[Bio] / Sprout / SproutDBD.xml Repository:
ViewVC logotype

Annotation of /Sprout/SproutDBD.xml

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.57 - (view) (download) (as text)

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 1.1 <Field name="unique-characterization" type="medium-string">
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 1.1 <Field name="access-code" type="key-string">
31 : parrello 1.52 <Notes>The access code field is deprecated. Its function has been replaced by
32 :     the account management system developed for the [[RapidAnnotationServer]].</Notes>
33 : parrello 1.8 </Field>
34 : parrello 1.15 <Field name="complete" type="boolean">
35 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
36 :     </Field>
37 : parrello 1.48 <Field name="dna-size" type="counter">
38 :     <Notes>number of base pairs in the genome</Notes>
39 :     </Field>
40 : parrello 1.8 <Field name="taxonomy" type="text">
41 : parrello 1.52 <Notes>The taxonomy string contains the full [[Wikipedia:taxonomy]] of the organism, while individual elements
42 : parrello 1.8 separated by semi-colons (and optional white space), starting with the domain and ending with
43 :     the disambiguated genus and species (which is the organism's scientific name plus an
44 :     identifying string).</Notes>
45 :     </Field>
46 : parrello 1.37 <Field name="primary-group" type="name-string">
47 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
48 : parrello 1.52 per organism (either based on the organism name or the default value =Supporting=). In general,
49 :     more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>
50 :     </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 :     <Notes>Number of [[protein encoding genes]] for this organism</Notes>
56 :     </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 1.1 </Fields>
61 :     <Indexes>
62 : parrello 1.45 <Index>
63 : parrello 1.1 <Notes>This index allows the applications to find all genomes associated with
64 :     a specific access code, so that a complete list of the genomes users can view
65 :     may be generated.</Notes>
66 :     <IndexFields>
67 :     <IndexField name="access-code" order="ascending" />
68 :     <IndexField name="genus" order="ascending" />
69 :     <IndexField name="species" order="ascending" />
70 :     <IndexField name="unique-characterization" order="ascending" />
71 :     </IndexFields>
72 :     </Index>
73 : parrello 1.45 <Index>
74 : parrello 1.37 <Notes>This index allows the applications to find all genomes associated with
75 :     a specific primary (NMPDR) group.</Notes>
76 :     <IndexFields>
77 :     <IndexField name="primary-group" order="ascending" />
78 :     <IndexField name="genus" order="ascending" />
79 :     <IndexField name="species" order="ascending" />
80 :     <IndexField name="unique-characterization" order="ascending" />
81 :     </IndexFields>
82 :     </Index>
83 : parrello 1.45 <Index>
84 : parrello 1.1 <Notes>This index allows the applications to find all genomes for a particular
85 :     species.</Notes>
86 :     <IndexFields>
87 :     <IndexField name="genus" order="ascending" />
88 :     <IndexField name="species" order="ascending" />
89 :     <IndexField name="unique-characterization" order="ascending" />
90 :     </IndexFields>
91 :     </Index>
92 :     </Indexes>
93 :     </Entity>
94 : parrello 1.50 <Entity name="CDD" keyType="key-string">
95 :     <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
96 : parrello 1.52 on a feature's protein. The ID is six-digit string assigned by the public
97 : parrello 1.55 Conserved Domain Database. A CDD
98 : parrello 1.52 can occur on multiple features and a feature generally has multiple CDDs.</Notes>
99 : parrello 1.50 </Entity>
100 : parrello 1.1 <Entity name="Source" keyType="medium-string">
101 : parrello 1.55 <Notes>A source describes a place from which genome data was taken. This can be an organization
102 : parrello 1.1 or a paper citation.</Notes>
103 :     <Fields>
104 :     <Field name="URL" type="string" relation="SourceURL">
105 : parrello 1.8 <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
106 :     </Field>
107 : parrello 1.1 <Field name="description" type="text">
108 : parrello 1.52 <Notes>Description of the source. The description can be a street address or a citation.</Notes>
109 : parrello 1.8 </Field>
110 : parrello 1.1 </Fields>
111 :     </Entity>
112 :     <Entity name="Contig" keyType="name-string">
113 : parrello 1.55 <DisplayInfo theme="nmpdr" col="1" row="1" />
114 :     <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
115 : parrello 1.1 genome ID followed by a name that identifies which contig this is for the parent genome. As
116 :     is the case with all keys in this database, the individual components are separated by a
