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1 : parrello 1.1 <Database>
2 :     <Title>Sprout Genome and Subsystem Database</Title>
3 : parrello 1.55 <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.
4 : parrello 1.51 The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external
5 :     servers available to the Sprout software. The Sprout database is reloaded approximately once
6 :     per month. There is significant redundancy in the Sprout database because it has been
7 :     optimized for searching. In particular, the Feature table contains an extra copy of the
8 :     feature's functional role and a list of possible search terms.</Notes>
9 : parrello 1.1 <Entities>
10 : parrello 1.61 <Entity name="Genome" keyType="float">
11 : parrello 1.55 <DisplayInfo theme="nmpdr" col="3" row="1" />
12 :     <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
13 : parrello 1.1 <Fields>
14 : parrello 1.60 <Field name="genus" type="string">
15 : parrello 1.1 <Notes>Genus of the relevant organism.</Notes>
16 :     </Field>
17 : parrello 1.60 <Field name="species" type="string">
18 : parrello 1.8 <Notes>Species of the relevant organism.</Notes>
19 :     </Field>
20 : parrello 1.60 <Field name="unique-characterization" type="string" default="">
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 1.60 <Field name="scientific-name" type="string">
26 :     <Notes>Scientific name of this genome, usually consisting of the genus,
27 :     species, and unique characterization.</Notes>
28 :     </Field>
29 :     <Field name="version" type="string">
30 :     <Notes>Version string for this genome, generally consisting of the genome ID followed
31 : parrello 1.48 by a period and a string of digits.</Notes>
32 :     </Field>
33 : parrello 1.15 <Field name="complete" type="boolean">
34 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
35 :     </Field>
36 : parrello 1.48 <Field name="dna-size" type="counter">
37 :     <Notes>number of base pairs in the genome</Notes>
38 :     </Field>
39 : parrello 1.8 <Field name="taxonomy" type="text">
40 : parrello 1.60 <Notes>The taxonomy string contains the full taxonomy of the organism, with individual elements
41 : parrello 1.8 separated by semi-colons (and optional white space), starting with the domain and ending with
42 :     the disambiguated genus and species (which is the organism's scientific name plus an
43 :     identifying string).</Notes>
44 :     </Field>
45 : parrello 1.60 <Field name="primary-group" type="string">
46 : parrello 1.37 <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
47 : parrello 1.60 per organism (either based on the organism name or a default value for supporting
48 :     genomes). In general, more data is kept on organisms in NMPDR groups than on supporting
49 :     organisms.</Notes>
50 : parrello 1.52 </Field>
51 :     <Field name="contigs" type="int">
52 :     <Notes>Number of contigs for this organism.</Notes>
53 :     </Field>
54 :     <Field name="pegs" type="int">
55 : parrello 1.60 <Notes>Number of protein encoding genes for this organism</Notes>
56 : parrello 1.52 </Field>
57 :     <Field name="rnas" type="int">
58 :     <Notes>Number of RNA features found for this organism.</Notes>
59 : parrello 1.37 </Field>
60 : parrello 1.60 <Field name="endospore" type="semi-boolean">
61 :     <Notes>Y/N/? flag indicating whether or not this organism produces endospores.</Notes>
62 :     </Field>
63 :     <Field name="gc-content" type="float">
64 :     <Notes>Percentage of the genome that consists of G and C base pairs.</Notes>
65 :     </Field>
66 :     <Field name="habitat" type="string">
67 :     <Notes>Preferred habitat of organism.</Notes>
68 :     </Field>
69 :     <Field name="gram-stain" type="semi-boolean">
70 :     <Notes>Gram stain behaviour of organism-- positive, negative, or unknown.</Notes>
71 :     </Field>
72 :     <Field name="motility" type="semi-boolean">
73 :     <Notes>Y/N/? flag indicating whether or not this organism can move under
74 :     its own power.</Notes>
75 :     </Field>
76 :     <Field name="oxygen" type="string">
77 :     <Notes>Indication of this organism's behavior relating to environmental oxygen.</Notes>
78 :     </Field>
79 :     <Field name="temperature-min" type="float">
80 :     <Notes>Minimum optimal temperature for this organism, in degrees Celsius.</Notes>
81 :     </Field>
82 :     <Field name="temperature-max" type="float">
83 :     <Notes>Maximum optimal temperature for this organism, in degrees Celsius.</Notes>
84 :     </Field>
85 :     <Field name="pathogenic" type="semi-boolean">
86 :     <Notes>Y/N/? flag indicating whether or not this organism is pathogenic.</Notes>
87 :     </Field>
88 :     <Field name="salinity" type="string">
89 :     <Notes>Indication of this organism's behavior relating to environmental
90 :     salinity.</Notes>
91 :     </Field>
92 :     <Field name="optimal-temperature-range" type="string">
93 :     <Notes>Indication of this organism's behavior relating to environmental
94 :     temperature.</Notes>
95 :     </Field>
96 : parrello 1.1 </Fields>
97 :     <Indexes>
98 : parrello 1.45 <Index>
99 : parrello 1.1 <Notes>This index allows the applications to find all genomes associated with
100 : parrello 1.37 a specific primary (NMPDR) group.</Notes>
101 :     <IndexFields>
102 :     <IndexField name="primary-group" order="ascending" />
103 :     <IndexField name="genus" order="ascending" />
104 :     <IndexField name="species" order="ascending" />
105 :     <IndexField name="unique-characterization" order="ascending" />
106 :     </IndexFields>
107 :     </Index>
108 : parrello 1.45 <Index>
109 : parrello 1.60 <Notes>This index allows the applications to retrieve all genomes by genus and species
110 :     groupings.</Notes>
111 : parrello 1.1 <IndexFields>
112 :     <IndexField name="genus" order="ascending" />
113 :     <IndexField name="species" order="ascending" />
114 :     <IndexField name="unique-characterization" order="ascending" />
115 :     </IndexFields>
116 :     </Index>
117 : parrello 1.60 <Index>
118 :     <Notes>This index allows the applications to search for genome by scientific
119 :     name.</Notes>
120 :     <IndexFields>
121 :     <IndexField name="scientific-name" order="ascending" />
122 :     </IndexFields>
123 :     </Index>
124 : parrello 1.1 </Indexes>
125 :     </Entity>
126 : parrello 1.60 <Entity name="ProteinFamily" keyType="string">
127 :     <Notes>A protein family represents a group of proteins with related
128 :     functions. Some protein families are downloaded from the PFAM database
129 :     and some are FIGfams. The protein family keys all begin with the letters
130 :     PF and the FIGfams with the letters FIG.</Notes>
131 :     <Fields>
132 :     <Field name="common-name" type="string" relation="ProteinFamilyName">
133 :     <Notes>Ontological name for the protein family. Not all families
134 :     have ontological names.</Notes>
135 :     </Field>
136 :     </Fields>
137 :     <Indexes>
138 :     <Index>
139 :     <Notes>This index allows the user to locate protein families
140 :     by name.</Notes>
141 :     <IndexFields>
142 :     <IndexField name="common-name" order="ascending" />
143 :     </IndexFields>
144 :     </Index>
145 :     </Indexes>
146 :     </Entity>
147 :     <Entity name="Host" keyType="string">
148 :     <Notes>A host is a particular type of creature in which an organism has
149 :     pathogenic behavior. Hosts can be specific (Human) or general
150 :     (Animal).</Notes>
151 :     </Entity>
152 :     <Entity name="CDD" keyType="string">
153 : parrello 1.50 <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
154 : parrello 1.52 on a feature's protein. The ID is six-digit string assigned by the public
155 : parrello 1.58 Conserved Domain Database. A CDD can occur on multiple features and a feature
156 :     generally has multiple CDDs.</Notes>
157 : parrello 1.50 </Entity>
158 : parrello 1.60 <Entity name="Source" keyType="string">
159 : parrello 1.55 <Notes>A source describes a place from which genome data was taken. This can be an organization
160 : parrello 1.1 or a paper citation.</Notes>
161 :     <Fields>
162 :     <Field name="URL" type="string" relation="SourceURL">
163 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
164 :     </Field>
165 : parrello 1.1 <Field name="description" type="text">
166 : parrello 1.52 <Notes>Description of the source. The description can be a street address or a citation.</Notes>
167 : parrello 1.8 </Field>
168 : parrello 1.1 </Fields>
169 :     </Entity>
170 : parrello 1.60 <Entity name="Contig" keyType="string">
171 : parrello 1.55 <DisplayInfo theme="nmpdr" col="1" row="1" />
172 :     <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
173 : parrello 1.1 genome ID followed by a name that identifies which contig this is for the parent genome. As
