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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 1.55 <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.
5 : parrello 1.51 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 : parrello 1.55 <DisplayInfo theme="nmpdr" col="3" row="1" />
13 :     <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
14 : parrello 1.1 <Fields>
15 :     <Field name="genus" type="name-string">
16 :     <Notes>Genus of the relevant organism.</Notes>
17 :     </Field>
18 :     <Field name="species" type="name-string">
19 : parrello 1.8 <Notes>Species of the relevant organism.</Notes>
20 :     </Field>
21 : parrello 1.58 <Field name="unique-characterization" type="medium-string" default="">
22 : parrello 1.8 <Notes>The unique characterization identifies the particular organism instance from which the
23 :     genome is taken. It is possible to have in the database more than one genome for a
24 : parrello 1.1 particular species, and every individual organism has variations in its DNA.</Notes>
25 :     </Field>
26 : parrello 1.48 <Field name="version" type="name-string">
27 :     <Notes>version string for this genome, generally consisting of the genome ID followed
28 :     by a period and a string of digits.</Notes>
29 :     </Field>
30 : parrello 1.15 <Field name="complete" type="boolean">
31 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
32 :     </Field>
33 : parrello 1.48 <Field name="dna-size" type="counter">
34 :     <Notes>number of base pairs in the genome</Notes>
35 :     </Field>
36 : parrello 1.8 <Field name="taxonomy" type="text">
37 : parrello 1.52 <Notes>The taxonomy string contains the full [[Wikipedia:taxonomy]] of the organism, while individual elements
38 : parrello 1.8 separated by semi-colons (and optional white space), starting with the domain and ending with
39 :     the disambiguated genus and species (which is the organism's scientific name plus an
40 :     identifying string).</Notes>
41 :     </Field>
42 : parrello 1.37 <Field name="primary-group" type="name-string">
43 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
44 : parrello 1.52 per organism (either based on the organism name or the default value =Supporting=). In general,
45 :     more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>
46 :     </Field>
47 :     <Field name="contigs" type="int">
48 :     <Notes>Number of contigs for this organism.</Notes>
49 :     </Field>
50 :     <Field name="pegs" type="int">
51 :     <Notes>Number of [[protein encoding genes]] for this organism</Notes>
52 :     </Field>
53 :     <Field name="rnas" type="int">
54 :     <Notes>Number of RNA features found for this organism.</Notes>
55 : parrello 1.37 </Field>
56 : parrello 1.1 </Fields>
57 :     <Indexes>
58 : parrello 1.45 <Index>
59 : parrello 1.1 <Notes>This index allows the applications to find all genomes associated with
60 : parrello 1.37 a specific primary (NMPDR) group.</Notes>
61 :     <IndexFields>
62 :     <IndexField name="primary-group" order="ascending" />
63 :     <IndexField name="genus" order="ascending" />
64 :     <IndexField name="species" order="ascending" />
65 :     <IndexField name="unique-characterization" order="ascending" />
66 :     </IndexFields>
67 :     </Index>
68 : parrello 1.45 <Index>
69 : parrello 1.1 <Notes>This index allows the applications to find all genomes for a particular
70 :     species.</Notes>
71 :     <IndexFields>
72 :     <IndexField name="genus" order="ascending" />
73 :     <IndexField name="species" order="ascending" />
74 :     <IndexField name="unique-characterization" order="ascending" />
75 :     </IndexFields>
76 :     </Index>
77 :     </Indexes>
78 :     </Entity>
79 : parrello 1.50 <Entity name="CDD" keyType="key-string">
80 :     <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
81 : parrello 1.52 on a feature's protein. The ID is six-digit string assigned by the public
82 : parrello 1.58 Conserved Domain Database. A CDD can occur on multiple features and a feature
83 :     generally has multiple CDDs.</Notes>
84 : parrello 1.50 </Entity>
85 : parrello 1.1 <Entity name="Source" keyType="medium-string">
86 : parrello 1.55 <Notes>A source describes a place from which genome data was taken. This can be an organization
87 : parrello 1.1 or a paper citation.</Notes>
88 :     <Fields>
89 :     <Field name="URL" type="string" relation="SourceURL">
90 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
91 :     </Field>
92 : parrello 1.1 <Field name="description" type="text">
93 : parrello 1.52 <Notes>Description of the source. The description can be a street address or a citation.</Notes>
94 : parrello 1.8 </Field>
95 : parrello 1.1 </Fields>
96 :     </Entity>
97 :     <Entity name="Contig" keyType="name-string">
98 : parrello 1.55 <DisplayInfo theme="nmpdr" col="1" row="1" />
99 :     <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
100 : parrello 1.1 genome ID followed by a name that identifies which contig this is for the parent genome. As
101 :     is the case with all keys in this database, the individual components are separated by a
102 : parrello 1.52 period. A contig can contain over a million residues. For performance reasons, therefore,
103 : parrello 1.55 the contig is split into multiple pieces called sequences. The sequences
104 : parrello 1.1 contain the characters that represent the residues as well as data on the quality of
105 :     the residue identification.</Notes>
106 :     </Entity>
107 :     <Entity name="Sequence" keyType="name-string">
108 : parrello 1.55 <Notes>A sequence is a continuous piece of a contig. Contigs are split into
109 : parrello 1.1 sequences so that we don't have to have the entire contig in memory when we are
110 :     manipulating it. The key of the sequence is the contig ID followed by the index of
111 :     the begin point.</Notes>
112 :     <Fields>
113 :     <Field name="sequence" type="text">
114 : parrello 1.52 <Notes>String consisting of the residues (base pairs). Each residue is described by a single
115 : parrello 1.8 character in the string.</Notes>
116 :     </Field>
117 : parrello 1.1 <Field name="quality-vector" type="text">
118 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
119 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
120 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
121 : parrello 1.52 10^-30. A higher quality number indicates a better chance of a correct match. It is
122 :     possible that the quality data is not known for a sequence. If that is the case, the
123 :     quality vector will contain the string =unknown=.</Notes>
124 : parrello 1.8 </Field>
125 : parrello 1.1 </Fields>
126 :     </Entity>
127 : parrello 1.54 <Entity name="Keyword" keyType="name-string">
128 : parrello 1.55 <Notes>A keyword is a word that can be used to search the feature table. This entity
129 :     contains the keyword's stem, its phonetic form, and the number of features that
130 :     can be found by searching for the word.</Notes>
131 :     <Fields>
132 :     <Field name="stem" type="name-string">
