
129 :     </Field>
130 : parrello 1.1 </Fields>
131 :     </Entity>
132 : parrello 1.25 <Entity name="Feature" keyType="id-string">
133 : parrello 1.1 <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
134 :     may be spread across multiple contigs of a genome, but never across more than
135 :     one genome. Features can be assigned to roles via spreadsheet cells,
136 :     and are the targets of annotation.</Notes>
137 :     <Fields>
138 : parrello 1.50 <Field name="feature-type" type="id-string">
139 : parrello 1.8 <Notes>Code indicating the type of this feature.</Notes>
140 :     </Field>
141 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
142 : parrello 1.8 <Notes>[i](optional)[/i] A translation of this feature's residues into character
143 :     codes, formed by concatenating the pieces of the feature together. For a
144 :     protein encoding group, this is the protein characters. For other types
145 :     it is the DNA characters.</Notes>
146 :     </Field>
147 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
148 : parrello 1.8 <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
149 :     the feature's initial residues.</Notes>
150 :     </Field>
151 : parrello 1.42 <Field name="assignment" type="text">
152 :     <Notes>Default functional assignment for this feature.</Notes>
153 :     </Field>
154 : parrello 1.1 <Field name="active" type="boolean">
155 : parrello 1.11 <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
156 : parrello 1.8 </Field>
157 : parrello 1.48 <Field name="assignment-maker" type="name-string">
158 :     <Notes>name of the user who made the functional assignment</Notes>
159 :     </Field>
160 :     <Field name="assignment-quality" type="char">
161 :     <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
162 :     (indicating experimental)</Notes>
163 :     </Field>
164 : parrello 1.41 <Field name="keywords" type="text" searchable="1">
165 :     <Notes>This is a list of search keywords for the feature. It includes the
166 :     functional assignment, subsystem roles, and special properties.</Notes>
167 : parrello 1.36 </Field>
168 : parrello 1.8 <Field name="link" type="text" relation="FeatureLink">
169 :     <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The
170 :     links are to other websites that have useful about the gene that the feature represents, and
171 :     are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
172 :     </Field>
173 : parrello 1.41 <Field name="conservation" type="float" relation="FeatureConservation">
174 :     <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
175 :     conserved in related genomes. A value of 1 indicates perfect conservation. A value less
176 : parrello 1.50 than 1 is a reflection of the degree to which gap characters interfere in the alignment
177 : parrello 1.41 between the feature and its close relatives.</Notes>
178 :     </Field>
179 : parrello 1.45 <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
180 :     <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
181 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
182 :     or potential (potential-essential), hyperlinked to the document from which the
183 :     essentiality was curated. If a feature is not essential, this field will have no
184 :     values; otherwise, it may have multiple values.</Notes>
185 :     </Field>
186 :     <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
187 :     <Notes>A value indicating the virulence of the feature, coded as HTML. In most
188 :     cases, this will be a phrase or SA number hyperlinked to the document from which
189 :     the virulence information was curated. If the feature is not virulent, this field
190 :     will have no values; otherwise, it may have multiple values.</Notes>
191 :     </Field>
192 : parrello 1.50 <Field name="cello" type="name-string">
193 :     <Notes>The cello value specifies the expected location of the protein: cytoplasm,
194 :     cell wall, inner membrane, and so forth.</Notes>
195 :     </Field>
196 : parrello 1.45 <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
197 :     <Notes>A value indicating whether or not the feature can be found in the
198 :     Immune Epitope Database. If the feature has not been matched to that database,
199 :     this field will have no values. Otherwise, it will have an epitope name and/or
200 :     sequence, hyperlinked to the database.</Notes>
201 :     </Field>
202 : parrello 1.50 <Field name="location-string" type="text">
203 :     <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
204 :     strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
205 :     we have to painstakingly paste together the IsLocatedIn records, which are themselves
206 :     designed to help look for genes in a particular region rather than to find the location
207 :     of a gene.</Notes>
208 :     </Field>
209 : parrello 1.1 </Fields>
210 : parrello 1.8 <Indexes>
211 :     <Index>
212 : parrello 1.50 <Notes>This index allows us to locate a feature by its CELLO value.</Notes>
213 : parrello 1.8 <IndexFields>