174 :     is the case with all keys in this database, the individual components are separated by a
175 : parrello 1.52 period. A contig can contain over a million residues. For performance reasons, therefore,
176 : parrello 1.55 the contig is split into multiple pieces called sequences. The sequences
177 : parrello 1.1 contain the characters that represent the residues as well as data on the quality of
178 :     the residue identification.</Notes>
179 : parrello 1.61 <Fields>
180 :     <Field name="length" type="counter">
181 :     <Notes>Number of base pairs in this contig.</Notes>
182 :     </Field>
183 :     </Fields>
184 : parrello 1.1 </Entity>
185 : parrello 1.60 <Entity name="Sequence" keyType="string">
186 : parrello 1.55 <Notes>A sequence is a continuous piece of a contig. Contigs are split into
187 : parrello 1.1 sequences so that we don't have to have the entire contig in memory when we are
188 :     manipulating it. The key of the sequence is the contig ID followed by the index of
189 :     the begin point.</Notes>
190 :     <Fields>
191 : parrello 1.60 <Field name="sequence" type="dna">
192 : parrello 1.52 <Notes>String consisting of the residues (base pairs). Each residue is described by a single
193 : parrello 1.8 character in the string.</Notes>
194 :     </Field>
195 : parrello 1.1 <Field name="quality-vector" type="text">
196 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
197 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
198 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
199 : parrello 1.52 10^-30. A higher quality number indicates a better chance of a correct match. It is
200 :     possible that the quality data is not known for a sequence. If that is the case, the
201 : parrello 1.60 quality vector will contain the string "unknown".</Notes>
202 : parrello 1.8 </Field>
203 : parrello 1.1 </Fields>
204 :     </Entity>
205 : parrello 1.60 <Entity name="Keyword" keyType="string">
206 : parrello 1.55 <Notes>A keyword is a word that can be used to search the feature table. This entity
207 :     contains the keyword's stem, its phonetic form, and the number of features that
208 :     can be found by searching for the word.</Notes>
209 :     <Fields>
210 : parrello 1.60 <Field name="stem" type="string">
211 : parrello 1.55 <Notes>The stem of a keyword is a normalized form that is independent of parts
212 :     of speech. The actual keywords stored in the database search index are stems.</Notes>
213 :     </Field>
214 : parrello 1.60 <Field name="phonex" type="string">
215 : parrello 1.55 <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
216 :     word stem. This can be used to find alternative spellings if an matching word is not
217 :     present.</Notes>
218 :     </Field>
219 : parrello 1.54 </Fields>
220 : parrello 1.55 <Indexes>
221 :     <Index>
222 :     <Notes>This index allows the user to find words by stem.</Notes>
223 :     <IndexFields>
224 :     <IndexField name="stem" order="ascending" />
225 :     </IndexFields>
226 :     </Index>
227 :     <Index>
228 :     <Notes>This index allows the user to find words by phonex.</Notes>
229 :     <IndexFields>
230 :     <IndexField name="phonex" order="ascending" />
231 :     </IndexFields>
232 :     </Index>
233 :     </Indexes>
234 :     </Entity>
235 : parrello 1.60 <Entity name="ExternalDatabase" keyType="string">
236 : parrello 1.55 <Notes>An external database identifies a biological database surveyed by PIR International
237 :     as part of an effort to determine which features are essentially identical between bioinformatics
238 :     organizations. Each feature in the database will have zero or more corresponding IDs that are
239 :     captured from the PIR data. Each corresponding ID is represented in a relationship between an external
240 :     database and the feature itself.</Notes>
241 : parrello 1.54 </Entity>
242 : parrello 1.60 <Entity name="Feature" keyType="string">
243 : parrello 1.55 <DisplayInfo theme="nmpdr" col="3" row="3" />
244 :     <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
245 : parrello 1.1 may be spread across multiple contigs of a genome, but never across more than
246 :     one genome. Features can be assigned to roles via spreadsheet cells,
247 : parrello 1.55 and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
248 : parrello 1.1 <Fields>
249 : parrello 1.60 <Field name="feature-type" type="string">
250 : parrello 1.52 <Notes>Code indicating the type of this feature. Among the codes currently
251 : parrello 1.60 supported are "peg" for a protein encoding gene, "bs" for a
252 :     binding site, "opr" for an operon, and so forth.</Notes>
253 : parrello 1.8 </Field>
254 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
255 : parrello 1.60 <Notes>(optional) A translation of this feature's residues into
256 :     protein character codes, formed by concatenating the pieces
257 :     of the feature together. Only protein encoding genes have
258 :     translations.</Notes>
259 : parrello 1.8 </Field>
260 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
261 : parrello 1.52 <Notes>Upstream sequence for the feature. This includes residues preceding the feature as
262 :     well as some of the feature's initial residues.</Notes>
263 : parrello 1.8 </Field>
264 : parrello 1.42 <Field name="assignment" type="text">
265 :     <Notes>Default functional assignment for this feature.</Notes>
266 :     </Field>
267 : parrello 1.60 <Field name="assignment-maker" type="string">
268 : parrello 1.48 <Notes>name of the user who made the functional assignment</Notes>
269 :     </Field>
270 :     <Field name="assignment-quality" type="char">
271 :     <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
272 :     (indicating experimental)</Notes>
273 :     </Field>
274 : parrello 1.41 <Field name="keywords" type="text" searchable="1">
275 :     <Notes>This is a list of search keywords for the feature. It includes the
276 :     functional assignment, subsystem roles, and special properties.</Notes>
277 : parrello 1.36 </Field>
278 : parrello 1.8 <Field name="link" type="text" relation="FeatureLink">
279 : parrello 1.52 <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
280 : parrello 1.8 links are to other websites that have useful about the gene that the feature represents, and
281 : parrello 1.60 are coded as raw HTML.</Notes>
282 : parrello 1.8 </Field>
283 : parrello 1.60 <Field name="essential" type="link" relation="FeatureEssential" special="property_search">
284 : parrello 1.45 <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
285 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
286 :     or potential (potential-essential), hyperlinked to the document from which the
287 :     essentiality was curated. If a feature is not essential, this field will have no
288 :     values; otherwise, it may have multiple values.</Notes>
289 :     </Field>
290 : parrello 1.60 <Field name="virulent" type="link" relation="FeatureVirulent" special="property_search">
291 : parrello 1.45 <Notes>A value indicating the virulence of the feature, coded as HTML. In most
292 :     cases, this will be a phrase or SA number hyperlinked to the document from which
293 :     the virulence information was curated. If the feature is not virulent, this field
294 :     will have no values; otherwise, it may have multiple values.</Notes>
295 :     </Field>
296 : parrello 1.60 <Field name="iedb" type="link" relation="FeatureIEDB" special="property_search">
297 : parrello 1.45 <Notes>A value indicating whether or not the feature can be found in the
298 :     Immune Epitope Database. If the feature has not been matched to that database,
299 :     this field will have no values. Otherwise, it will have an epitope name and/or
300 :     sequence, hyperlinked to the database.</Notes>
301 :     </Field>
302 : parrello 1.50 <Field name="location-string" type="text">
303 :     <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
304 :     strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
305 : parrello 1.60 we have to painstakingly paste together the IsLocatedIn records, which are themselves
306 : parrello 1.52 designed to help look for features in a particular region rather than to find the location
307 :     of a feature.</Notes>
308 : parrello 1.50 </Field>
309 : parrello 1.60 <Field name="signal-peptide" type="string">
310 : parrello 1.55 <Notes>The signal peptide location for this feature. This is expressed as start and end
311 :     numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
312 :     peptide at the beginning of the feature's protein and extending through 22 amino acid
313 :     positions. An empty string means no signal peptide is present.</Notes>
314 :     </Field>
315 :     <Field name="transmembrane-map" type="text">
316 :     <Notes>A map indicating which sections of a protein will be embedded in a membrane.