117 : parrello 1.52 period. A contig can contain over a million residues. For performance reasons, therefore,
118 : parrello 1.55 the contig is split into multiple pieces called sequences. The sequences
119 : parrello 1.1 contain the characters that represent the residues as well as data on the quality of
120 :     the residue identification.</Notes>
121 :     </Entity>
122 :     <Entity name="Sequence" keyType="name-string">
123 : parrello 1.55 <Notes>A sequence is a continuous piece of a contig. Contigs are split into
124 : parrello 1.1 sequences so that we don't have to have the entire contig in memory when we are
125 :     manipulating it. The key of the sequence is the contig ID followed by the index of
126 :     the begin point.</Notes>
127 :     <Fields>
128 :     <Field name="sequence" type="text">
129 : parrello 1.52 <Notes>String consisting of the residues (base pairs). Each residue is described by a single
130 : parrello 1.8 character in the string.</Notes>
131 :     </Field>
132 : parrello 1.1 <Field name="quality-vector" type="text">
133 : parrello 1.9 <Notes>String describing the quality data for each base pair. Individual values will
134 : parrello 1.8 be separated by periods. The value represents negative exponent of the probability
135 :     of error. Thus, for example, a quality of 30 indicates the probability of error is
136 : parrello 1.52 10^-30. A higher quality number indicates a better chance of a correct match. It is
137 :     possible that the quality data is not known for a sequence. If that is the case, the
138 :     quality vector will contain the string =unknown=.</Notes>
139 : parrello 1.8 </Field>
140 : parrello 1.1 </Fields>
141 :     </Entity>
142 : parrello 1.54 <Entity name="Keyword" keyType="name-string">
143 : parrello 1.55 <Notes>A keyword is a word that can be used to search the feature table. This entity
144 :     contains the keyword's stem, its phonetic form, and the number of features that
145 :     can be found by searching for the word.</Notes>
146 :     <Fields>
147 :     <Field name="stem" type="name-string">
148 :     <Notes>The stem of a keyword is a normalized form that is independent of parts
149 :     of speech. The actual keywords stored in the database search index are stems.</Notes>
150 :     </Field>
151 : parrello 1.54 <Field name="count" type="counter">
152 :     <Notes>Number of features that can be found by searching for the specified
153 :     keyword.</Notes>
154 :     </Field>
155 : parrello 1.55 <Field name="phonex" type="name-string">
156 :     <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
157 :     word stem. This can be used to find alternative spellings if an matching word is not
158 :     present.</Notes>
159 :     </Field>
160 : parrello 1.54 </Fields>
161 : parrello 1.55 <Indexes>
162 :     <Index>
163 :     <Notes>This index allows the user to find words by stem.</Notes>
164 :     <IndexFields>
165 :     <IndexField name="stem" order="ascending" />
166 :     </IndexFields>
167 :     </Index>
168 :     <Index>
169 :     <Notes>This index allows the user to find words by phonex.</Notes>
170 :     <IndexFields>
171 :     <IndexField name="phonex" order="ascending" />
172 :     <IndexField name="count" order="descending" />
173 :     </IndexFields>
174 :     </Index>
175 :     </Indexes>
176 :     </Entity>
177 :     <Entity name="ExternalDatabase" keyType="key-string">
178 :     <Notes>An external database identifies a biological database surveyed by PIR International
179 :     as part of an effort to determine which features are essentially identical between bioinformatics
180 :     organizations. Each feature in the database will have zero or more corresponding IDs that are
181 :     captured from the PIR data. Each corresponding ID is represented in a relationship between an external
182 :     database and the feature itself.</Notes>
183 : parrello 1.54 </Entity>
184 : parrello 1.25 <Entity name="Feature" keyType="id-string">
185 : parrello 1.55 <DisplayInfo theme="nmpdr" col="3" row="3" />
186 :     <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
187 : parrello 1.1 may be spread across multiple contigs of a genome, but never across more than
188 :     one genome. Features can be assigned to roles via spreadsheet cells,
189 : parrello 1.55 and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
190 : parrello 1.1 <Fields>
191 : parrello 1.50 <Field name="feature-type" type="id-string">
192 : parrello 1.52 <Notes>Code indicating the type of this feature. Among the codes currently
193 :     supported are =peg= for a [[protein encoding gene]], =bs= for a
194 :     binding site, =opr= for an operon, and so forth.</Notes>
195 : parrello 1.8 </Field>
196 : parrello 1.1 <Field name="translation" type="text" relation="FeatureTranslation">
197 : parrello 1.52 <Notes>_(optional)_ A translation of this feature's residues into character