133 :     <Notes>The stem of a keyword is a normalized form that is independent of parts
134 :     of speech. The actual keywords stored in the database search index are stems.</Notes>
135 :     </Field>
136 :     <Field name="phonex" type="name-string">
137 :     <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
138 :     word stem. This can be used to find alternative spellings if an matching word is not
139 :     present.</Notes>
140 :     </Field>
141 : parrello 1.54 </Fields>
142 : parrello 1.55 <Indexes>
143 :     <Index>
144 :     <Notes>This index allows the user to find words by stem.</Notes>
145 :     <IndexFields>
146 :     <IndexField name="stem" order="ascending" />
147 :     </IndexFields>
148 :     </Index>
149 :     <Index>
150 :     <Notes>This index allows the user to find words by phonex.</Notes>
151 :     <IndexFields>
152 :     <IndexField name="phonex" order="ascending" />
153 :     </IndexFields>
154 :     </Index>
155 :     </Indexes>
156 :     </Entity>
157 :     <Entity name="ExternalDatabase" keyType="key-string">
158 :     <Notes>An external database identifies a biological database surveyed by PIR International
159 :     as part of an effort to determine which features are essentially identical between bioinformatics
160 :     organizations. Each feature in the database will have zero or more corresponding IDs that are
161 :     captured from the PIR data. Each corresponding ID is represented in a relationship between an external
162 :     database and the feature itself.</Notes>
163 : parrello 1.54 </Entity>
164 : parrello 1.25 <Entity name="Feature" keyType="id-string">
165 : parrello 1.55 <DisplayInfo theme="nmpdr" col="3" row="3" />
166 :     <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
167 : parrello 1.1 may be spread across multiple contigs of a genome, but never across more than
168 :     one genome. Features can be assigned to roles via spreadsheet cells,
169 : parrello 1.55 and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
170 : parrello 1.1 <Fields>
171 : parrello 1.50 <Field name="feature-type" type="id-string">
172 : parrello 1.52 <Notes>Code indicating the type of this feature. Among the codes currently
173 :     supported are =peg= for a [[protein encoding gene]], =bs= for a
174 :     binding site, =opr= for an operon, and so forth.</Notes>
175 : parrello 1.8 </Field>
176 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
177 : parrello 1.52 <Notes>_(optional)_ A translation of this feature's residues into character
178 : parrello 1.8 codes, formed by concatenating the pieces of the feature together. For a
179 : parrello 1.52 [[protein encoding gene]], the translation contains protein characters. For other types
180 :     it contains DNA characters.</Notes>
181 : parrello 1.8 </Field>
182 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
183 : parrello 1.52 <Notes>Upstream sequence for the feature. This includes residues preceding the feature as
184 :     well as some of the feature's initial residues.</Notes>
185 : parrello 1.8 </Field>
186 : parrello 1.42 <Field name="assignment" type="text">
187 :     <Notes>Default functional assignment for this feature.</Notes>
188 :     </Field>
189 : parrello 1.48 <Field name="assignment-maker" type="name-string">
190 :     <Notes>name of the user who made the functional assignment</Notes>
191 :     </Field>
192 :     <Field name="assignment-quality" type="char">
193 :     <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
194 :     (indicating experimental)</Notes>
195 :     </Field>
196 : parrello 1.41 <Field name="keywords" type="text" searchable="1">
197 :     <Notes>This is a list of search keywords for the feature. It includes the
198 :     functional assignment, subsystem roles, and special properties.</Notes>
199 : parrello 1.36 </Field>
200 : parrello 1.8 <Field name="link" type="text" relation="FeatureLink">
201 : parrello 1.52 <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
202 : parrello 1.8 links are to other websites that have useful about the gene that the feature represents, and
203 : parrello 1.52 are coded as raw HTML, using &lt;a href="_link_"&gt;_text_&lt;/a&gt; notation.</Notes>
204 : parrello 1.8 </Field>
205 : parrello 1.41 <Field name="conservation" type="float" relation="FeatureConservation">
206 : parrello 1.52 <Notes>_(optional)_ A number between 0 and 1 that indicates the degree to which this feature's DNA is
207 : parrello 1.41 conserved in related genomes. A value of 1 indicates perfect conservation. A value less
208 : parrello 1.50 than 1 is a reflection of the degree to which gap characters interfere in the alignment
209 : parrello 1.41 between the feature and its close relatives.</Notes>
210 :     </Field>
211 : parrello 1.45 <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
212 :     <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
213 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
214 :     or potential (potential-essential), hyperlinked to the document from which the
215 :     essentiality was curated. If a feature is not essential, this field will have no
216 :     values; otherwise, it may have multiple values.</Notes>
217 :     </Field>
218 :     <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
219 :     <Notes>A value indicating the virulence of the feature, coded as HTML. In most
220 :     cases, this will be a phrase or SA number hyperlinked to the document from which
221 :     the virulence information was curated. If the feature is not virulent, this field
222 :     will have no values; otherwise, it may have multiple values.</Notes>
223 :     </Field>
224 :     <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
225 :     <Notes>A value indicating whether or not the feature can be found in the
226 :     Immune Epitope Database. If the feature has not been matched to that database,
227 :     this field will have no values. Otherwise, it will have an epitope name and/or
228 :     sequence, hyperlinked to the database.</Notes>
229 :     </Field>
230 : parrello 1.50 <Field name="location-string" type="text">
231 :     <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
232 :     strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
233 : parrello 1.52 we have to painstakingly paste together the [[#IsLocatedIn]] records, which are themselves
234 :     designed to help look for features in a particular region rather than to find the location
235 :     of a feature.</Notes>
236 : parrello 1.50 </Field>
237 : parrello 1.55 <Field name="signal-peptide" type="name-string">
238 :     <Notes>The signal peptide location for this feature. This is expressed as start and end
239 :     numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
240 :     peptide at the beginning of the feature's protein and extending through 22 amino acid
241 :     positions. An empty string means no signal peptide is present.</Notes>
242 :     </Field>
243 :     <Field name="transmembrane-map" type="text">
244 :     <Notes>A map indicating which sections of a protein will be embedded in a membrane.