317 :     This is expressed as a comma-separated list of as start and end numbers with hyphens
318 :     for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
319 :     sections of the protein that become embedded in a membrane: the 10th through 12th
320 :     amino acids, and the 40th through the 60th. An empty string means no
321 :     transmembrane regions are known.</Notes>
322 :     </Field>
323 :     <Field name="similar-to-human" type="boolean">
324 :     <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
325 :     else FALSE</Notes>
326 :     </Field>
327 :     <Field name="isoelectric-point" type="float">
328 :     <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
329 :     If the pH of the medium is lower than this value, the protein will have a net
330 :     positive charge. If the pH of the medium is higher, then the protein will have a
331 :     net negative charge.</Notes>
332 :     </Field>
333 :     <Field name="molecular-weight" type="float">
334 :     <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
335 :     indicates that no protein is created.</Notes>
336 :     </Field>
337 :     <Field name="sequence-length" type="counter">
338 :     <Notes>Number of base pairs in this feature.</Notes>
339 :     </Field>
340 :     <Field name="locked" type="boolean">
341 :     <Notes>TRUE if a feature's assignment is locked. A locked feature's functional
342 :     role cannot be changed by automated programs.</Notes>
343 :     </Field>
344 :     <Field name="in-genbank" type="boolean">
345 :     <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
346 :     </Field>
347 : parrello 1.60 <Field name="conserved-neighbors" type="int">
348 :     <Notes>number of coupled features</Notes>
349 :     </Field>
350 :     <Field name="transmembrane-domain-count" type="int">
351 :     <Notes>number of sections in the feature's protein that
352 :     become embedded in the cell membrane</Notes>
353 :     </Field>
354 :     <Field name="ec" type="string" relation="FeatureEC">
355 :     <Notes>An EC number associated with this feature.</Notes>
356 :     </Field>
357 : parrello 1.1 </Fields>
358 : parrello 1.60 <Indexes>
359 :     <Index>
360 :     <Notes>This index supports looking up features by EC
361 :     number.</Notes>
362 :     <IndexFields>
363 :     <IndexField name="ec" order="ascending" />
364 :     </IndexFields>
365 :     </Index>
366 :     </Indexes>
367 : parrello 1.1 </Entity>
368 : parrello 1.60 <Entity name="FeatureAlias" keyType="string">
369 : parrello 1.50 <Notes>Alternative names for features. A feature can have many aliases. In general,
370 : parrello 1.52 each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
371 :     </Entity>
372 : parrello 1.60 <Entity name="SproutUser" keyType="string">
373 : parrello 1.55 <Notes>A user is a person who can make annotations and view data in the database. The
374 : parrello 1.52 user object is keyed on the user's login name.</Notes>
375 :     <Fields>
376 :     <Field name="description" type="string">
377 :     <Notes>Full name or description of this user.</Notes>
378 :     </Field>
379 :     </Fields>
380 : parrello 1.50 </Entity>
381 : parrello 1.60 <Entity name="SynonymGroup" keyType="string">
382 : parrello 1.55 <Notes>A synonym group represents a group of features. Features that represent substantially
383 : parrello 1.52 identical proteins or DNA sequences are mapped to the same synonym group, and this information is
384 :     used to expand similarities.</Notes>
385 : parrello 1.27 </Entity>
386 : parrello 1.1 <Entity name="Role" keyType="string">
387 : parrello 1.55 <DisplayInfo theme="web" col="7" row="3" />
388 :     <Notes>A role describes a biological function that may be fulfilled by a feature.
389 : parrello 1.1 One of the main goals of the database is to record the roles of the various features.</Notes>
390 : parrello 1.50 </Entity>
391 :     <Entity name="RoleEC" keyType="string">
392 :     <Notes>EC code for a role.</Notes>
393 : parrello 1.1 </Entity>
394 : parrello 1.60 <Entity name="Annotation" keyType="string">
395 : parrello 1.55 <DisplayInfo theme="seed" col="1" row="3" />
396 :     <Notes>An annotation contains supplementary information about a feature. The most
397 : parrello 1.60 important type of annotation is the assignment of a functional role; however,
398 : parrello 1.52 other types of annotations are also possible.</Notes>
399 : parrello 1.8 <Fields>
400 :     <Field name="time" type="date">
401 :     <Notes>Date and time of the annotation.</Notes>
402 :     </Field>
403 :     <Field name="annotation" type="text">
404 :     <Notes>Text of the annotation.</Notes>
405 :     </Field>
406 : parrello 1.1 </Fields>
407 : parrello 1.26 <Indexes>
408 :     <Index>
409 :     <Notes>This index allows the user to find recent annotations.</Notes>
410 :     <IndexFields>
411 :     <IndexField name="time" order="descending" />
412 :     </IndexFields>
413 :     </Index>
414 :     </Indexes>
415 : parrello 1.1 </Entity>
416 : parrello 1.60 <Entity name="Reaction" keyType="string">
417 : parrello 1.55 <DisplayInfo theme="web" col="7" row="5" />
418 :     <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
419 : parrello 1.15 is generally a small number preceded by a letter.</Notes>
420 :     <Fields>
421 :     <Field name="url" type="string" relation="ReactionURL">
422 :     <Notes>HTML string containing a link to a web location that describes the
423 :     reaction. This field is optional.</Notes>
424 :     </Field>
425 :     <Field name="rev" type="boolean">
426 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
427 :     </Field>
428 :     </Fields>
429 :     </Entity>
430 : parrello 1.60 <Entity name="Compound" keyType="string">
431 : parrello 1.55 <DisplayInfo theme="web" col="7" row="7" />
432 :     <Notes>A compound is a chemical that participates in a reaction.