214 : parrello 1.50 <IndexField name="cello" order="ascending" />
215 : parrello 1.8 </IndexFields>
216 :     </Index>
217 :     </Indexes>
218 : parrello 1.1 </Entity>
219 : parrello 1.50 <Entity name="FeatureAlias" keyType="medium-string">
220 :     <Notes>Alternative names for features. A feature can have many aliases. In general,
221 :     each alias corresponds to only one feature, but there are exceptionsis is not strictly enforced.</Notes>
222 :     </Entity>
223 : parrello 1.27 <Entity name="SynonymGroup" keyType="id-string">
224 :     <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
225 :     are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
226 :     </Entity>
227 : parrello 1.1 <Entity name="Role" keyType="string">
228 :     <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
229 :     One of the main goals of the database is to record the roles of the various features.</Notes>
230 : parrello 1.50 </Entity>
231 :     <Entity name="RoleEC" keyType="string">
232 :     <Notes>EC code for a role.</Notes>
233 : parrello 1.1 </Entity>
234 :     <Entity name="Annotation" keyType="name-string">
235 :     <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
236 : parrello 1.8 are currently the only objects that may be inserted directly into the database. All other
237 : parrello 1.24 information is loaded from data exported by the SEED.</Notes>
238 : parrello 1.8 <Fields>
239 :     <Field name="time" type="date">
240 :     <Notes>Date and time of the annotation.</Notes>
241 :     </Field>
242 :     <Field name="annotation" type="text">
243 :     <Notes>Text of the annotation.</Notes>
244 :     </Field>
245 : parrello 1.1 </Fields>
246 : parrello 1.26 <Indexes>
247 :     <Index>
248 :     <Notes>This index allows the user to find recent annotations.</Notes>
249 :     <IndexFields>
250 :     <IndexField name="time" order="descending" />
251 :     </IndexFields>
252 :     </Index>
253 :     </Indexes>
254 : parrello 1.1 </Entity>
255 : parrello 1.15 <Entity name="Reaction" keyType="key-string">
256 :     <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
257 :     is generally a small number preceded by a letter.</Notes>
258 :     <Fields>
259 :     <Field name="url" type="string" relation="ReactionURL">
260 :     <Notes>HTML string containing a link to a web location that describes the
261 :     reaction. This field is optional.</Notes>
262 :     </Field>
263 :     <Field name="rev" type="boolean">
264 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
265 :     </Field>
266 :     </Fields>
267 :     </Entity>
268 :     <Entity name="Compound" keyType="name-string">
269 :     <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
270 :     All compounds have a unique ID and may also have one or more names.</Notes>
271 :     <Fields>
272 : parrello 1.50 <Field name="label" type="string">
273 : parrello 1.19 <Notes>Name used in reaction display strings.
274 :     It is the same as the name possessing a priority of 1, but it is placed
275 :     here to speed up the query used to create the display strings.</Notes>
276 :     </Field>
277 : parrello 1.15 </Fields>
278 : parrello 1.50 </Entity>
279 :     <Entity name="CompoundName" keyType="string">
280 :     <Notes>A [i]compound name[/i] is a common name for the chemical represented by a
281 :     compound.</Notes>
282 :     </Entity>
283 :     <Entity name="CompoundCAS" keyType="name-string">
284 :     <Notes>This entity represents the Chemical Abstract Service ID for a compound. Each
285 :     Compound has at most one CAS ID.</Notes>
286 : parrello 1.15 </Entity>
287 : parrello 1.5 <Entity name="Subsystem" keyType="string">
288 : parrello 1.1 <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
289 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
290 : parrello 1.15 <Fields>
291 :     <Field name="curator" type="string">
292 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
293 :     </Field>
294 :     <Field name="notes" type="text">
295 :     <Notes>Descriptive notes about the subsystem.</Notes>
296 :     </Field>
297 : parrello 1.28 <Field name="classification" type="string" relation="SubsystemClass">
298 : parrello 1.44 <Notes>Classification string, colon-delimited. This string organizes the
299 : parrello 1.42 subsystems into a hierarchy.</Notes>
300 : parrello 1.28 </Field>
301 : parrello 1.15 </Fields>
302 :     </Entity>
303 :     <Entity name="RoleSubset" keyType="string">
304 :     <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
305 :     subset names are generally very short, non-unique strings. The ID of the parent
306 :     subsystem is prefixed to the subset ID in order to make it unique.</Notes>
307 :     </Entity>
308 :     <Entity name="GenomeSubset" keyType="string">
309 :     <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
310 :     in a particular subsystem. The subset names are generally very short, non-unique
311 :     strings. The ID of the parent subsystem is prefixed to the subset ID in order
312 :     to make it unique.</Notes>
313 : parrello 1.1 </Entity>