245 :     This is expressed as a comma-separated list of as start and end numbers with hyphens
246 :     for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
247 :     sections of the protein that become embedded in a membrane: the 10th through 12th
248 :     amino acids, and the 40th through the 60th. An empty string means no
249 :     transmembrane regions are known.</Notes>
250 :     </Field>
251 :     <Field name="similar-to-human" type="boolean">
252 :     <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
253 :     else FALSE</Notes>
254 :     </Field>
255 :     <Field name="isoelectric-point" type="float">
256 :     <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
257 :     If the pH of the medium is lower than this value, the protein will have a net
258 :     positive charge. If the pH of the medium is higher, then the protein will have a
259 :     net negative charge.</Notes>
260 :     </Field>
261 :     <Field name="molecular-weight" type="float">
262 :     <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
263 :     indicates that no protein is created.</Notes>
264 :     </Field>
265 :     <Field name="sequence-length" type="counter">
266 :     <Notes>Number of base pairs in this feature.</Notes>
267 :     </Field>
268 :     <Field name="locked" type="boolean">
269 :     <Notes>TRUE if a feature's assignment is locked. A locked feature's functional
270 :     role cannot be changed by automated programs.</Notes>
271 :     </Field>
272 :     <Field name="in-genbank" type="boolean">
273 :     <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
274 :     </Field>
275 : parrello 1.1 </Fields>
276 :     </Entity>
277 : parrello 1.50 <Entity name="FeatureAlias" keyType="medium-string">
278 :     <Notes>Alternative names for features. A feature can have many aliases. In general,
279 : parrello 1.52 each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
280 :     </Entity>
281 :     <Entity name="SproutUser" keyType="name-string">
282 : parrello 1.55 <Notes>A user is a person who can make annotations and view data in the database. The
283 : parrello 1.52 user object is keyed on the user's login name.</Notes>
284 :     <Fields>
285 :     <Field name="description" type="string">
286 :     <Notes>Full name or description of this user.</Notes>
287 :     </Field>
288 :     </Fields>
289 : parrello 1.50 </Entity>
290 : parrello 1.27 <Entity name="SynonymGroup" keyType="id-string">
291 : parrello 1.55 <Notes>A synonym group represents a group of features. Features that represent substantially
292 : parrello 1.52 identical proteins or DNA sequences are mapped to the same synonym group, and this information is
293 :     used to expand similarities.</Notes>
294 : parrello 1.27 </Entity>
295 : parrello 1.1 <Entity name="Role" keyType="string">
296 : parrello 1.55 <DisplayInfo theme="web" col="7" row="3" />
297 :     <Notes>A role describes a biological function that may be fulfilled by a feature.
298 : parrello 1.1 One of the main goals of the database is to record the roles of the various features.</Notes>
299 : parrello 1.50 </Entity>
300 :     <Entity name="RoleEC" keyType="string">
301 :     <Notes>EC code for a role.</Notes>
302 : parrello 1.1 </Entity>
303 :     <Entity name="Annotation" keyType="name-string">
304 : parrello 1.55 <DisplayInfo theme="seed" col="1" row="3" />
305 :     <Notes>An annotation contains supplementary information about a feature. The most
306 : parrello 1.52 important type of annotation is the assignment of a [[functional role]]; however,
307 :     other types of annotations are also possible.</Notes>
308 : parrello 1.8 <Fields>
309 :     <Field name="time" type="date">
310 :     <Notes>Date and time of the annotation.</Notes>
311 :     </Field>
312 :     <Field name="annotation" type="text">
313 :     <Notes>Text of the annotation.</Notes>
314 :     </Field>
315 : parrello 1.1 </Fields>
316 : parrello 1.26 <Indexes>
317 :     <Index>
318 :     <Notes>This index allows the user to find recent annotations.</Notes>
319 :     <IndexFields>
320 :     <IndexField name="time" order="descending" />
321 :     </IndexFields>
322 :     </Index>
323 :     </Indexes>
324 : parrello 1.1 </Entity>
325 : parrello 1.15 <Entity name="Reaction" keyType="key-string">
326 : parrello 1.55 <DisplayInfo theme="web" col="7" row="5" />
327 :     <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
328 : parrello 1.15 is generally a small number preceded by a letter.</Notes>
329 :     <Fields>
330 :     <Field name="url" type="string" relation="ReactionURL">
331 :     <Notes>HTML string containing a link to a web location that describes the
332 :     reaction. This field is optional.</Notes>
333 :     </Field>
334 :     <Field name="rev" type="boolean">
335 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
336 :     </Field>
337 :     </Fields>
338 :     </Entity>
339 :     <Entity name="Compound" keyType="name-string">
340 : parrello 1.55 <DisplayInfo theme="web" col="7" row="7" />
341 :     <Notes>A compound is a chemical that participates in a reaction.