433 : parrello 1.15 All compounds have a unique ID and may also have one or more names.</Notes>
434 :     <Fields>
435 : parrello 1.50 <Field name="label" type="string">
436 : parrello 1.52 <Notes>Name used in reaction display strings. This is the same as the name
437 :     possessing a priority of 1, but it is placed here to speed up the query
438 :     used to create the display strings.</Notes>
439 : parrello 1.19 </Field>
440 : parrello 1.15 </Fields>
441 : parrello 1.50 </Entity>
442 :     <Entity name="CompoundName" keyType="string">
443 : parrello 1.55 <Notes>A compound name is a common name for the chemical represented by a
444 : parrello 1.50 compound.</Notes>
445 :     </Entity>
446 : parrello 1.60 <Entity name="CompoundCAS" keyType="string">
447 : parrello 1.55 <Notes>This entity represents the Chemical Abstract Service ID for a
448 : parrello 1.52 compound. Each Compound has at most one CAS ID.</Notes>
449 : parrello 1.15 </Entity>
450 : parrello 1.5 <Entity name="Subsystem" keyType="string">
451 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="1" />
452 :     <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
453 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
454 :     <Fields>
455 :     <Field name="version" type="int">
456 :     <Notes>Version number for the subsystem. This value is incremented each time the subsystem
457 :     is backed up.</Notes>
458 :     </Field>
459 : parrello 1.15 <Field name="curator" type="string">
460 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
461 :     </Field>
462 :     <Field name="notes" type="text">
463 :     <Notes>Descriptive notes about the subsystem.</Notes>
464 :     </Field>
465 : parrello 1.52 <Field name="description" type="text">
466 : parrello 1.55 <Notes>Description of the subsystem's function in the cell.</Notes>
467 : parrello 1.52 </Field>
468 : parrello 1.28 <Field name="classification" type="string" relation="SubsystemClass">
469 : parrello 1.44 <Notes>Classification string, colon-delimited. This string organizes the
470 : parrello 1.42 subsystems into a hierarchy.</Notes>
471 : parrello 1.28 </Field>
472 : parrello 1.55 <Field name="hope-curation-notes" type="text" relation="SubsystemHopeNotes">
473 :     <Notes>Text description of how the scenarios were curated.</Notes>
474 :     </Field>
475 : parrello 1.15 </Fields>
476 :     </Entity>
477 :     <Entity name="RoleSubset" keyType="string">
478 : parrello 1.55 <Notes>A role subset is a named collection of roles in a particular subsystem. The
479 : parrello 1.15 subset names are generally very short, non-unique strings. The ID of the parent
480 :     subsystem is prefixed to the subset ID in order to make it unique.</Notes>
481 :     </Entity>
482 :     <Entity name="GenomeSubset" keyType="string">
483 : parrello 1.55 <Notes>A genome subset is a named collection of genomes that participate
484 : parrello 1.15 in a particular subsystem. The subset names are generally very short, non-unique
485 :     strings. The ID of the parent subsystem is prefixed to the subset ID in order
486 :     to make it unique.</Notes>
487 : parrello 1.1 </Entity>
488 : parrello 1.24 <Entity name="SSCell" keyType="hash-string">
489 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="3" />
490 :     <Notes>Part of the process of subsystem annotation of features
491 :     is creating a spreadsheet of genomes and roles to which features are assigned.
492 :     A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
493 : parrello 1.60 <Fields>
494 :     <Field name="column-number" type="int">
495 :     <Notes>Column number of this cell. This value is put here to
496 :     improve the performance of an essential query.</Notes>
497 :     </Field>
498 :     </Fields>
499 : parrello 1.1 </Entity>
500 : parrello 1.8 <Entity name="Property" keyType="int">
501 : parrello 1.55 <Notes>A property is a type of assertion that could be made about the properties of
502 : parrello 1.8 a particular feature. Each property instance is a key/value pair and can be associated
503 :     with many different features. Conversely, a feature can be associated with many key/value
504 :     pairs, even some that notionally contradict each other. For example, there can be evidence
505 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
506 :     <Fields>
507 : parrello 1.60 <Field name="property-name" type="string">
508 : parrello 1.8 <Notes>Name of this property.</Notes>
509 :     </Field>
510 : parrello 1.60 <Field name="property-value" type="text">
511 : parrello 1.8 <Notes>Value associated with this property. For each property
512 :     name, there must by a property record for all of its possible
513 :     values.</Notes>
514 :     </Field>
515 :     </Fields>
516 :     <Indexes>
517 :     <Index>
518 :     <Notes>This index enables the application to find all values for a specified property
519 :     name, or any given name/value pair.</Notes>
520 :     <IndexFields>
521 :     <IndexField name="property-name" order="ascending" />
522 :     <IndexField name="property-value" order="ascending" />
523 :     </IndexFields>
524 :     </Index>
525 :     </Indexes>
526 :     </Entity>
527 : parrello 1.60 <Entity name="Diagram" keyType="string">
528 : parrello 1.55 <DisplayInfo theme="web" col="7" row="1" />
529 :     <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
530 : parrello 1.8 subsystem. A diagram is identified by a short name and contains a longer descriptive name.
531 :     The actual diagram shows which functional roles guide the reactions along with the inputs
532 : parrello 1.52 and outputs; the database, however, only indicates which roles belong to a particular
533 :     diagram's map.</Notes>
534 : parrello 1.8 <Fields>
535 :     <Field name="name" type="text">
536 :     <Notes>Descriptive name of this diagram.</Notes>
537 :     </Field>
538 :     </Fields>
539 :     </Entity>
540 : parrello 1.60 <Entity name="PDB" keyType="string">
541 : parrello 1.55 <DisplayInfo theme="web" col="3" row="5" />
542 : parrello 1.52 <Notes>A PDB is a protein data bank entry containing information that can be used
543 :     to determine the shape of the protein and the energies required to dock with it.