314 : parrello 1.24 <Entity name="SSCell" keyType="hash-string">
315 : parrello 1.1 <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
316 :     genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
317 :     of the positions on the spreadsheet.</Notes>
318 :     </Entity>
319 :     <Entity name="SproutUser" keyType="name-string">
320 :     <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The
321 :     user object is keyed on the user's login name.</Notes>
322 :     <Fields>
323 : parrello 1.8 <Field name="description" type="string">
324 :     <Notes>Full name or description of this user.</Notes>
325 :     </Field>
326 : parrello 1.1 <Field name="access-code" type="key-string" relation="UserAccess">
327 : parrello 1.8 <Notes>Access code possessed by this
328 : parrello 1.1 user. A user can have many access codes; a genome is accessible to the user if its
329 :     access code matches any one of the user's access codes.</Notes>
330 : parrello 1.8 </Field>
331 : parrello 1.1 </Fields>
332 :     </Entity>
333 : parrello 1.8 <Entity name="Property" keyType="int">
334 :     <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of
335 :     a particular feature. Each property instance is a key/value pair and can be associated
336 :     with many different features. Conversely, a feature can be associated with many key/value
337 :     pairs, even some that notionally contradict each other. For example, there can be evidence
338 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
339 :     <Fields>
340 :     <Field name="property-name" type="name-string">
341 :     <Notes>Name of this property.</Notes>
342 :     </Field>
343 :     <Field name="property-value" type="string">
344 :     <Notes>Value associated with this property. For each property
345 :     name, there must by a property record for all of its possible
346 :     values.</Notes>
347 :     </Field>
348 :     </Fields>
349 :     <Indexes>
350 :     <Index>
351 :     <Notes>This index enables the application to find all values for a specified property
352 :     name, or any given name/value pair.</Notes>
353 :     <IndexFields>
354 :     <IndexField name="property-name" order="ascending" />
355 :     <IndexField name="property-value" order="ascending" />
356 :     </IndexFields>
357 :     </Index>
358 :     </Indexes>
359 :     </Entity>
360 :     <Entity name="Diagram" keyType="name-string">
361 :     <Notes>A functional diagram describes the chemical reactions, often comprising a single
362 :     subsystem. A diagram is identified by a short name and contains a longer descriptive name.
363 :     The actual diagram shows which functional roles guide the reactions along with the inputs
364 :     and outputs; the database, however, only indicate which roles belong to a particular
365 :     map.</Notes>
366 :     <Fields>
367 :     <Field name="name" type="text">
368 :     <Notes>Descriptive name of this diagram.</Notes>
369 :     </Field>
370 :     </Fields>
371 :     </Entity>
372 :     <Entity name="ExternalAliasOrg" keyType="name-string">
373 :     <Notes>An external alias is a feature name for a functional assignment that is not a
374 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
375 :     the database. This table contains a description of the relevant organism for an
376 :     external alias functional assignment.</Notes>
377 :     <Fields>
378 :     <Field name="org" type="text">
379 :     <Notes>Descriptive name of the target organism for this external alias.</Notes>
380 :     </Field>
381 :     </Fields>
382 :     </Entity>
383 :     <Entity name="ExternalAliasFunc" keyType="name-string">
384 :     <Notes>An external alias is a feature name for a functional assignment that is not a
385 :     FIG ID. Functional assignments for external aliases are kept in a separate section of
386 :     the database. This table contains the functional role for the external alias functional
387 :     assignment.</Notes>
388 :     <Fields>
389 :     <Field name="func" type="text">
390 :     <Notes>Functional role for this external alias.</Notes>
391 :     </Field>
392 :     </Fields>
393 :     </Entity>
394 : parrello 1.31 <Entity name="Family" keyType="id-string">
395 :     <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
396 :     families provide a mechanism for verifying the accuracy of functional assignments
397 :     and are also used in determining phylogenetic trees.</Notes>
398 :     <Fields>
399 : parrello 1.32 <Field name="function" type="text">
400 : parrello 1.31 <Notes>The functional assignment expected for all PEGs in this family.</Notes>
401 :     </Field>
402 : parrello 1.33 <Field name="size" type="int">
403 : parrello 1.31 <Notes>The number of proteins in this family. This may be larger than the
404 :     number of PEGs included in the family, since the family may also contain external
405 :     IDs.</Notes>
406 :     </Field>
407 :     </Fields>
408 :     </Entity>
409 : parrello 1.49 <Entity name="PDB" keyType="id-string">
410 :     <Notes>A PDB is a protein database containing information that can be used to determine