198 : parrello 1.8 codes, formed by concatenating the pieces of the feature together. For a
199 : parrello 1.52 [[protein encoding gene]], the translation contains protein characters. For other types
200 :     it contains DNA characters.</Notes>
201 : parrello 1.8 </Field>
202 : parrello 1.1 <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
203 : parrello 1.52 <Notes>Upstream sequence for the feature. This includes residues preceding the feature as
204 :     well as some of the feature's initial residues.</Notes>
205 : parrello 1.8 </Field>
206 : parrello 1.42 <Field name="assignment" type="text">
207 :     <Notes>Default functional assignment for this feature.</Notes>
208 :     </Field>
209 : parrello 1.1 <Field name="active" type="boolean">
210 : parrello 1.52 <Notes>(This field is deprecated.) TRUE if this feature is still considered valid,
211 :     FALSE if it has been logically deleted.</Notes>
212 : parrello 1.8 </Field>
213 : parrello 1.48 <Field name="assignment-maker" type="name-string">
214 :     <Notes>name of the user who made the functional assignment</Notes>
215 :     </Field>
216 :     <Field name="assignment-quality" type="char">
217 :     <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
218 :     (indicating experimental)</Notes>
219 :     </Field>
220 : parrello 1.41 <Field name="keywords" type="text" searchable="1">
221 :     <Notes>This is a list of search keywords for the feature. It includes the
222 :     functional assignment, subsystem roles, and special properties.</Notes>
223 : parrello 1.36 </Field>
224 : parrello 1.8 <Field name="link" type="text" relation="FeatureLink">
225 : parrello 1.52 <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
226 : parrello 1.8 links are to other websites that have useful about the gene that the feature represents, and
227 : parrello 1.52 are coded as raw HTML, using &lt;a href="_link_"&gt;_text_&lt;/a&gt; notation.</Notes>
228 : parrello 1.8 </Field>
229 : parrello 1.41 <Field name="conservation" type="float" relation="FeatureConservation">
230 : parrello 1.52 <Notes>_(optional)_ A number between 0 and 1 that indicates the degree to which this feature's DNA is
231 : parrello 1.41 conserved in related genomes. A value of 1 indicates perfect conservation. A value less
232 : parrello 1.50 than 1 is a reflection of the degree to which gap characters interfere in the alignment
233 : parrello 1.41 between the feature and its close relatives.</Notes>
234 :     </Field>
235 : parrello 1.45 <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
236 :     <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
237 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
238 :     or potential (potential-essential), hyperlinked to the document from which the
239 :     essentiality was curated. If a feature is not essential, this field will have no
240 :     values; otherwise, it may have multiple values.</Notes>
241 :     </Field>
242 :     <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
243 :     <Notes>A value indicating the virulence of the feature, coded as HTML. In most
244 :     cases, this will be a phrase or SA number hyperlinked to the document from which
245 :     the virulence information was curated. If the feature is not virulent, this field
246 :     will have no values; otherwise, it may have multiple values.</Notes>
247 :     </Field>
248 :     <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
249 :     <Notes>A value indicating whether or not the feature can be found in the
250 :     Immune Epitope Database. If the feature has not been matched to that database,
251 :     this field will have no values. Otherwise, it will have an epitope name and/or
252 :     sequence, hyperlinked to the database.</Notes>
253 :     </Field>
254 : parrello 1.50 <Field name="location-string" type="text">
255 :     <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
256 :     strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
257 : parrello 1.52 we have to painstakingly paste together the [[#IsLocatedIn]] records, which are themselves
258 :     designed to help look for features in a particular region rather than to find the location
259 :     of a feature.</Notes>
260 : parrello 1.50 </Field>
261 : parrello 1.55 <Field name="signal-peptide" type="name-string">
262 :     <Notes>The signal peptide location for this feature. This is expressed as start and end
263 :     numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
264 :     peptide at the beginning of the feature's protein and extending through 22 amino acid
265 :     positions. An empty string means no signal peptide is present.</Notes>
266 :     </Field>
267 :     <Field name="transmembrane-map" type="text">
268 :     <Notes>A map indicating which sections of a protein will be embedded in a membrane.