342 : parrello 1.15 All compounds have a unique ID and may also have one or more names.</Notes>
343 :     <Fields>
344 : parrello 1.50 <Field name="label" type="string">
345 : parrello 1.52 <Notes>Name used in reaction display strings. This is the same as the name
346 :     possessing a priority of 1, but it is placed here to speed up the query
347 :     used to create the display strings.</Notes>
348 : parrello 1.19 </Field>
349 : parrello 1.15 </Fields>
350 : parrello 1.50 </Entity>
351 :     <Entity name="CompoundName" keyType="string">
352 : parrello 1.55 <Notes>A compound name is a common name for the chemical represented by a
353 : parrello 1.50 compound.</Notes>
354 :     </Entity>
355 :     <Entity name="CompoundCAS" keyType="name-string">
356 : parrello 1.55 <Notes>This entity represents the Chemical Abstract Service ID for a
357 : parrello 1.52 compound. Each Compound has at most one CAS ID.</Notes>
358 : parrello 1.15 </Entity>
359 : parrello 1.5 <Entity name="Subsystem" keyType="string">
360 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="1" />
361 :     <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
362 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
363 :     <Fields>
364 :     <Field name="version" type="int">
365 :     <Notes>Version number for the subsystem. This value is incremented each time the subsystem
366 :     is backed up.</Notes>
367 :     </Field>
368 : parrello 1.15 <Field name="curator" type="string">
369 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
370 :     </Field>
371 :     <Field name="notes" type="text">
372 :     <Notes>Descriptive notes about the subsystem.</Notes>
373 :     </Field>
374 : parrello 1.52 <Field name="description" type="text">
375 : parrello 1.55 <Notes>Description of the subsystem's function in the cell.</Notes>
376 : parrello 1.52 </Field>
377 : parrello 1.28 <Field name="classification" type="string" relation="SubsystemClass">
378 : parrello 1.44 <Notes>Classification string, colon-delimited. This string organizes the
379 : parrello 1.42 subsystems into a hierarchy.</Notes>
380 : parrello 1.28 </Field>
381 : parrello 1.55 <Field name="hope-curation-notes" type="text" relation="SubsystemHopeNotes">
382 :     <Notes>Text description of how the scenarios were curated.</Notes>
383 :     </Field>
384 : parrello 1.15 </Fields>
385 :     </Entity>
386 :     <Entity name="RoleSubset" keyType="string">
387 : parrello 1.55 <Notes>A role subset is a named collection of roles in a particular subsystem. The
388 : parrello 1.15 subset names are generally very short, non-unique strings. The ID of the parent
389 :     subsystem is prefixed to the subset ID in order to make it unique.</Notes>
390 :     </Entity>
391 :     <Entity name="GenomeSubset" keyType="string">
392 : parrello 1.55 <Notes>A genome subset is a named collection of genomes that participate
393 : parrello 1.15 in a particular subsystem. The subset names are generally very short, non-unique
394 :     strings. The ID of the parent subsystem is prefixed to the subset ID in order
395 :     to make it unique.</Notes>
396 : parrello 1.1 </Entity>
397 : parrello 1.24 <Entity name="SSCell" keyType="hash-string">
398 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="3" />
399 :     <Notes>Part of the process of subsystem annotation of features
400 :     is creating a spreadsheet of genomes and roles to which features are assigned.
401 :     A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
402 : parrello 1.1 </Entity>
403 : parrello 1.8 <Entity name="Property" keyType="int">
404 : parrello 1.55 <Notes>A property is a type of assertion that could be made about the properties of
405 : parrello 1.8 a particular feature. Each property instance is a key/value pair and can be associated
406 :     with many different features. Conversely, a feature can be associated with many key/value
407 :     pairs, even some that notionally contradict each other. For example, there can be evidence
408 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
409 :     <Fields>
410 :     <Field name="property-name" type="name-string">
411 :     <Notes>Name of this property.</Notes>
412 :     </Field>
413 :     <Field name="property-value" type="string">
414 :     <Notes>Value associated with this property. For each property
415 :     name, there must by a property record for all of its possible
416 :     values.</Notes>
417 :     </Field>
418 :     </Fields>
419 :     <Indexes>
420 :     <Index>
421 :     <Notes>This index enables the application to find all values for a specified property
422 :     name, or any given name/value pair.</Notes>
423 :     <IndexFields>
424 :     <IndexField name="property-name" order="ascending" />
425 :     <IndexField name="property-value" order="ascending" />
426 :     </IndexFields>
427 :     </Index>
428 :     </Indexes>
429 :     </Entity>
430 :     <Entity name="Diagram" keyType="name-string">
431 : parrello 1.55 <DisplayInfo theme="web" col="7" row="1" />
432 :     <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
433 : parrello 1.8 subsystem. A diagram is identified by a short name and contains a longer descriptive name.
434 :     The actual diagram shows which functional roles guide the reactions along with the inputs
435 : parrello 1.52 and outputs; the database, however, only indicates which roles belong to a particular
436 :     diagram's map.</Notes>
437 : parrello 1.8 <Fields>
438 :     <Field name="name" type="text">
439 :     <Notes>Descriptive name of this diagram.</Notes>
440 :     </Field>
441 :     </Fields>
442 :     </Entity>
443 : parrello 1.49 <Entity name="PDB" keyType="id-string">
444 : parrello 1.55 <DisplayInfo theme="web" col="3" row="5" />
445 : parrello 1.52 <Notes>A PDB is a protein data bank entry containing information that can be used
446 :     to determine the shape of the protein and the energies required to dock with it.
447 : parrello 1.55 The ID is the four-character name used on the PDB web site.</Notes>
448 : parrello 1.49 <Fields>
449 :     <Field name="docking-count" type="int">
450 :     <Notes>The number of ligands that have been docked against this PDB.</Notes>
451 :     </Field>
452 :     </Fields>
453 :     <Indexes>
454 :     <Index>
455 :     <IndexFields>
456 :     <IndexField name="docking-count" order="descending" />
457 :     <IndexField name="id" order="ascending" />
458 :     </IndexFields>
459 :     </Index>
460 :     </Indexes>
461 :     </Entity>
462 :     <Entity name="Ligand" keyType="id-string">
463 : parrello 1.55 <DisplayInfo theme="web" col="3" row="7" />
464 : parrello 1.49 <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
465 : parrello 1.52 The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>
466 : parrello 1.49 <Fields>
467 :     <Field name="name" type="long-string">
468 :     <Notes>Chemical name of this ligand.</Notes>
469 :     </Field>
470 :     </Fields>
471 :     </Entity>
472 : parrello 1.55 <Entity name="CellLocation" keyType="key-string">
473 :     <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
474 :     membrane, outside the cell, inside the cell, and so forth.</Notes>
475 :     </Entity>
476 :     <Entity name="Scenario" keyType="string">
477 :     <Notes>A scenario used to verify the validity of subsystem assignments. Each
478 :     scenario converrts input compounds to output compounds using reactions.
479 :     The scenario may use all of the reactions controlled by a subsystem or only
480 :     some, and may also incorporate additional reactions.</Notes>
481 :     </Entity>
482 : parrello 1.1 </Entities>
483 :     <Relationships>
484 : parrello 1.55 <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
485 :     <DisplayInfo theme="web" />
486 :     <Notes>This relationship connects a role to the reactions it catalyzes.