544 : parrello 1.55 The ID is the four-character name used on the PDB web site.</Notes>
545 : parrello 1.49 <Fields>
546 :     <Field name="docking-count" type="int">
547 :     <Notes>The number of ligands that have been docked against this PDB.</Notes>
548 :     </Field>
549 :     </Fields>
550 :     <Indexes>
551 :     <Index>
552 :     <IndexFields>
553 :     <IndexField name="docking-count" order="descending" />
554 :     <IndexField name="id" order="ascending" />
555 :     </IndexFields>
556 :     </Index>
557 :     </Indexes>
558 :     </Entity>
559 : parrello 1.60 <Entity name="Ligand" keyType="string">
560 : parrello 1.55 <DisplayInfo theme="web" col="3" row="7" />
561 : parrello 1.49 <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
562 : parrello 1.60 The ID of the ligand is an 8-digit ID number in the ZINC database.</Notes>
563 : parrello 1.49 <Fields>
564 :     <Field name="name" type="long-string">
565 :     <Notes>Chemical name of this ligand.</Notes>
566 :     </Field>
567 :     </Fields>
568 :     </Entity>
569 : parrello 1.60 <Entity name="CellLocation" keyType="string">
570 : parrello 1.55 <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
571 :     membrane, outside the cell, inside the cell, and so forth.</Notes>
572 :     </Entity>
573 :     <Entity name="Scenario" keyType="string">
574 :     <Notes>A scenario used to verify the validity of subsystem assignments. Each
575 :     scenario converrts input compounds to output compounds using reactions.
576 :     The scenario may use all of the reactions controlled by a subsystem or only
577 :     some, and may also incorporate additional reactions.</Notes>
578 :     </Entity>
579 : parrello 1.1 </Entities>
580 :     <Relationships>
581 : parrello 1.62 <Relationship name="IsRepresentativeOf" from="Genome" to="Genome" arity="1M">
582 :     <Notes>This relationship connects a genome to its representative. Genomes
583 :     are partitioned into multiple sets of close strains, each having a
584 :     single representative. In certain situations, it is desirable to
585 :     analyze only representative genomes rather than the full suite.</Notes>
586 :     </Relationship>
587 : parrello 1.60 <Relationship name="IsPathogenicIn" from="Genome" to="Host" arity="MM">
588 :     <Notes>This relationship connects a genome to a host in which it is
589 :     pathogenic. Many genomes do not have a pathogenic host; some have
590 :     multiple hosts.</Notes>
591 :     </Relationship>
592 :     <Relationship name="IsFamilyForFeature" from="ProteinFamily" to="Feature"
593 :     arity="MM" converse="IsInFamily">
594 :     <Notes>This relationship connects a feature to its protein
595 :     families.</Notes>
596 :     <Fields>
597 :     <Field name="range" type="string">
598 :     <Notes>Location in the feature of the matching protein.</Notes>
599 :     </Field>
600 :     </Fields>
601 :     </Relationship>
602 :     <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM"
603 :     converse="IsCatalyzedBy">
604 : parrello 1.55 <DisplayInfo theme="web" />
605 :     <Notes>This relationship connects a role to the reactions it catalyzes.
606 :     The purpose of a role is to create proteins that trigger certain
607 :     chemical reactions. A single reaction can be triggered by many roles,
608 :     and a role can trigger many reactions.</Notes>
609 :     </Relationship>
610 :     <Relationship name="ExcludesReaction" from="Scenario" to="Reaction" arity="MM">
611 :     <Notes>This relationship connects a scenario to reactions of the parent
612 :     subsystem that do not participate in it.</Notes>
613 :     </Relationship>
614 :     <Relationship name="IncludesReaction" from="Scenario" to="Reaction" arity="MM">
615 :     <Notes>This relationship connects a scenario to reactions that participate
616 :     in it but are not part of the parent subsystem.</Notes>
617 :     </Relationship>
618 :     <Relationship name="HasScenario" from="Subsystem" to="Scenario" arity="MM">
619 :     <Notes>This relationship connects a role to the scenarios used to
620 :     validate it.</Notes>
621 :     </Relationship>
622 :     <Relationship name="IsInputFor" from="Compound" to="Scenario" arity="MM">
623 :     <Notes>This relationship connects a scenario to its input compounds.</Notes>
624 :     </Relationship>
625 :     <Relationship name="IsOutputOf" from="Compound" to="Scenario" arity="MM">
626 :     <Notes>This relationship connects a scenario to its output compounds</Notes>
627 :     <Fields>
628 :     <Field name="auxiliary" type="boolean">
629 :     <Notes>TRUE if this is an auxiliary output compound, FALSE if it is a
630 :     main output compound.</Notes>
631 :     </Field>
632 :     </Fields>
633 :     </Relationship>
634 :     <Relationship name="IsOnDiagram" from="Scenario" to="Diagram" arity="MM">
635 :     <Notes>This relationship connects a scenario to related diagrams.</Notes>
636 :     </Relationship>
637 :     <Relationship name="IsPossiblePlaceFor" from="CellLocation" to="Feature" arity="MM">
638 :     <Notes>This relationship connects a feature with the various places in a cell that the feature
639 :     might be found. The confidence factor is included as intersection data.</Notes>
640 :     <Fields>
641 :     <Field name="confidence" type="float">
642 :     <Notes>Confidence that the protein will be found in this location, expressed as a
643 :     value from 0 to 10.</Notes>
644 :     </Field>
645 :     </Fields>
646 :     </Relationship>
647 : parrello 1.50 <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
648 :     <Notes>This relationship connects a feature to its CDD protein domains. The
649 :     match score is included as intersection data.</Notes>
650 :     <Fields>
651 :     <Field name="score" type="float">
652 :     <Notes>This is the match score between the feature and the CDD. A
653 :     lower score is a better match.</Notes>
654 :     </Field>
655 :     </Fields>
656 :     <FromIndex>
657 :     <IndexFields>
658 :     <IndexField name="score" order="ascending" />
659 :     </IndexFields>
660 :     </FromIndex>
661 :     </Relationship>
662 :     <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
663 :     <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
664 :     associated with a compound, and some are associated with two compounds, but not
665 :     all compounds have CAS IDs.</Notes>
666 :     </Relationship>
667 :     <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
668 :     <Notes>Relates a role to its EC number. Every EC number is associated with a
669 :     role, but not all roles have EC numbers.</Notes>
670 :     </Relationship>
671 :     <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
672 :     <Notes>Connects an alias to the feature it represents. Every alias connects
673 :     to at least 1 feature, and a feature connects to many aliases.</Notes>
674 :     </Relationship>
675 :     <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
676 :     <Notes>Connects a compound to its names. A compound generally has several
677 :     names</Notes>
678 :     <Fields>
679 :     <Field name="priority" type="int">
680 :     <Notes>Priority of this name, with 1 being the highest priority, 2
681 :     the next highest, and so forth.</Notes>
682 :     </Field>
683 :     </Fields>
684 :     <FromIndex>
685 :     <Notes>This index enables the application to view the names of a compound
686 :     in priority order.</Notes>
687 :     <IndexFields>
688 :     <IndexField name="priority" order="ascending" />
689 :     </IndexFields>
690 :     </FromIndex>
691 :     </Relationship>
692 : parrello 1.49 <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
693 : parrello 1.55 <DisplayInfo caption="Is Protein\nFor Feature" theme="web" />
694 : parrello 1.49 <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
695 :     <Fields>
696 :     <Field name="score" type="float">
697 :     <Notes>Similarity score for the comparison between the feature and
698 :     the PDB protein. A lower score indicates a better match.</Notes>
699 :     </Field>
700 :     <Field name="start-location" type="int">
701 :     <Notes>Starting location within the feature of the matching region.</Notes>
702 :     </Field>
703 :     <Field name="end-location" type="int">
704 :     <Notes>Ending location within the feature of the matching region.</Notes>
705 :     </Field>
706 :     </Fields>
707 :     <ToIndex>
708 :     <Notes>This index enables the application to view the PDBs of a
709 :     feature in order from the closest match to the furthest.</Notes>
710 :     <IndexFields>
711 :     <IndexField name="score" order="ascending" />
712 :     </IndexFields>
713 :     </ToIndex>
714 :     <FromIndex>
715 :     <Notes>This index enables the application to view the features of
716 :     a PDB in order from the closest match to the furthest.</Notes>
717 :     <IndexFields>
718 :     <IndexField name="score" order="ascending" />
719 :     </IndexFields>
720 :     </FromIndex>
721 :     </Relationship>
722 :     <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
723 : parrello 1.55 <DisplayInfo caption="Docks With" theme="web" />
724 :     <Notes>Indicates that a docking result exists between a PDB and a ligand. The
725 : parrello 1.49 docking result describes the energy required for the ligand to dock with
726 :     the protein described by the PDB. A lower energy indicates the ligand has a
727 :     good chance of disabling the protein. At the current time, only the best
728 :     docking results are kept.</Notes>
729 :     <Fields>
730 : parrello 1.60 <Field name="reason" type="string">
731 : parrello 1.49 <Notes>Indication of the reason for determining the docking result.