269 :     This is expressed as a comma-separated list of as start and end numbers with hyphens
270 :     for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
271 :     sections of the protein that become embedded in a membrane: the 10th through 12th
272 :     amino acids, and the 40th through the 60th. An empty string means no
273 :     transmembrane regions are known.</Notes>
274 :     </Field>
275 :     <Field name="similar-to-human" type="boolean">
276 :     <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
277 :     else FALSE</Notes>
278 :     </Field>
279 :     <Field name="isoelectric-point" type="float">
280 :     <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
281 :     If the pH of the medium is lower than this value, the protein will have a net
282 :     positive charge. If the pH of the medium is higher, then the protein will have a
283 :     net negative charge.</Notes>
284 :     </Field>
285 :     <Field name="molecular-weight" type="float">
286 :     <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
287 :     indicates that no protein is created.</Notes>
288 :     </Field>
289 :     <Field name="sequence-length" type="counter">
290 :     <Notes>Number of base pairs in this feature.</Notes>
291 :     </Field>
292 :     <Field name="locked" type="boolean">
293 :     <Notes>TRUE if a feature's assignment is locked. A locked feature's functional
294 :     role cannot be changed by automated programs.</Notes>
295 :     </Field>
296 :     <Field name="in-genbank" type="boolean">
297 :     <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
298 :     </Field>
299 : parrello 1.1 </Fields>
300 :     </Entity>
301 : parrello 1.50 <Entity name="FeatureAlias" keyType="medium-string">
302 :     <Notes>Alternative names for features. A feature can have many aliases. In general,
303 : parrello 1.52 each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
304 :     </Entity>
305 :     <Entity name="SproutUser" keyType="name-string">
306 : parrello 1.55 <Notes>A user is a person who can make annotations and view data in the database. The
307 : parrello 1.52 user object is keyed on the user's login name.</Notes>
308 :     <Fields>
309 :     <Field name="description" type="string">
310 :     <Notes>Full name or description of this user.</Notes>
311 :     </Field>
312 :     <Field name="access-code" type="key-string" relation="UserAccess">
313 :     <Notes>This field is deprecated.</Notes>
314 :     </Field>
315 :     </Fields>
316 : parrello 1.50 </Entity>
317 : parrello 1.27 <Entity name="SynonymGroup" keyType="id-string">
318 : parrello 1.55 <Notes>A synonym group represents a group of features. Features that represent substantially
319 : parrello 1.52 identical proteins or DNA sequences are mapped to the same synonym group, and this information is
320 :     used to expand similarities.</Notes>
321 : parrello 1.27 </Entity>
322 : parrello 1.1 <Entity name="Role" keyType="string">
323 : parrello 1.55 <DisplayInfo theme="web" col="7" row="3" />
324 :     <Notes>A role describes a biological function that may be fulfilled by a feature.
325 : parrello 1.1 One of the main goals of the database is to record the roles of the various features.</Notes>
326 : parrello 1.50 </Entity>
327 :     <Entity name="RoleEC" keyType="string">
328 :     <Notes>EC code for a role.</Notes>
329 : parrello 1.1 </Entity>
330 :     <Entity name="Annotation" keyType="name-string">
331 : parrello 1.55 <DisplayInfo theme="seed" col="1" row="3" />
332 :     <Notes>An annotation contains supplementary information about a feature. The most
333 : parrello 1.52 important type of annotation is the assignment of a [[functional role]]; however,
334 :     other types of annotations are also possible.</Notes>
335 : parrello 1.8 <Fields>
336 :     <Field name="time" type="date">
337 :     <Notes>Date and time of the annotation.</Notes>
338 :     </Field>
339 :     <Field name="annotation" type="text">
340 :     <Notes>Text of the annotation.</Notes>
341 :     </Field>
342 : parrello 1.1 </Fields>
343 : parrello 1.26 <Indexes>
344 :     <Index>
345 :     <Notes>This index allows the user to find recent annotations.</Notes>
346 :     <IndexFields>
347 :     <IndexField name="time" order="descending" />
348 :     </IndexFields>
349 :     </Index>
350 :     </Indexes>
351 : parrello 1.1 </Entity>
352 : parrello 1.15 <Entity name="Reaction" keyType="key-string">
353 : parrello 1.55 <DisplayInfo theme="web" col="7" row="5" />
354 :     <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
355 : parrello 1.15 is generally a small number preceded by a letter.</Notes>
356 :     <Fields>
357 :     <Field name="url" type="string" relation="ReactionURL">
358 :     <Notes>HTML string containing a link to a web location that describes the
359 :     reaction. This field is optional.</Notes>
360 :     </Field>
361 :     <Field name="rev" type="boolean">
362 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
363 :     </Field>
364 :     </Fields>
365 :     </Entity>
366 :     <Entity name="Compound" keyType="name-string">
367 : parrello 1.55 <DisplayInfo theme="web" col="7" row="7" />
368 :     <Notes>A compound is a chemical that participates in a reaction.