487 :     The purpose of a role is to create proteins that trigger certain
488 :     chemical reactions. A single reaction can be triggered by many roles,
489 :     and a role can trigger many reactions.</Notes>
490 :     </Relationship>
491 :     <Relationship name="ExcludesReaction" from="Scenario" to="Reaction" arity="MM">
492 :     <Notes>This relationship connects a scenario to reactions of the parent
493 :     subsystem that do not participate in it.</Notes>
494 :     </Relationship>
495 :     <Relationship name="IncludesReaction" from="Scenario" to="Reaction" arity="MM">
496 :     <Notes>This relationship connects a scenario to reactions that participate
497 :     in it but are not part of the parent subsystem.</Notes>
498 :     </Relationship>
499 :     <Relationship name="HasScenario" from="Subsystem" to="Scenario" arity="MM">
500 :     <Notes>This relationship connects a role to the scenarios used to
501 :     validate it.</Notes>
502 :     </Relationship>
503 :     <Relationship name="IsInputFor" from="Compound" to="Scenario" arity="MM">
504 :     <Notes>This relationship connects a scenario to its input compounds.</Notes>
505 :     </Relationship>
506 :     <Relationship name="IsOutputOf" from="Compound" to="Scenario" arity="MM">
507 :     <Notes>This relationship connects a scenario to its output compounds</Notes>
508 :     <Fields>
509 :     <Field name="auxiliary" type="boolean">
510 :     <Notes>TRUE if this is an auxiliary output compound, FALSE if it is a
511 :     main output compound.</Notes>
512 :     </Field>
513 :     </Fields>
514 :     </Relationship>
515 :     <Relationship name="IsOnDiagram" from="Scenario" to="Diagram" arity="MM">
516 :     <Notes>This relationship connects a scenario to related diagrams.</Notes>
517 :     </Relationship>
518 :     <Relationship name="IsPossiblePlaceFor" from="CellLocation" to="Feature" arity="MM">
519 :     <Notes>This relationship connects a feature with the various places in a cell that the feature
520 :     might be found. The confidence factor is included as intersection data.</Notes>
521 :     <Fields>
522 :     <Field name="confidence" type="float">
523 :     <Notes>Confidence that the protein will be found in this location, expressed as a
524 :     value from 0 to 10.</Notes>
525 :     </Field>
526 :     </Fields>
527 :     </Relationship>
528 : parrello 1.50 <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
529 :     <Notes>This relationship connects a feature to its CDD protein domains. The
530 :     match score is included as intersection data.</Notes>
531 :     <Fields>
532 :     <Field name="score" type="float">
533 :     <Notes>This is the match score between the feature and the CDD. A
534 :     lower score is a better match.</Notes>
535 :     </Field>
536 :     </Fields>
537 :     <FromIndex>
538 :     <IndexFields>
539 :     <IndexField name="score" order="ascending" />
540 :     </IndexFields>
541 :     </FromIndex>
542 :     </Relationship>
543 :     <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
544 :     <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
545 :     associated with a compound, and some are associated with two compounds, but not
546 :     all compounds have CAS IDs.</Notes>
547 :     </Relationship>
548 :     <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
549 :     <Notes>Relates a role to its EC number. Every EC number is associated with a
550 :     role, but not all roles have EC numbers.</Notes>
551 :     </Relationship>
552 :     <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
553 :     <Notes>Connects an alias to the feature it represents. Every alias connects
554 :     to at least 1 feature, and a feature connects to many aliases.</Notes>
555 :     </Relationship>
556 :     <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
557 :     <Notes>Connects a compound to its names. A compound generally has several
558 :     names</Notes>
559 :     <Fields>
560 :     <Field name="priority" type="int">
561 :     <Notes>Priority of this name, with 1 being the highest priority, 2
562 :     the next highest, and so forth.</Notes>
563 :     </Field>
564 :     </Fields>
565 :     <FromIndex>
566 :     <Notes>This index enables the application to view the names of a compound
567 :     in priority order.</Notes>
568 :     <IndexFields>
569 :     <IndexField name="priority" order="ascending" />
570 :     </IndexFields>
571 :     </FromIndex>
572 :     </Relationship>
573 : parrello 1.49 <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
574 : parrello 1.55 <DisplayInfo caption="Is Protein\nFor Feature" theme="web" />
575 : parrello 1.49 <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
576 :     <Fields>
577 :     <Field name="score" type="float">
578 :     <Notes>Similarity score for the comparison between the feature and
579 :     the PDB protein. A lower score indicates a better match.</Notes>
580 :     </Field>
581 :     <Field name="start-location" type="int">
582 :     <Notes>Starting location within the feature of the matching region.</Notes>
583 :     </Field>
584 :     <Field name="end-location" type="int">
585 :     <Notes>Ending location within the feature of the matching region.</Notes>
586 :     </Field>
587 :     </Fields>
588 :     <ToIndex>
589 :     <Notes>This index enables the application to view the PDBs of a
590 :     feature in order from the closest match to the furthest.</Notes>
591 :     <IndexFields>
592 :     <IndexField name="score" order="ascending" />
593 :     </IndexFields>
594 :     </ToIndex>
595 :     <FromIndex>
596 :     <Notes>This index enables the application to view the features of
597 :     a PDB in order from the closest match to the furthest.</Notes>
598 :     <IndexFields>
599 :     <IndexField name="score" order="ascending" />
600 :     </IndexFields>
601 :     </FromIndex>
602 :     </Relationship>
603 :     <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
604 : parrello 1.55 <DisplayInfo caption="Docks With" theme="web" />
605 :     <Notes>Indicates that a docking result exists between a PDB and a ligand. The
606 : parrello 1.49 docking result describes the energy required for the ligand to dock with
607 :     the protein described by the PDB. A lower energy indicates the ligand has a
608 :     good chance of disabling the protein. At the current time, only the best
609 :     docking results are kept.</Notes>
610 :     <Fields>
611 :     <Field name="reason" type="id-string">
612 :     <Notes>Indication of the reason for determining the docking result.