732 : parrello 1.52 A value of =Random= indicates the docking was attempted as a part
733 : parrello 1.49 of a random survey used to determine the docking characteristics of the
734 : parrello 1.52 PDB. A value of =Rich= indicates the docking was attempted because
735 : parrello 1.49 a low-energy docking result was predicted for the ligand with respect
736 :     to the PDB.</Notes>
737 :     </Field>
738 : parrello 1.60 <Field name="tool" type="string">
739 : parrello 1.49 <Notes>Name of the tool used to produce the docking result.</Notes>
740 :     </Field>
741 :     <Field name="total-energy" type="float">
742 :     <Notes>Total energy required for the ligand to dock with the PDB
743 :     protein, in kcal/mol. A negative value means energy is released.</Notes>
744 :     </Field>
745 : parrello 1.59 <Field name="vanderwaals-energy" type="float">
746 : parrello 1.49 <Notes>Docking energy in kcal/mol that results from the geometric fit
747 :     (Van der Waals force) between the PDB and the ligand.</Notes>
748 :     </Field>
749 :     <Field name="electrostatic-energy" type="float">
750 :     <Notes>Docking energy in kcal/mol that results from the movement of
751 : parrello 1.52 electrons (electrostatic force) between the PDB and the ligand.</Notes>
752 : parrello 1.49 </Field>
753 :     </Fields>
754 :     <FromIndex>
755 :     <Notes>This index enables the application to view a PDB's docking results from
756 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
757 :     <IndexFields>
758 :     <IndexField name="total-energy" order="ascending" />
759 :     </IndexFields>
760 :     </FromIndex>
761 :     <ToIndex>
762 :     <Notes>This index enables the application to view a ligand's docking results from
763 : parrello 1.52 the lowest energy (best docking) to highest energy (worst docking).</Notes>
764 : parrello 1.49 </ToIndex>
765 :     </Relationship>
766 : parrello 1.55 <Relationship name="IsAlsoFoundIn" from="Feature" to="ExternalDatabase" arity="MM">
767 :     <Notes>This relationship connects a feature to external databases that contain
768 :     essentially identical features. The name used in the external database is stored
769 :     in the relationship as intersection data.</Notes>
770 :     <Fields>
771 : parrello 1.60 <Field name="alias" type="string">
772 : parrello 1.55 <Notes>ID of the feature in the specified external database.</Notes>
773 :     </Field>
774 :     </Fields>
775 :     <Indexes>
776 :     <Index>
777 :     <Notes>This index allows direct access to features by external ID.</Notes>
778 :     <IndexFields>
779 :     <IndexField name="alias" order="ascending" />
780 :     </IndexFields>
781 :     </Index>
782 :     </Indexes>
783 :     </Relationship>
784 : parrello 1.50 <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
785 : parrello 1.27 <Notes>This relation connects a synonym group to the features that make it
786 :     up.</Notes>
787 :     </Relationship>
788 : parrello 1.60 <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M" converse="IsInGenome">
789 : parrello 1.55 <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
790 : parrello 1.24 <Notes>This relationship connects a genome to all of its features. This
791 :     relationship is redundant in a sense, because the genome ID is part
792 :     of the feature ID; however, it makes the creation of certain queries more
793 :     convenient because you can drag in filtering information for a feature's
794 :     genome.</Notes>
795 :     <Fields>
796 : parrello 1.60 <Field name="type" type="string">
797 : parrello 1.24 <Notes>Feature type (eg. peg, rna)</Notes>
798 :     </Field>
799 :     </Fields>
800 : parrello 1.38 <FromIndex>
801 : parrello 1.24 <Notes>This index enables the application to view the features of a
802 :     Genome sorted by type.</Notes>
803 :     <IndexFields>
804 :     <IndexField name="type" order="ascending" />
805 :     </IndexFields>
806 : parrello 1.38 </FromIndex>
807 : parrello 1.24 </Relationship>
808 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
809 : parrello 1.55 <DisplayInfo caption="Is Part Of" theme="nmpdr" />
810 : parrello 1.1 <Notes>This relationship connects a genome to the contigs that contain the actual genetic
811 :     information.</Notes>
812 :     </Relationship>
813 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
814 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
815 :     come from a single source or from a cooperation among multiple sources.</Notes>
816 :     </Relationship>
817 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
818 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
819 :     contig into sequences, we get a performance boost from only needing to keep small portions
820 :     of a contig in memory at any one time. This relationship connects the contig to its
821 :     constituent sequences.</Notes>
822 :     <Fields>
823 :     <Field name="len" type="int">
824 : parrello 1.15 <Notes>Length of the sequence.</Notes>
825 :     </Field>
826 : parrello 1.1 <Field name="start-position" type="int">
827 : parrello 1.15 <Notes>Index (1-based) of the point in the contig where this
828 :     sequence starts.</Notes>
829 :     </Field>
830 : parrello 1.1 </Fields>
831 :     <FromIndex>
832 :     <Notes>This index enables the application to find all of the sequences in
833 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
834 : parrello 1.1 <IndexFields>
835 :     <IndexField name="start-position" order="ascending" />
836 :     <IndexField name="len" order="ascending" />
837 :     </IndexFields>
838 :     </FromIndex>
839 :     </Relationship>
840 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
841 : parrello 1.55 <DisplayInfo caption="Targets" theme="seed" />
842 : parrello 1.1 <Notes>This relationship connects a feature to its annotations.</Notes>
843 :     </Relationship>
844 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
845 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
846 :     </Relationship>
847 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
848 : parrello 1.55 <DisplayInfo caption="\nParticipates\nIn" theme="seed" />
849 : parrello 1.1 <Notes>This relationship connects subsystems to the genomes that use
850 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
851 : parrello 1.52 connected to the genome features through the *SSCell* object.</Notes>
852 : parrello 1.15 <Fields>
853 : parrello 1.60 <Field name="variant-code" type="string">
854 : parrello 1.20 <Notes>Code indicating the subsystem variant to which this
855 : parrello 1.15 genome belongs. Each subsystem can have multiple variants. A variant
856 : parrello 1.60 code of -1 indicates that the genome does not have a functional
857 :     variant of the subsystem. A variant code of 0 indicates that
858 : parrello 1.20 the genome's participation is considered iffy.</Notes>
859 : parrello 1.15 </Field>
860 :     </Fields>
861 :     <ToIndex>
862 :     <Notes>This index enables the application to find all of the genomes using
863 :     a subsystem in order by variant code, which is how we wish to display them
864 :     in the spreadsheets.</Notes>
865 :     <IndexFields>
866 :     <IndexField name="variant-code" order="ascending" />
867 :     </IndexFields>
868 :     </ToIndex>
869 : parrello 1.1 </Relationship>
870 : parrello 1.60 <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM" converse="Uses">
871 : parrello 1.55 <DisplayInfo caption="Uses" theme="seed" />
872 :     <Notes>This relationship connects roles to the subsystems that implement them.</Notes>
873 : parrello 1.15 <Fields>
874 : parrello 1.60 <Field name="abbr" type="string">
875 : parrello 1.50 <Notes>Abbreviated name for the role, generally non-unique, but useful
876 :     in column headings for HTML tables.</Notes>
877 :     </Field>
878 : parrello 1.15 <Field name="column-number" type="int">
879 :     <Notes>Column number for this role in the specified subsystem's
880 :     spreadsheet.</Notes>
881 :     </Field>
882 : parrello 1.55 <Field name="auxiliary" type="boolean">
883 :     <Notes>If TRUE, then this role is ancillary to the purpose of the subsystem.