369 : parrello 1.15 All compounds have a unique ID and may also have one or more names.</Notes>
370 :     <Fields>
371 : parrello 1.50 <Field name="label" type="string">
372 : parrello 1.52 <Notes>Name used in reaction display strings. This is the same as the name
373 :     possessing a priority of 1, but it is placed here to speed up the query
374 :     used to create the display strings.</Notes>
375 : parrello 1.19 </Field>
376 : parrello 1.15 </Fields>
377 : parrello 1.50 </Entity>
378 :     <Entity name="CompoundName" keyType="string">
379 : parrello 1.55 <Notes>A compound name is a common name for the chemical represented by a
380 : parrello 1.50 compound.</Notes>
381 :     </Entity>
382 :     <Entity name="CompoundCAS" keyType="name-string">
383 : parrello 1.55 <Notes>This entity represents the Chemical Abstract Service ID for a
384 : parrello 1.52 compound. Each Compound has at most one CAS ID.</Notes>
385 : parrello 1.15 </Entity>
386 : parrello 1.5 <Entity name="Subsystem" keyType="string">
387 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="1" />
388 :     <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
389 :     is an important tool for recognizing parallel genetic features in different organisms.</Notes>
390 :     <Fields>
391 :     <Field name="version" type="int">
392 :     <Notes>Version number for the subsystem. This value is incremented each time the subsystem
393 :     is backed up.</Notes>
394 :     </Field>
395 : parrello 1.15 <Field name="curator" type="string">
396 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
397 :     </Field>
398 :     <Field name="notes" type="text">
399 :     <Notes>Descriptive notes about the subsystem.</Notes>
400 :     </Field>
401 : parrello 1.52 <Field name="description" type="text">
402 : parrello 1.55 <Notes>Description of the subsystem's function in the cell.</Notes>
403 : parrello 1.52 </Field>
404 : parrello 1.28 <Field name="classification" type="string" relation="SubsystemClass">
405 : parrello 1.44 <Notes>Classification string, colon-delimited. This string organizes the
406 : parrello 1.42 subsystems into a hierarchy.</Notes>
407 : parrello 1.28 </Field>
408 : parrello 1.55 <Field name="hope-curation-notes" type="text" relation="SubsystemHopeNotes">
409 :     <Notes>Text description of how the scenarios were curated.</Notes>
410 :     </Field>
411 : parrello 1.15 </Fields>
412 :     </Entity>
413 :     <Entity name="RoleSubset" keyType="string">
414 : parrello 1.55 <Notes>A role subset is a named collection of roles in a particular subsystem. The
415 : parrello 1.15 subset names are generally very short, non-unique strings. The ID of the parent
416 :     subsystem is prefixed to the subset ID in order to make it unique.</Notes>
417 :     </Entity>
418 :     <Entity name="GenomeSubset" keyType="string">
419 : parrello 1.55 <Notes>A genome subset is a named collection of genomes that participate
420 : parrello 1.15 in a particular subsystem. The subset names are generally very short, non-unique
421 :     strings. The ID of the parent subsystem is prefixed to the subset ID in order
422 :     to make it unique.</Notes>
423 : parrello 1.1 </Entity>
424 : parrello 1.24 <Entity name="SSCell" keyType="hash-string">
425 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="3" />
426 :     <Notes>Part of the process of subsystem annotation of features
427 :     is creating a spreadsheet of genomes and roles to which features are assigned.
428 :     A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
429 : parrello 1.1 </Entity>
430 : parrello 1.8 <Entity name="Property" keyType="int">
431 : parrello 1.55 <Notes>A property is a type of assertion that could be made about the properties of
432 : parrello 1.8 a particular feature. Each property instance is a key/value pair and can be associated
433 :     with many different features. Conversely, a feature can be associated with many key/value
434 :     pairs, even some that notionally contradict each other. For example, there can be evidence
435 :     that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
436 :     <Fields>
437 :     <Field name="property-name" type="name-string">
438 :     <Notes>Name of this property.</Notes>
439 :     </Field>
440 :     <Field name="property-value" type="string">
441 :     <Notes>Value associated with this property. For each property
442 :     name, there must by a property record for all of its possible
443 :     values.</Notes>
444 :     </Field>
445 :     </Fields>
446 :     <Indexes>
447 :     <Index>
448 :     <Notes>This index enables the application to find all values for a specified property
449 :     name, or any given name/value pair.</Notes>
450 :     <IndexFields>
451 :     <IndexField name="property-name" order="ascending" />
452 :     <IndexField name="property-value" order="ascending" />
453 :     </IndexFields>
454 :     </Index>
455 :     </Indexes>
456 :     </Entity>
457 :     <Entity name="Diagram" keyType="name-string">
458 : parrello 1.55 <DisplayInfo theme="web" col="7" row="1" />
459 :     <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
460 : parrello 1.8 subsystem. A diagram is identified by a short name and contains a longer descriptive name.