613 : parrello 1.52 A value of =Random= indicates the docking was attempted as a part
614 : parrello 1.49 of a random survey used to determine the docking characteristics of the
615 : parrello 1.52 PDB. A value of =Rich= indicates the docking was attempted because
616 : parrello 1.49 a low-energy docking result was predicted for the ligand with respect
617 :     to the PDB.</Notes>
618 :     </Field>
619 :     <Field name="tool" type="id-string">
620 :     <Notes>Name of the tool used to produce the docking result.</Notes>
621 :     </Field>
622 :     <Field name="total-energy" type="float">
623 :     <Notes>Total energy required for the ligand to dock with the PDB
624 :     protein, in kcal/mol. A negative value means energy is released.</Notes>
625 :     </Field>
626 : parrello 1.59 <Field name="vanderwaals-energy" type="float">
627 : parrello 1.49 <Notes>Docking energy in kcal/mol that results from the geometric fit
628 :     (Van der Waals force) between the PDB and the ligand.</Notes>
629 :     </Field>
630 :     <Field name="electrostatic-energy" type="float">
631 :     <Notes>Docking energy in kcal/mol that results from the movement of
632 : parrello 1.52 electrons (electrostatic force) between the PDB and the ligand.</Notes>
633 : parrello 1.49 </Field>
634 :     </Fields>
635 :     <FromIndex>
636 :     <Notes>This index enables the application to view a PDB's docking results from
637 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
638 :     <IndexFields>
639 :     <IndexField name="total-energy" order="ascending" />
640 :     </IndexFields>
641 :     </FromIndex>
642 :     <ToIndex>
643 :     <Notes>This index enables the application to view a ligand's docking results from
644 : parrello 1.52 the lowest energy (best docking) to highest energy (worst docking).</Notes>
645 : parrello 1.49 </ToIndex>
646 :     </Relationship>
647 : parrello 1.55 <Relationship name="IsAlsoFoundIn" from="Feature" to="ExternalDatabase" arity="MM">
648 :     <Notes>This relationship connects a feature to external databases that contain
649 :     essentially identical features. The name used in the external database is stored
650 :     in the relationship as intersection data.</Notes>
651 :     <Fields>
652 :     <Field name="alias" type="name-string">
653 :     <Notes>ID of the feature in the specified external database.</Notes>
654 :     </Field>
655 :     </Fields>
656 :     <Indexes>
657 :     <Index>
658 :     <Notes>This index allows direct access to features by external ID.</Notes>
659 :     <IndexFields>
660 :     <IndexField name="alias" order="ascending" />
661 :     </IndexFields>
662 :     </Index>
663 :     </Indexes>
664 :     </Relationship>
665 : parrello 1.50 <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
666 : parrello 1.27 <Notes>This relation connects a synonym group to the features that make it
667 :     up.</Notes>
668 :     </Relationship>
669 : parrello 1.24 <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
670 : parrello 1.55 <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
671 : parrello 1.24 <Notes>This relationship connects a genome to all of its features. This
672 :     relationship is redundant in a sense, because the genome ID is part
673 :     of the feature ID; however, it makes the creation of certain queries more
674 :     convenient because you can drag in filtering information for a feature's
675 :     genome.</Notes>
676 :     <Fields>
677 :     <Field name="type" type="key-string">
678 :     <Notes>Feature type (eg. peg, rna)</Notes>
679 :     </Field>
680 :     </Fields>
681 : parrello 1.38 <FromIndex>
682 : parrello 1.24 <Notes>This index enables the application to view the features of a
683 :     Genome sorted by type.</Notes>
684 :     <IndexFields>
685 :     <IndexField name="type" order="ascending" />
686 :     </IndexFields>
687 : parrello 1.38 </FromIndex>
688 : parrello 1.24 </Relationship>
689 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
690 : parrello 1.55 <DisplayInfo caption="Is Part Of" theme="nmpdr" />
691 : parrello 1.1 <Notes>This relationship connects a genome to the contigs that contain the actual genetic
692 :     information.</Notes>
693 :     </Relationship>
694 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
695 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
696 :     come from a single source or from a cooperation among multiple sources.</Notes>
697 :     </Relationship>
698 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
699 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
700 :     contig into sequences, we get a performance boost from only needing to keep small portions
701 :     of a contig in memory at any one time. This relationship connects the contig to its
702 :     constituent sequences.</Notes>
703 :     <Fields>
704 :     <Field name="len" type="int">
705 : parrello 1.15 <Notes>Length of the sequence.</Notes>
706 :     </Field>
707 : parrello 1.1 <Field name="start-position" type="int">
708 : parrello 1.15 <Notes>Index (1-based) of the point in the contig where this
709 :     sequence starts.</Notes>
710 :     </Field>
711 : parrello 1.1 </Fields>
712 :     <FromIndex>
713 :     <Notes>This index enables the application to find all of the sequences in
714 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
715 : parrello 1.1 <IndexFields>
716 :     <IndexField name="start-position" order="ascending" />
717 :     <IndexField name="len" order="ascending" />
718 :     </IndexFields>
719 :     </FromIndex>
720 :     </Relationship>
721 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
722 : parrello 1.55 <DisplayInfo caption="Targets" theme="seed" />
723 : parrello 1.1 <Notes>This relationship connects a feature to its annotations.</Notes>
724 :     </Relationship>
725 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
726 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
727 :     </Relationship>
728 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
729 : parrello 1.55 <DisplayInfo caption="\nParticipates\nIn" theme="seed" />
730 : parrello 1.1 <Notes>This relationship connects subsystems to the genomes that use
731 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
732 : parrello 1.52 connected to the genome features through the *SSCell* object.</Notes>
733 : parrello 1.15 <Fields>
734 :     <Field name="variant-code" type="key-string">
735 : parrello 1.20 <Notes>Code indicating the subsystem variant to which this
736 : parrello 1.15 genome belongs. Each subsystem can have multiple variants. A variant
737 : parrello 1.52 code of =-1= indicates that the genome does not have a functional
738 :     variant of the subsystem. A variant code of =0= indicates that
739 : parrello 1.20 the genome's participation is considered iffy.</Notes>
740 : parrello 1.15 </Field>
741 :     </Fields>
742 :     <ToIndex>
743 :     <Notes>This index enables the application to find all of the genomes using
744 :     a subsystem in order by variant code, which is how we wish to display them
745 :     in the spreadsheets.</Notes>
746 :     <IndexFields>
747 :     <IndexField name="variant-code" order="ascending" />
748 :     </IndexFields>
749 :     </ToIndex>
750 : parrello 1.1 </Relationship>
751 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
752 : parrello 1.55 <DisplayInfo caption="Uses" theme="seed" />
753 :     <Notes>This relationship connects roles to the subsystems that implement them.</Notes>
754 : parrello 1.15 <Fields>
755 : parrello 1.50 <Field name="abbr" type="name-string">
756 :     <Notes>Abbreviated name for the role, generally non-unique, but useful
757 :     in column headings for HTML tables.</Notes>
758 :     </Field>
759 : parrello 1.15 <Field name="column-number" type="int">
760 :     <Notes>Column number for this role in the specified subsystem's
761 :     spreadsheet.</Notes>
762 :     </Field>
763 : parrello 1.55 <Field name="auxiliary" type="boolean">
764 :     <Notes>If TRUE, then this role is ancillary to the purpose of the subsystem.