884 :     If FALSE, it is essential to its metabolic pathway.</Notes>
885 :     </Field>
886 : parrello 1.57 <Field name="hope-reaction-note" type="text">
887 : parrello 1.55 <Notes>A description of the status of a role in relation to the
888 :     reactions it produces as determined by the scenarios. If present,
889 :     will indicate if the role has been determined to be auxiliary,
890 :     if it has been examined to verify an automatic assignment, and so
891 :     forth.</Notes>
892 :     </Field>
893 : parrello 1.15 </Fields>
894 :     <ToIndex>
895 :     <Notes>This index enables the application to see the subsystem roles
896 :     in column order. The ordering of the roles is usually significant,
897 :     so it is important to preserve it.</Notes>
898 :     <IndexFields>
899 :     <IndexField name="column-number" order="ascending" />
900 :     </IndexFields>
901 :     </ToIndex>
902 : parrello 1.1 </Relationship>
903 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
904 : parrello 1.55 <DisplayInfo caption="Is Row Of" theme="seed" />
905 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
906 :     genome for the spreadsheet column.</Notes>
907 :     </Relationship>
908 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
909 : parrello 1.55 <DisplayInfo caption="Is In\nColumn\nFor" theme="seed" />
910 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
911 :     role for the spreadsheet row.</Notes>
912 :     </Relationship>
913 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
914 : parrello 1.55 <DisplayInfo caption="Is\nContained\nIn" theme="seed" />
915 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
916 :     features assigned to it.</Notes>
917 : parrello 1.15 <Fields>
918 :     <Field name="cluster-number" type="int">
919 :     <Notes>ID of this feature's cluster. Clusters represent families of
920 :     related proteins participating in a subsystem.</Notes>
921 :     </Field>
922 :     </Fields>
923 :     </Relationship>
924 :     <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
925 : parrello 1.55 <DisplayInfo caption="Involves" theme="web" />
926 : parrello 1.15 <Notes>This relationship connects a reaction to the compounds that participate
927 :     in it.</Notes>
928 :     <Fields>
929 :     <Field name="product" type="boolean">
930 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
931 :     it is a substrate. When a reaction is written on paper in
932 :     chemical notation, the substrates are left of the arrow and the
933 :     products are to the right. Sorting on this field will cause
934 :     the substrates to appear first, followed by the products. If the
935 :     reaction is reversible, then the notion of substrates and products
936 :     is not at intuitive; however, a value here of FALSE still puts the
937 :     compound left of the arrow and a value of TRUE still puts it to the
938 :     right.</Notes>
939 :     </Field>
940 : parrello 1.60 <Field name="stoichiometry" type="string">
941 : parrello 1.15 <Notes>Number of molecules of the compound that participate in a
942 :     single instance of the reaction. For example, if a reaction
943 : parrello 1.19 produces two water molecules, the stoichiometry of water for the
944 : parrello 1.15 reaction would be two. When a reaction is written on paper in
945 : parrello 1.19 chemical notation, the stoichiometry is the number next to the
946 : parrello 1.15 chemical formula of the compound.</Notes>
947 :     </Field>
948 :     <Field name="main" type="boolean">
949 :     <Notes>TRUE if this compound is one of the main participants in
950 :     the reaction, else FALSE. It is permissible for none of the
951 :     compounds in the reaction to be considered main, in which
952 :     case this value would be FALSE for all of the relevant
953 :     compounds.</Notes>
954 :     </Field>
955 : parrello 1.60 <Field name="loc" type="string">
956 : parrello 1.15 <Notes>An optional character string that indicates the relative
957 :     position of this compound in the reaction's chemical formula. The
958 :     location affects the way the compounds present as we cross the
959 :     relationship from the reaction side. The product/substrate flag
960 :     comes first, then the value of this field, then the main flag.
961 :     The default value is an empty string; however, the empty string
962 :     sorts first, so if this field is used, it should probably be
963 :     used for every compound in the reaction.</Notes>
964 :     </Field>
965 : parrello 1.19 <Field name="discriminator" type="int">
966 :     <Notes>A unique ID for this record. The discriminator does not
967 :     provide any useful data, but it prevents identical records from
968 :     being collapsed by the SELECT DISTINCT command used by ERDB to
969 :     retrieve data.</Notes>
970 :     </Field>
971 : parrello 1.15 </Fields>
972 :     <ToIndex>
973 :     <Notes>This index presents the compounds in the reaction in the
974 :     order they should be displayed when writing it in chemical notation.