411 :     the shape of the protein and the energies required to dock with it. The ID is the
412 :     four-character name used on the PDB web site.</Notes>
413 :     <Fields>
414 :     <Field name="docking-count" type="int">
415 :     <Notes>The number of ligands that have been docked against this PDB.</Notes>
416 :     </Field>
417 :     </Fields>
418 :     <Indexes>
419 :     <Index>
420 :     <IndexFields>
421 :     <IndexField name="docking-count" order="descending" />
422 :     <IndexField name="id" order="ascending" />
423 :     </IndexFields>
424 :     </Index>
425 :     </Indexes>
426 :     </Entity>
427 :     <Entity name="Ligand" keyType="id-string">
428 :     <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
429 :     The ID of the ligand is an 8-digit ZINC ID number.</Notes>
430 :     <Fields>
431 :     <Field name="name" type="long-string">
432 :     <Notes>Chemical name of this ligand.</Notes>
433 :     </Field>
434 :     </Fields>
435 :     </Entity>
436 : parrello 1.1 </Entities>
437 :     <Relationships>
438 : parrello 1.50 <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
439 :     <Notes>This relationship connects a feature to its CDD protein domains. The
440 :     match score is included as intersection data.</Notes>
441 :     <Fields>
442 :     <Field name="score" type="float">
443 :     <Notes>This is the match score between the feature and the CDD. A
444 :     lower score is a better match.</Notes>
445 :     </Field>
446 :     </Fields>
447 :     <FromIndex>
448 :     <IndexFields>
449 :     <IndexField name="score" order="ascending" />
450 :     </IndexFields>
451 :     </FromIndex>
452 :     </Relationship>
453 :     <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
454 :     <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
455 :     associated with a compound, and some are associated with two compounds, but not
456 :     all compounds have CAS IDs.</Notes>
457 :     </Relationship>
458 :     <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
459 :     <Notes>Relates a role to its EC number. Every EC number is associated with a
460 :     role, but not all roles have EC numbers.</Notes>
461 :     </Relationship>
462 :     <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
463 :     <Notes>Connects an alias to the feature it represents. Every alias connects
464 :     to at least 1 feature, and a feature connects to many aliases.</Notes>
465 :     </Relationship>
466 :     <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
467 :     <Notes>Connects a compound to its names. A compound generally has several
468 :     names</Notes>
469 :     <Fields>
470 :     <Field name="priority" type="int">
471 :     <Notes>Priority of this name, with 1 being the highest priority, 2
472 :     the next highest, and so forth.</Notes>
473 :     </Field>
474 :     </Fields>
475 :     <FromIndex>
476 :     <Notes>This index enables the application to view the names of a compound
477 :     in priority order.</Notes>
478 :     <IndexFields>
479 :     <IndexField name="priority" order="ascending" />
480 :     </IndexFields>
481 :     </FromIndex>
482 :     </Relationship>
483 : parrello 1.49 <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
484 :     <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
485 :     <Fields>
486 :     <Field name="score" type="float">
487 :     <Notes>Similarity score for the comparison between the feature and
488 :     the PDB protein. A lower score indicates a better match.</Notes>
489 :     </Field>
490 :     <Field name="start-location" type="int">
491 :     <Notes>Starting location within the feature of the matching region.</Notes>
492 :     </Field>
493 :     <Field name="end-location" type="int">
494 :     <Notes>Ending location within the feature of the matching region.</Notes>
495 :     </Field>
496 :     </Fields>
497 :     <ToIndex>
498 :     <Notes>This index enables the application to view the PDBs of a
499 :     feature in order from the closest match to the furthest.</Notes>
500 :     <IndexFields>
501 :     <IndexField name="score" order="ascending" />
502 :     </IndexFields>
503 :     </ToIndex>
504 :     <FromIndex>
505 :     <Notes>This index enables the application to view the features of
506 :     a PDB in order from the closest match to the furthest.</Notes>
507 :     <IndexFields>
508 :     <IndexField name="score" order="ascending" />
509 :     </IndexFields>
510 :     </FromIndex>
511 :     </Relationship>
512 :     <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
513 :     <Notes>Indicates that a docking result exists between a PDB and a ligand. The
514 :     docking result describes the energy required for the ligand to dock with
515 :     the protein described by the PDB. A lower energy indicates the ligand has a
516 :     good chance of disabling the protein. At the current time, only the best
517 :     docking results are kept.</Notes>
518 :     <Fields>
519 :     <Field name="reason" type="id-string">
520 :     <Notes>Indication of the reason for determining the docking result.