461 :     The actual diagram shows which functional roles guide the reactions along with the inputs
462 : parrello 1.52 and outputs; the database, however, only indicates which roles belong to a particular
463 :     diagram's map.</Notes>
464 : parrello 1.8 <Fields>
465 :     <Field name="name" type="text">
466 :     <Notes>Descriptive name of this diagram.</Notes>
467 :     </Field>
468 :     </Fields>
469 :     </Entity>
470 : parrello 1.31 <Entity name="Family" keyType="id-string">
471 : parrello 1.55 <DisplayInfo theme="seed" col="5" row="5" />
472 :     <Notes>A family (also called a FigFam) is a group of homologous features believed to have
473 :     the same function. Families provide a mechanism for verifying the accuracy of functional
474 :     assignments and are also used in Rapid Annotation and in determining phylogenetic trees.</Notes>
475 : parrello 1.31 <Fields>
476 : parrello 1.32 <Field name="function" type="text">
477 : parrello 1.31 <Notes>The functional assignment expected for all PEGs in this family.</Notes>
478 :     </Field>
479 : parrello 1.33 <Field name="size" type="int">
480 : parrello 1.31 <Notes>The number of proteins in this family. This may be larger than the
481 :     number of PEGs included in the family, since the family may also contain external
482 :     IDs.</Notes>
483 :     </Field>
484 :     </Fields>
485 :     </Entity>
486 : parrello 1.49 <Entity name="PDB" keyType="id-string">
487 : parrello 1.55 <DisplayInfo theme="web" col="3" row="5" />
488 : parrello 1.52 <Notes>A PDB is a protein data bank entry containing information that can be used
489 :     to determine the shape of the protein and the energies required to dock with it.
490 : parrello 1.55 The ID is the four-character name used on the PDB web site.</Notes>
491 : parrello 1.49 <Fields>
492 :     <Field name="docking-count" type="int">
493 :     <Notes>The number of ligands that have been docked against this PDB.</Notes>
494 :     </Field>
495 :     </Fields>
496 :     <Indexes>
497 :     <Index>
498 :     <IndexFields>
499 :     <IndexField name="docking-count" order="descending" />
500 :     <IndexField name="id" order="ascending" />
501 :     </IndexFields>
502 :     </Index>
503 :     </Indexes>
504 :     </Entity>
505 :     <Entity name="Ligand" keyType="id-string">
506 : parrello 1.55 <DisplayInfo theme="web" col="3" row="7" />
507 : parrello 1.49 <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
508 : parrello 1.52 The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>
509 : parrello 1.49 <Fields>
510 :     <Field name="name" type="long-string">
511 :     <Notes>Chemical name of this ligand.</Notes>
512 :     </Field>
513 :     </Fields>
514 :     </Entity>
515 : parrello 1.55 <Entity name="CellLocation" keyType="key-string">
516 :     <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
517 :     membrane, outside the cell, inside the cell, and so forth.</Notes>
518 :     </Entity>
519 :     <Entity name="Scenario" keyType="string">
520 :     <Notes>A scenario used to verify the validity of subsystem assignments. Each
521 :     scenario converrts input compounds to output compounds using reactions.
522 :     The scenario may use all of the reactions controlled by a subsystem or only
523 :     some, and may also incorporate additional reactions.</Notes>
524 :     </Entity>
525 : parrello 1.1 </Entities>
526 :     <Relationships>
527 : parrello 1.55 <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
528 :     <DisplayInfo theme="web" />
529 :     <Notes>This relationship connects a role to the reactions it catalyzes.