975 :     All the substrates appear before all the products, and within that
976 :     ordering, the main compounds appear first.</Notes>
977 : parrello 1.19 <IndexFields>
978 :     <IndexField name="product" order="ascending" />
979 :     <IndexField name="loc" order="ascending" />
980 :     <IndexField name="main" order="descending" />
981 :     </IndexFields>
982 : parrello 1.15 </ToIndex>
983 : parrello 1.1 </Relationship>
984 : parrello 1.61 <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM" converse="IsLocusFor">
985 : parrello 1.55 <DisplayInfo caption="Is\nLocation\nOf" theme="nmpdr" />
986 : parrello 1.1 <Notes>This relationship connects a feature to the contig segments that work together
987 :     to effect it. The segments are numbered sequentially starting from 1. The database is
988 :     required to place an upper limit on the length of each segment. If a segment is longer
989 : parrello 1.52 than the maximum, it can be broken into smaller bits. The upper limit enables applications
990 :     to locate all features that contain a specific residue. For example, if the upper limit
991 :     is 100 and we are looking for a feature that contains residue 234 of contig *ABC*, we
992 :     can look for features with a begin point between 135 and 333. The results can then be
993 :     filtered by direction and length of the segment.</Notes>
994 : parrello 1.1 <Fields>
995 :     <Field name="locN" type="int">
996 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
997 :     </Field>
998 : parrello 1.1 <Field name="beg" type="int">
999 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
1000 :     belongs to the segment.</Notes>
1001 :     </Field>
1002 : parrello 1.1 <Field name="len" type="int">
1003 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
1004 :     a specific point between residues. This is the point before the residue if the direction
1005 :     is forward and the point after the residue if the direction is backward.</Notes>
1006 :     </Field>
1007 : parrello 1.1 <Field name="dir" type="char">
1008 : parrello 1.52 <Notes>Direction of the segment: =+= if it is forward and
1009 :     =-= if it is backward.</Notes>
1010 : parrello 1.8 </Field>
1011 : parrello 1.1 </Fields>
1012 : parrello 1.45 <FromIndex>
1013 : parrello 1.1 <Notes>This index allows the application to find all the segments of a feature in
1014 : parrello 1.8 the proper order.</Notes>
1015 : parrello 1.1 <IndexFields>
1016 :     <IndexField name="locN" order="ascending" />
1017 :     </IndexFields>
1018 :     </FromIndex>
1019 :     <ToIndex>
1020 :     <Notes>This index is the one used by applications to find all the feature
1021 :     segments that contain a specific residue.</Notes>
1022 :     <IndexFields>
1023 :     <IndexField name="beg" order="ascending" />
1024 :     </IndexFields>
1025 :     </ToIndex>
1026 :     </Relationship>
1027 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
1028 :     <Notes>This relationship connects a feature to its known property values.
1029 :     The relationship contains text data that indicates the paper or organization
1030 :     that discovered evidence that the feature possesses the property. So, for
1031 :     example, if two papers presented evidence that a feature is essential,
1032 :     there would be an instance of this relationship for both.</Notes>
1033 :     <Fields>
1034 :     <Field name="evidence" type="text">
1035 :     <Notes>URL or citation of the paper or
1036 :     institution that reported evidence of the relevant feature possessing
1037 :     the specified property value.</Notes>
1038 :     </Field>
1039 :     </Fields>
1040 :     </Relationship>
1041 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
1042 : parrello 1.55 <DisplayInfo caption="Shows" theme="web" />
1043 : parrello 1.8 <Notes>This relationship connects a role to the diagrams on which it
1044 :     appears. A role frequently identifies an enzyme, and can appear in many
1045 :     diagrams. A diagram generally contains many different roles.</Notes>
1046 :     </Relationship>
1047 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
1048 : parrello 1.55 <DisplayInfo caption="Is Container Of" theme="seed" />
1049 : parrello 1.8 <Notes>This relationship connects a subsystem to the spreadsheet cells
1050 :     used to analyze and display it. The cells themselves can be thought of
1051 :     as a grid with Roles on one axis and Genomes on the other. The
1052 :     various features of the subsystem are then assigned to the cells.</Notes>
1053 :     </Relationship>
1054 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
1055 :     <Notes>This relationship identifies the users trusted by each
1056 :     particular user. When viewing functional assignments, the
1057 :     assignment displayed is the most recent one by a user trusted
1058 :     by the current user. The current user implicitly trusts himself.
1059 :     If no trusted users are specified in the database, the user
1060 : parrello 1.52 also implicitly trusts the user =FIG=.</Notes>
1061 : parrello 1.8 </Relationship>
1062 : parrello 1.15 <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
1063 :     <Notes>This relationship connects a role subset to the roles that it covers.
1064 :     A subset is, essentially, a named group of roles belonging to a specific
1065 :     subsystem, and this relationship effects that. Note that will a role
1066 :     may belong to many subsystems, a subset belongs to only one subsystem,
1067 :     and all roles in the subset must have that subsystem in common.</Notes>
1068 :     </Relationship>
1069 :     <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
1070 :     <Notes>This relationship connects a subset to the genomes that it covers.
1071 :     A subset is, essentially, a named group of genomes participating in a specific
1072 :     subsystem, and this relationship effects that. Note that while a genome
1073 :     may belong to many subsystems, a subset belongs to only one subsystem,
1074 :     and all genomes in the subset must have that subsystem in common.</Notes>
1075 :     </Relationship>
1076 :     <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
1077 :     <Notes>This relationship connects a subsystem to its constituent
1078 :     role subsets. Note that some roles in a subsystem may not belong to a
1079 :     subset, so the relationship between roles and subsystems cannot be
1080 :     derived from the relationships going through the subset.</Notes>
1081 :     </Relationship>
1082 :     <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
1083 :     <Notes>This relationship connects a subsystem to its constituent
1084 :     genome subsets. Note that some genomes in a subsystem may not belong to a
1085 :     subset, so the relationship between genomes and subsystems cannot be
1086 :     derived from the relationships going through the subset.</Notes>
1087 :     </Relationship>
1088 : parrello 1.39 <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
1089 :     <Notes>This relationship connects a feature to the subsystems in which it
1090 :     participates. This is technically redundant information, but it is used
1091 : parrello 1.52 so often that it gets its own table for performance reasons.</Notes>
1092 : parrello 1.40 <Fields>
1093 : parrello 1.60 <Field name="genome" type="string">
1094 : parrello 1.40 <Notes>ID of the genome containing the feature</Notes>
1095 :     </Field>
1096 : parrello 1.60 <Field name="type" type="string">
1097 : parrello 1.40 <Notes>Feature type (eg. peg, rna)</Notes>
1098 :     </Field>
1099 :     </Fields>
1100 :     <ToIndex>
1101 :     <Notes>This index enables the application to view the features of a
1102 :     subsystem sorted by genome and feature type.</Notes>
1103 :     <IndexFields>
1104 :     <IndexField name="genome" order="ascending" />
1105 :     <IndexField name="type" order="ascending" />
1106 :     </IndexFields>
1107 :     </ToIndex>
1108 : parrello 1.39 </Relationship>
1109 : parrello 1.1 </Relationships>
1110 : parrello 1.56 <Shapes>
1111 :     <Shape type="oval" name="Pins">
1112 :     <DisplayInfo theme="nmpdr" col="1" row="4.5" fixed="1" />
1113 :     <Notes>The Pin Server provides information about functional couplings between features.</Notes>
1114 :     </Shape>
1115 :     <Shape type="oval" name="Sims">
1116 :     <DisplayInfo theme="nmpdr" col="1.5" row="5" fixed="1" />
1117 :     <Notes>The Similarity Server contains a high-performance custom database of similarities between features.</Notes>
1118 :     </Shape>
1119 :     <Shape type="oval" name="BBHs">
1120 :     <DisplayInfo theme="nmpdr" col="2" row="5.5" fixed="1" />
1121 :     <Notes>For each feature, the BBH Server has that feature's bidirectional best hits in other genomes.</Notes>
1122 :     </Shape>
1123 :     <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1124 :     <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1125 : parrello 1.60 <Notes>HTTP services are used to transmit data between the servers and the
1126 :     NMPDR.</Notes>
1127 : parrello 1.56 </Shape>
1128 :     </Shapes>
1129 : parrello 1.1 </Database>

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