765 :     If FALSE, it is essential to its metabolic pathway.</Notes>
766 :     </Field>
767 : parrello 1.57 <Field name="hope-reaction-note" type="text">
768 : parrello 1.55 <Notes>A description of the status of a role in relation to the
769 :     reactions it produces as determined by the scenarios. If present,
770 :     will indicate if the role has been determined to be auxiliary,
771 :     if it has been examined to verify an automatic assignment, and so
772 :     forth.</Notes>
773 :     </Field>
774 : parrello 1.15 </Fields>
775 :     <ToIndex>
776 :     <Notes>This index enables the application to see the subsystem roles
777 :     in column order. The ordering of the roles is usually significant,
778 :     so it is important to preserve it.</Notes>
779 :     <IndexFields>
780 :     <IndexField name="column-number" order="ascending" />
781 :     </IndexFields>
782 :     </ToIndex>
783 : parrello 1.1 </Relationship>
784 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
785 : parrello 1.55 <DisplayInfo caption="Is Row Of" theme="seed" />
786 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
787 :     genome for the spreadsheet column.</Notes>
788 :     </Relationship>
789 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
790 : parrello 1.55 <DisplayInfo caption="Is In\nColumn\nFor" theme="seed" />
791 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
792 :     role for the spreadsheet row.</Notes>
793 :     </Relationship>
794 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
795 : parrello 1.55 <DisplayInfo caption="Is\nContained\nIn" theme="seed" />
796 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
797 :     features assigned to it.</Notes>
798 : parrello 1.15 <Fields>
799 :     <Field name="cluster-number" type="int">
800 :     <Notes>ID of this feature's cluster. Clusters represent families of
801 :     related proteins participating in a subsystem.</Notes>
802 :     </Field>
803 :     </Fields>
804 :     </Relationship>
805 :     <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
806 : parrello 1.55 <DisplayInfo caption="Involves" theme="web" />
807 : parrello 1.15 <Notes>This relationship connects a reaction to the compounds that participate
808 :     in it.</Notes>
809 :     <Fields>
810 :     <Field name="product" type="boolean">
811 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
812 :     it is a substrate. When a reaction is written on paper in
813 :     chemical notation, the substrates are left of the arrow and the
814 :     products are to the right. Sorting on this field will cause
815 :     the substrates to appear first, followed by the products. If the
816 :     reaction is reversible, then the notion of substrates and products
817 :     is not at intuitive; however, a value here of FALSE still puts the
818 :     compound left of the arrow and a value of TRUE still puts it to the
819 :     right.</Notes>
820 :     </Field>
821 : parrello 1.19 <Field name="stoichiometry" type="key-string">
822 : parrello 1.15 <Notes>Number of molecules of the compound that participate in a
823 :     single instance of the reaction. For example, if a reaction
824 : parrello 1.19 produces two water molecules, the stoichiometry of water for the
825 : parrello 1.15 reaction would be two. When a reaction is written on paper in
826 : parrello 1.19 chemical notation, the stoichiometry is the number next to the
827 : parrello 1.15 chemical formula of the compound.</Notes>
828 :     </Field>
829 :     <Field name="main" type="boolean">
830 :     <Notes>TRUE if this compound is one of the main participants in
831 :     the reaction, else FALSE. It is permissible for none of the
832 :     compounds in the reaction to be considered main, in which
833 :     case this value would be FALSE for all of the relevant
834 :     compounds.</Notes>
835 :     </Field>
836 :     <Field name="loc" type="key-string">
837 :     <Notes>An optional character string that indicates the relative
838 :     position of this compound in the reaction's chemical formula. The
839 :     location affects the way the compounds present as we cross the
840 :     relationship from the reaction side. The product/substrate flag
841 :     comes first, then the value of this field, then the main flag.
842 :     The default value is an empty string; however, the empty string
843 :     sorts first, so if this field is used, it should probably be
844 :     used for every compound in the reaction.</Notes>
845 :     </Field>
846 : parrello 1.19 <Field name="discriminator" type="int">
847 :     <Notes>A unique ID for this record. The discriminator does not
848 :     provide any useful data, but it prevents identical records from
849 :     being collapsed by the SELECT DISTINCT command used by ERDB to
850 :     retrieve data.</Notes>
851 :     </Field>
852 : parrello 1.15 </Fields>
853 :     <ToIndex>
854 :     <Notes>This index presents the compounds in the reaction in the
855 :     order they should be displayed when writing it in chemical notation.
856 :     All the substrates appear before all the products, and within that
857 :     ordering, the main compounds appear first.</Notes>
858 : parrello 1.19 <IndexFields>
859 :     <IndexField name="product" order="ascending" />
860 :     <IndexField name="loc" order="ascending" />
861 :     <IndexField name="main" order="descending" />
862 :     </IndexFields>
863 : parrello 1.15 </ToIndex>
864 : parrello 1.1 </Relationship>
865 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
866 : parrello 1.55 <DisplayInfo caption="Is\nLocation\nOf" theme="nmpdr" />
867 : parrello 1.1 <Notes>This relationship connects a feature to the contig segments that work together
868 :     to effect it. The segments are numbered sequentially starting from 1. The database is
869 :     required to place an upper limit on the length of each segment. If a segment is longer
870 : parrello 1.52 than the maximum, it can be broken into smaller bits. The upper limit enables applications
871 :     to locate all features that contain a specific residue. For example, if the upper limit
872 :     is 100 and we are looking for a feature that contains residue 234 of contig *ABC*, we
873 :     can look for features with a begin point between 135 and 333. The results can then be
874 :     filtered by direction and length of the segment.</Notes>
875 : parrello 1.1 <Fields>
876 :     <Field name="locN" type="int">
877 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
878 :     </Field>
879 : parrello 1.1 <Field name="beg" type="int">
880 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
881 :     belongs to the segment.</Notes>
882 :     </Field>
883 : parrello 1.1 <Field name="len" type="int">
884 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
885 :     a specific point between residues. This is the point before the residue if the direction
886 :     is forward and the point after the residue if the direction is backward.</Notes>
887 :     </Field>
888 : parrello 1.1 <Field name="dir" type="char">
889 : parrello 1.52 <Notes>Direction of the segment: =+= if it is forward and
890 :     =-= if it is backward.</Notes>
891 : parrello 1.8 </Field>
892 : parrello 1.1 </Fields>
893 : parrello 1.45 <FromIndex>
894 : parrello 1.1 <Notes>This index allows the application to find all the segments of a feature in
895 : parrello 1.8 the proper order.</Notes>
896 : parrello 1.1 <IndexFields>
897 :     <IndexField name="locN" order="ascending" />
898 :     </IndexFields>
899 :     </FromIndex>
900 :     <ToIndex>
901 :     <Notes>This index is the one used by applications to find all the feature
902 :     segments that contain a specific residue.</Notes>
903 :     <IndexFields>
904 :     <IndexField name="beg" order="ascending" />
905 :     </IndexFields>
906 :     </ToIndex>
907 :     </Relationship>
908 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
909 :     <Notes>This relationship connects a feature to its known property values.