521 :     A value of [b]Random[/b] indicates the docking was attempted as a part
522 :     of a random survey used to determine the docking characteristics of the
523 :     PDB. A value of [b]Rich[/b] indicates the docking was attempted because
524 :     a low-energy docking result was predicted for the ligand with respect
525 :     to the PDB.</Notes>
526 :     </Field>
527 :     <Field name="tool" type="id-string">
528 :     <Notes>Name of the tool used to produce the docking result.</Notes>
529 :     </Field>
530 :     <Field name="total-energy" type="float">
531 :     <Notes>Total energy required for the ligand to dock with the PDB
532 :     protein, in kcal/mol. A negative value means energy is released.</Notes>
533 :     </Field>
534 :     <Field name="vanderwalls-energy" type="float">
535 :     <Notes>Docking energy in kcal/mol that results from the geometric fit
536 :     (Van der Waals force) between the PDB and the ligand.</Notes>
537 :     </Field>
538 :     <Field name="electrostatic-energy" type="float">
539 :     <Notes>Docking energy in kcal/mol that results from the movement of
540 :     electrons (electrostatic force) between the PDB and the ligan.</Notes>
541 :     </Field>
542 :     </Fields>
543 :     <FromIndex>
544 :     <Notes>This index enables the application to view a PDB's docking results from
545 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
546 :     <IndexFields>
547 :     <IndexField name="total-energy" order="ascending" />
548 :     </IndexFields>
549 :     </FromIndex>
550 :     <ToIndex>
551 :     <Notes>This index enables the application to view a ligand's docking results from
552 :     the lowest energy (best docking) to highest energy (worst docking). Note that
553 :     since we only keep the best docking results for a PDB, this index is not likely
554 :     to provide useful results.</Notes>
555 :     </ToIndex>
556 :     </Relationship>
557 : parrello 1.34 <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
558 : parrello 1.31 <Notes>This relationship connects a protein family to all of its PEGs and connects
559 :     each PEG to all of its protein families.</Notes>
560 :     </Relationship>
561 : parrello 1.50 <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
562 : parrello 1.27 <Notes>This relation connects a synonym group to the features that make it
563 :     up.</Notes>
564 :     </Relationship>
565 : parrello 1.24 <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
566 :     <Notes>This relationship connects a genome to all of its features. This
567 :     relationship is redundant in a sense, because the genome ID is part
568 :     of the feature ID; however, it makes the creation of certain queries more
569 :     convenient because you can drag in filtering information for a feature's
570 :     genome.</Notes>
571 :     <Fields>
572 :     <Field name="type" type="key-string">
573 :     <Notes>Feature type (eg. peg, rna)</Notes>
574 :     </Field>
575 :     </Fields>
576 : parrello 1.38 <FromIndex>
577 : parrello 1.24 <Notes>This index enables the application to view the features of a
578 :     Genome sorted by type.</Notes>
579 :     <IndexFields>
580 :     <IndexField name="type" order="ascending" />
581 :     </IndexFields>
582 : parrello 1.38 </FromIndex>
583 : parrello 1.24 </Relationship>
584 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
585 :     <Notes>This relationship connects a genome to the contigs that contain the actual genetic
586 :     information.</Notes>
587 :     </Relationship>
588 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
589 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
590 :     come from a single source or from a cooperation among multiple sources.</Notes>
591 :     </Relationship>
592 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
593 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
594 :     contig into sequences, we get a performance boost from only needing to keep small portions
595 :     of a contig in memory at any one time. This relationship connects the contig to its
596 :     constituent sequences.</Notes>
597 :     <Fields>
598 :     <Field name="len" type="int">
599 : parrello 1.15 <Notes>Length of the sequence.</Notes>
600 :     </Field>
601 : parrello 1.1 <Field name="start-position" type="int">
602 : parrello 1.15 <Notes>Index (1-based) of the point in the contig where this
603 :     sequence starts.</Notes>
604 :     </Field>
605 : parrello 1.1 </Fields>
606 :     <FromIndex>
607 :     <Notes>This index enables the application to find all of the sequences in
608 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
609 : parrello 1.1 <IndexFields>
610 :     <IndexField name="start-position" order="ascending" />
611 :     <IndexField name="len" order="ascending" />
612 :     </IndexFields>
613 :     </FromIndex>
614 :     </Relationship>
615 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
616 :     <Notes>This relationship connects a feature to its annotations.</Notes>
617 :     </Relationship>
618 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
619 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
620 :     </Relationship>
621 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