530 :     The purpose of a role is to create proteins that trigger certain
531 :     chemical reactions. A single reaction can be triggered by many roles,
532 :     and a role can trigger many reactions.</Notes>
533 :     </Relationship>
534 :     <Relationship name="ExcludesReaction" from="Scenario" to="Reaction" arity="MM">
535 :     <Notes>This relationship connects a scenario to reactions of the parent
536 :     subsystem that do not participate in it.</Notes>
537 :     </Relationship>
538 :     <Relationship name="IncludesReaction" from="Scenario" to="Reaction" arity="MM">
539 :     <Notes>This relationship connects a scenario to reactions that participate
540 :     in it but are not part of the parent subsystem.</Notes>
541 :     </Relationship>
542 :     <Relationship name="HasScenario" from="Subsystem" to="Scenario" arity="MM">
543 :     <Notes>This relationship connects a role to the scenarios used to
544 :     validate it.</Notes>
545 :     </Relationship>
546 :     <Relationship name="IsInputFor" from="Compound" to="Scenario" arity="MM">
547 :     <Notes>This relationship connects a scenario to its input compounds.</Notes>
548 :     </Relationship>
549 :     <Relationship name="IsOutputOf" from="Compound" to="Scenario" arity="MM">
550 :     <Notes>This relationship connects a scenario to its output compounds</Notes>
551 :     <Fields>
552 :     <Field name="auxiliary" type="boolean">
553 :     <Notes>TRUE if this is an auxiliary output compound, FALSE if it is a
554 :     main output compound.</Notes>
555 :     </Field>
556 :     </Fields>
557 :     </Relationship>
558 :     <Relationship name="IsOnDiagram" from="Scenario" to="Diagram" arity="MM">
559 :     <Notes>This relationship connects a scenario to related diagrams.</Notes>
560 :     </Relationship>
561 :     <Relationship name="IsPossiblePlaceFor" from="CellLocation" to="Feature" arity="MM">
562 :     <Notes>This relationship connects a feature with the various places in a cell that the feature
563 :     might be found. The confidence factor is included as intersection data.</Notes>
564 :     <Fields>
565 :     <Field name="confidence" type="float">
566 :     <Notes>Confidence that the protein will be found in this location, expressed as a
567 :     value from 0 to 10.</Notes>
568 :     </Field>
569 :     </Fields>
570 :     </Relationship>
571 : parrello 1.50 <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
572 :     <Notes>This relationship connects a feature to its CDD protein domains. The
573 :     match score is included as intersection data.</Notes>
574 :     <Fields>
575 :     <Field name="score" type="float">
576 :     <Notes>This is the match score between the feature and the CDD. A
577 :     lower score is a better match.</Notes>
578 :     </Field>
579 :     </Fields>
580 :     <FromIndex>
581 :     <IndexFields>
582 :     <IndexField name="score" order="ascending" />
583 :     </IndexFields>
584 :     </FromIndex>
585 :     </Relationship>
586 :     <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
587 :     <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
588 :     associated with a compound, and some are associated with two compounds, but not
589 :     all compounds have CAS IDs.</Notes>
590 :     </Relationship>
591 :     <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
592 :     <Notes>Relates a role to its EC number. Every EC number is associated with a
593 :     role, but not all roles have EC numbers.</Notes>
594 :     </Relationship>
595 :     <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
596 :     <Notes>Connects an alias to the feature it represents. Every alias connects
597 :     to at least 1 feature, and a feature connects to many aliases.</Notes>
598 :     </Relationship>
599 :     <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
600 :     <Notes>Connects a compound to its names. A compound generally has several
601 :     names</Notes>
602 :     <Fields>
603 :     <Field name="priority" type="int">
604 :     <Notes>Priority of this name, with 1 being the highest priority, 2
605 :     the next highest, and so forth.</Notes>
606 :     </Field>
607 :     </Fields>
608 :     <FromIndex>
609 :     <Notes>This index enables the application to view the names of a compound
610 :     in priority order.</Notes>
611 :     <IndexFields>
612 :     <IndexField name="priority" order="ascending" />
613 :     </IndexFields>
614 :     </FromIndex>
615 :     </Relationship>
616 : parrello 1.49 <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
617 : parrello 1.55 <DisplayInfo caption="Is Protein\nFor Feature" theme="web" />
618 : parrello 1.49 <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
619 :     <Fields>
620 :     <Field name="score" type="float">
621 :     <Notes>Similarity score for the comparison between the feature and
622 :     the PDB protein. A lower score indicates a better match.</Notes>
623 :     </Field>
624 :     <Field name="start-location" type="int">
625 :     <Notes>Starting location within the feature of the matching region.</Notes>
626 :     </Field>
627 :     <Field name="end-location" type="int">
628 :     <Notes>Ending location within the feature of the matching region.</Notes>
629 :     </Field>
630 :     </Fields>
631 :     <ToIndex>
632 :     <Notes>This index enables the application to view the PDBs of a
633 :     feature in order from the closest match to the furthest.</Notes>
634 :     <IndexFields>
635 :     <IndexField name="score" order="ascending" />
636 :     </IndexFields>
637 :     </ToIndex>
638 :     <FromIndex>
639 :     <Notes>This index enables the application to view the features of
640 :     a PDB in order from the closest match to the furthest.</Notes>
641 :     <IndexFields>
642 :     <IndexField name="score" order="ascending" />
643 :     </IndexFields>
644 :     </FromIndex>
645 :     </Relationship>
646 :     <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
647 : parrello 1.55 <DisplayInfo caption="Docks With" theme="web" />
648 :     <Notes>Indicates that a docking result exists between a PDB and a ligand. The
649 : parrello 1.49 docking result describes the energy required for the ligand to dock with
650 :     the protein described by the PDB. A lower energy indicates the ligand has a
651 :     good chance of disabling the protein. At the current time, only the best
652 :     docking results are kept.</Notes>
653 :     <Fields>
654 :     <Field name="reason" type="id-string">
655 :     <Notes>Indication of the reason for determining the docking result.