910 :     The relationship contains text data that indicates the paper or organization
911 :     that discovered evidence that the feature possesses the property. So, for
912 :     example, if two papers presented evidence that a feature is essential,
913 :     there would be an instance of this relationship for both.</Notes>
914 :     <Fields>
915 :     <Field name="evidence" type="text">
916 :     <Notes>URL or citation of the paper or
917 :     institution that reported evidence of the relevant feature possessing
918 :     the specified property value.</Notes>
919 :     </Field>
920 :     </Fields>
921 :     </Relationship>
922 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
923 : parrello 1.55 <DisplayInfo caption="Shows" theme="web" />
924 : parrello 1.8 <Notes>This relationship connects a role to the diagrams on which it
925 :     appears. A role frequently identifies an enzyme, and can appear in many
926 :     diagrams. A diagram generally contains many different roles.</Notes>
927 :     </Relationship>
928 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
929 : parrello 1.55 <DisplayInfo caption="Is Container Of" theme="seed" />
930 : parrello 1.8 <Notes>This relationship connects a subsystem to the spreadsheet cells
931 :     used to analyze and display it. The cells themselves can be thought of
932 :     as a grid with Roles on one axis and Genomes on the other. The
933 :     various features of the subsystem are then assigned to the cells.</Notes>
934 :     </Relationship>
935 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
936 :     <Notes>This relationship identifies the users trusted by each
937 :     particular user. When viewing functional assignments, the
938 :     assignment displayed is the most recent one by a user trusted
939 :     by the current user. The current user implicitly trusts himself.
940 :     If no trusted users are specified in the database, the user
941 : parrello 1.52 also implicitly trusts the user =FIG=.</Notes>
942 : parrello 1.8 </Relationship>
943 : parrello 1.15 <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
944 :     <Notes>This relationship connects a role subset to the roles that it covers.
945 :     A subset is, essentially, a named group of roles belonging to a specific
946 :     subsystem, and this relationship effects that. Note that will a role
947 :     may belong to many subsystems, a subset belongs to only one subsystem,
948 :     and all roles in the subset must have that subsystem in common.</Notes>
949 :     </Relationship>
950 :     <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
951 :     <Notes>This relationship connects a subset to the genomes that it covers.
952 :     A subset is, essentially, a named group of genomes participating in a specific
953 :     subsystem, and this relationship effects that. Note that while a genome
954 :     may belong to many subsystems, a subset belongs to only one subsystem,
955 :     and all genomes in the subset must have that subsystem in common.</Notes>
956 :     </Relationship>
957 :     <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
958 :     <Notes>This relationship connects a subsystem to its constituent
959 :     role subsets. Note that some roles in a subsystem may not belong to a
960 :     subset, so the relationship between roles and subsystems cannot be
961 :     derived from the relationships going through the subset.</Notes>
962 :     </Relationship>
963 :     <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
964 :     <Notes>This relationship connects a subsystem to its constituent
965 :     genome subsets. Note that some genomes in a subsystem may not belong to a
966 :     subset, so the relationship between genomes and subsystems cannot be
967 :     derived from the relationships going through the subset.</Notes>
968 :     </Relationship>
969 : parrello 1.39 <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
970 :     <Notes>This relationship connects a feature to the subsystems in which it
971 :     participates. This is technically redundant information, but it is used
972 : parrello 1.52 so often that it gets its own table for performance reasons.</Notes>
973 : parrello 1.40 <Fields>
974 :     <Field name="genome" type="name-string">
975 :     <Notes>ID of the genome containing the feature</Notes>
976 :     </Field>
977 :     <Field name="type" type="key-string">
978 :     <Notes>Feature type (eg. peg, rna)</Notes>
979 :     </Field>
980 :     </Fields>
981 :     <ToIndex>
982 :     <Notes>This index enables the application to view the features of a
983 :     subsystem sorted by genome and feature type.</Notes>
984 :     <IndexFields>
985 :     <IndexField name="genome" order="ascending" />
986 :     <IndexField name="type" order="ascending" />
987 :     </IndexFields>
988 :     </ToIndex>
989 : parrello 1.39 </Relationship>
990 : parrello 1.1 </Relationships>
991 : parrello 1.56 <Shapes>
992 :     <Shape type="oval" name="Pins">
993 :     <DisplayInfo theme="nmpdr" col="1" row="4.5" fixed="1" />
994 :     <Notes>The Pin Server provides information about functional couplings between features.</Notes>
995 :     </Shape>
996 :     <Shape type="oval" name="Sims">
997 :     <DisplayInfo theme="nmpdr" col="1.5" row="5" fixed="1" />
998 :     <Notes>The Similarity Server contains a high-performance custom database of similarities between features.</Notes>
999 :     </Shape>
1000 :     <Shape type="oval" name="BBHs">
1001 :     <DisplayInfo theme="nmpdr" col="2" row="5.5" fixed="1" />
1002 :     <Notes>For each feature, the BBH Server has that feature's bidirectional best hits in other genomes.</Notes>
1003 :     </Shape>
1004 :     <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1005 :     <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1006 :     </Shape>
1007 :     </Shapes>
1008 : parrello 1.1 </Database>

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