622 :     <Notes>This relationship connects subsystems to the genomes that use
623 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
624 :     connected to the genome features through the [b]SSCell[/b] object.</Notes>
625 : parrello 1.15 <Fields>
626 :     <Field name="variant-code" type="key-string">
627 : parrello 1.20 <Notes>Code indicating the subsystem variant to which this
628 : parrello 1.15 genome belongs. Each subsystem can have multiple variants. A variant
629 : parrello 1.20 code of [b]-1[/b] indicates that the genome does not have a functional
630 :     variant of the subsystem. A variant code of [b]0[/b] indicates that
631 :     the genome's participation is considered iffy.</Notes>
632 : parrello 1.15 </Field>
633 :     </Fields>
634 :     <ToIndex>
635 :     <Notes>This index enables the application to find all of the genomes using
636 :     a subsystem in order by variant code, which is how we wish to display them
637 :     in the spreadsheets.</Notes>
638 :     <IndexFields>
639 :     <IndexField name="variant-code" order="ascending" />
640 :     </IndexFields>
641 :     </ToIndex>
642 : parrello 1.1 </Relationship>
643 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
644 :     <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
645 : parrello 1.15 <Fields>
646 : parrello 1.50 <Field name="abbr" type="name-string">
647 :     <Notes>Abbreviated name for the role, generally non-unique, but useful
648 :     in column headings for HTML tables.</Notes>
649 :     </Field>
650 : parrello 1.15 <Field name="column-number" type="int">
651 :     <Notes>Column number for this role in the specified subsystem's
652 :     spreadsheet.</Notes>
653 :     </Field>
654 :     </Fields>
655 :     <ToIndex>
656 :     <Notes>This index enables the application to see the subsystem roles
657 :     in column order. The ordering of the roles is usually significant,
658 :     so it is important to preserve it.</Notes>
659 :     <IndexFields>
660 :     <IndexField name="column-number" order="ascending" />
661 :     </IndexFields>
662 :     </ToIndex>
663 : parrello 1.1 </Relationship>
664 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
665 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
666 :     genome for the spreadsheet column.</Notes>
667 :     </Relationship>
668 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
669 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
670 :     role for the spreadsheet row.</Notes>
671 :     </Relationship>
672 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
673 :     <Notes>This relationship connects a subsystem's spreadsheet cell to the
674 :     features assigned to it.</Notes>
675 : parrello 1.15 <Fields>
676 :     <Field name="cluster-number" type="int">
677 :     <Notes>ID of this feature's cluster. Clusters represent families of
678 :     related proteins participating in a subsystem.</Notes>
679 :     </Field>
680 :     </Fields>
681 :     </Relationship>
682 :     <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
683 :     <Notes>This relationship connects a reaction to the compounds that participate
684 :     in it.</Notes>
685 :     <Fields>
686 :     <Field name="product" type="boolean">
687 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
688 :     it is a substrate. When a reaction is written on paper in
689 :     chemical notation, the substrates are left of the arrow and the
690 :     products are to the right. Sorting on this field will cause
691 :     the substrates to appear first, followed by the products. If the
692 :     reaction is reversible, then the notion of substrates and products
693 :     is not at intuitive; however, a value here of FALSE still puts the
694 :     compound left of the arrow and a value of TRUE still puts it to the
695 :     right.</Notes>
696 :     </Field>
697 : parrello 1.19 <Field name="stoichiometry" type="key-string">
698 : parrello 1.15 <Notes>Number of molecules of the compound that participate in a
699 :     single instance of the reaction. For example, if a reaction
700 : parrello 1.19 produces two water molecules, the stoichiometry of water for the
701 : parrello 1.15 reaction would be two. When a reaction is written on paper in
702 : parrello 1.19 chemical notation, the stoichiometry is the number next to the
703 : parrello 1.15 chemical formula of the compound.</Notes>
704 :     </Field>
705 :     <Field name="main" type="boolean">
706 :     <Notes>TRUE if this compound is one of the main participants in
707 :     the reaction, else FALSE. It is permissible for none of the
708 :     compounds in the reaction to be considered main, in which
709 :     case this value would be FALSE for all of the relevant
710 :     compounds.</Notes>
711 :     </Field>
712 :     <Field name="loc" type="key-string">
713 :     <Notes>An optional character string that indicates the relative
714 :     position of this compound in the reaction's chemical formula. The
715 :     location affects the way the compounds present as we cross the
716 :     relationship from the reaction side. The product/substrate flag
717 :     comes first, then the value of this field, then the main flag.
718 :     The default value is an empty string; however, the empty string
719 :     sorts first, so if this field is used, it should probably be
720 :     used for every compound in the reaction.</Notes>
721 :     </Field>
722 : parrello 1.19 <Field name="discriminator" type="int">
723 :     <Notes>A unique ID for this record. The discriminator does not
724 :     provide any useful data, but it prevents identical records from
725 :     being collapsed by the SELECT DISTINCT command used by ERDB to
726 :     retrieve data.</Notes>
727 :     </Field>
728 : parrello 1.15 </Fields>
729 :     <ToIndex>
730 :     <Notes>This index presents the compounds in the reaction in the
731 :     order they should be displayed when writing it in chemical notation.
732 :     All the substrates appear before all the products, and within that
733 :     ordering, the main compounds appear first.</Notes>
734 : parrello 1.19 <IndexFields>
735 :     <IndexField name="product" order="ascending" />
736 :     <IndexField name="loc" order="ascending" />
737 :     <IndexField name="main" order="descending" />
738 :     </IndexFields>
739 : parrello 1.15 </ToIndex>
740 : parrello 1.1 </Relationship>
741 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
742 :     <Notes>This relationship connects a feature to the contig segments that work together
743 :     to effect it. The segments are numbered sequentially starting from 1. The database is
744 :     required to place an upper limit on the length of each segment. If a segment is longer
745 :     than the maximum, it can be broken into smaller bits.
746 :     [p]The upper limit enables applications to locate all features that contain a specific
747 :     residue. For example, if the upper limit is 100 and we are looking for a feature that
748 :     contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point
749 :     between 135 and 333. The results can then be filtered by direction and length of the
750 :     segment.</Notes>
751 :     <Fields>
752 :     <Field name="locN" type="int">
753 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
754 :     </Field>
755 : parrello 1.1 <Field name="beg" type="int">
756 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
757 :     belongs to the segment.</Notes>
758 :     </Field>
759 : parrello 1.1 <Field name="len" type="int">
760 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
761 :     a specific point between residues. This is the point before the residue if the direction
762 :     is forward and the point after the residue if the direction is backward.</Notes>
763 :     </Field>
764 : parrello 1.1 <Field name="dir" type="char">
765 : parrello 1.8 <Notes>Direction of the segment: [b]+[/b] if it is forward and
766 :     [b]-[/b] if it is backward.</Notes>
767 :     </Field>
768 : parrello 1.1 </Fields>
769 : parrello 1.45 <FromIndex>
770 : parrello 1.1 <Notes>This index allows the application to find all the segments of a feature in
771 : parrello 1.8 the proper order.</Notes>
772 : parrello 1.1 <IndexFields>
773 :     <IndexField name="locN" order="ascending" />
774 :     </IndexFields>
775 :     </FromIndex>
776 :     <ToIndex>
777 :     <Notes>This index is the one used by applications to find all the feature
778 :     segments that contain a specific residue.</Notes>
779 :     <IndexFields>
780 :     <IndexField name="beg" order="ascending" />
781 :     </IndexFields>
782 :     </ToIndex>
783 :     </Relationship>
784 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
785 :     <Notes>This relationship connects a feature to its known property values.
786 :     The relationship contains text data that indicates the paper or organization
787 :     that discovered evidence that the feature possesses the property. So, for
788 :     example, if two papers presented evidence that a feature is essential,
789 :     there would be an instance of this relationship for both.</Notes>
790 :     <Fields>
791 :     <Field name="evidence" type="text">
792 :     <Notes>URL or citation of the paper or
793 :     institution that reported evidence of the relevant feature possessing
794 :     the specified property value.</Notes>
795 :     </Field>
796 :     </Fields>
797 :     </Relationship>
798 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
799 :     <Notes>This relationship connects a role to the diagrams on which it
800 :     appears. A role frequently identifies an enzyme, and can appear in many
801 :     diagrams. A diagram generally contains many different roles.</Notes>
802 :     </Relationship>
803 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
804 :     <Notes>This relationship connects a subsystem to the spreadsheet cells
805 :     used to analyze and display it. The cells themselves can be thought of
806 :     as a grid with Roles on one axis and Genomes on the other. The
807 :     various features of the subsystem are then assigned to the cells.</Notes>
808 :     </Relationship>
809 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
810 :     <Notes>This relationship identifies the users trusted by each
811 :     particular user. When viewing functional assignments, the
812 :     assignment displayed is the most recent one by a user trusted
813 :     by the current user. The current user implicitly trusts himself.
814 :     If no trusted users are specified in the database, the user
815 :     also implicitly trusts the user [b]FIG[/b].</Notes>
816 :     </Relationship>
817 : parrello 1.15 <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
818 :     <Notes>This relationship connects a role subset to the roles that it covers.
819 :     A subset is, essentially, a named group of roles belonging to a specific
820 :     subsystem, and this relationship effects that. Note that will a role
821 :     may belong to many subsystems, a subset belongs to only one subsystem,
822 :     and all roles in the subset must have that subsystem in common.</Notes>
823 :     </Relationship>
824 :     <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
825 :     <Notes>This relationship connects a subset to the genomes that it covers.
826 :     A subset is, essentially, a named group of genomes participating in a specific
827 :     subsystem, and this relationship effects that. Note that while a genome
828 :     may belong to many subsystems, a subset belongs to only one subsystem,
829 :     and all genomes in the subset must have that subsystem in common.</Notes>
830 :     </Relationship>
831 :     <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
832 :     <Notes>This relationship connects a subsystem to its constituent
833 :     role subsets. Note that some roles in a subsystem may not belong to a
834 :     subset, so the relationship between roles and subsystems cannot be
835 :     derived from the relationships going through the subset.</Notes>
836 :     </Relationship>
837 :     <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
838 :     <Notes>This relationship connects a subsystem to its constituent
839 :     genome subsets. Note that some genomes in a subsystem may not belong to a
840 :     subset, so the relationship between genomes and subsystems cannot be
841 :     derived from the relationships going through the subset.</Notes>
842 :     </Relationship>
843 :     <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
844 :     <Notes>This relationship connects a role to the reactions it catalyzes.
845 :     The purpose of a role is to create proteins that trigger certain
846 :     chemical reactions. A single reaction can be triggered by many roles,
847 :     and a role can trigger many reactions.</Notes>
848 :     </Relationship>
849 : parrello 1.39 <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
850 :     <Notes>This relationship connects a feature to the subsystems in which it
851 :     participates. This is technically redundant information, but it is used
852 :     so often that it deserves its own table.</Notes>
853 : parrello 1.40 <Fields>
854 :     <Field name="genome" type="name-string">
855 :     <Notes>ID of the genome containing the feature</Notes>
856 :     </Field>
857 :     <Field name="type" type="key-string">
858 :     <Notes>Feature type (eg. peg, rna)</Notes>
859 :     </Field>
860 :     </Fields>
861 :     <ToIndex>
862 :     <Notes>This index enables the application to view the features of a
863 :     subsystem sorted by genome and feature type.</Notes>
864 :     <IndexFields>
865 :     <IndexField name="genome" order="ascending" />
866 :     <IndexField name="type" order="ascending" />
867 :     </IndexFields>
868 :     </ToIndex>
869 : parrello 1.39 </Relationship>
870 : parrello 1.1 </Relationships>
871 :     </Database>

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