656 : parrello 1.52 A value of =Random= indicates the docking was attempted as a part
657 : parrello 1.49 of a random survey used to determine the docking characteristics of the
658 : parrello 1.52 PDB. A value of =Rich= indicates the docking was attempted because
659 : parrello 1.49 a low-energy docking result was predicted for the ligand with respect
660 :     to the PDB.</Notes>
661 :     </Field>
662 :     <Field name="tool" type="id-string">
663 :     <Notes>Name of the tool used to produce the docking result.</Notes>
664 :     </Field>
665 :     <Field name="total-energy" type="float">
666 :     <Notes>Total energy required for the ligand to dock with the PDB
667 :     protein, in kcal/mol. A negative value means energy is released.</Notes>
668 :     </Field>
669 :     <Field name="vanderwalls-energy" type="float">
670 :     <Notes>Docking energy in kcal/mol that results from the geometric fit
671 :     (Van der Waals force) between the PDB and the ligand.</Notes>
672 :     </Field>
673 :     <Field name="electrostatic-energy" type="float">
674 :     <Notes>Docking energy in kcal/mol that results from the movement of
675 : parrello 1.52 electrons (electrostatic force) between the PDB and the ligand.</Notes>
676 : parrello 1.49 </Field>
677 :     </Fields>
678 :     <FromIndex>
679 :     <Notes>This index enables the application to view a PDB's docking results from
680 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
681 :     <IndexFields>
682 :     <IndexField name="total-energy" order="ascending" />
683 :     </IndexFields>
684 :     </FromIndex>
685 :     <ToIndex>
686 :     <Notes>This index enables the application to view a ligand's docking results from
687 : parrello 1.52 the lowest energy (best docking) to highest energy (worst docking).</Notes>
688 : parrello 1.49 </ToIndex>
689 :     </Relationship>
690 : parrello 1.55 <Relationship name="IsAlsoFoundIn" from="Feature" to="ExternalDatabase" arity="MM">
691 :     <Notes>This relationship connects a feature to external databases that contain
692 :     essentially identical features. The name used in the external database is stored
693 :     in the relationship as intersection data.</Notes>
694 :     <Fields>
695 :     <Field name="alias" type="name-string">
696 :     <Notes>ID of the feature in the specified external database.</Notes>
697 :     </Field>
698 :     </Fields>
699 :     <Indexes>
700 :     <Index>
701 :     <Notes>This index allows direct access to features by external ID.</Notes>
702 :     <IndexFields>
703 :     <IndexField name="alias" order="ascending" />
704 :     </IndexFields>
705 :     </Index>
706 :     </Indexes>
707 :     </Relationship>
708 : parrello 1.34 <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
709 : parrello 1.55 <DisplayInfo caption="Belongs To" theme="seed" />
710 : parrello 1.31 <Notes>This relationship connects a protein family to all of its PEGs and connects
711 :     each PEG to all of its protein families.</Notes>
712 :     </Relationship>
713 : parrello 1.50 <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
714 : parrello 1.27 <Notes>This relation connects a synonym group to the features that make it
715 :     up.</Notes>
716 :     </Relationship>
717 : parrello 1.24 <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
718 : parrello 1.55 <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
719 : parrello 1.24 <Notes>This relationship connects a genome to all of its features. This
720 :     relationship is redundant in a sense, because the genome ID is part
721 :     of the feature ID; however, it makes the creation of certain queries more
722 :     convenient because you can drag in filtering information for a feature's
723 :     genome.</Notes>
724 :     <Fields>
725 :     <Field name="type" type="key-string">
726 :     <Notes>Feature type (eg. peg, rna)</Notes>
727 :     </Field>
728 :     </Fields>
729 : parrello 1.38 <FromIndex>
730 : parrello 1.24 <Notes>This index enables the application to view the features of a
731 :     Genome sorted by type.</Notes>
732 :     <IndexFields>
733 :     <IndexField name="type" order="ascending" />
734 :     </IndexFields>
735 : parrello 1.38 </FromIndex>
736 : parrello 1.24 </Relationship>
737 : parrello 1.1 <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
738 : parrello 1.55 <DisplayInfo caption="Is Part Of" theme="nmpdr" />
739 : parrello 1.1 <Notes>This relationship connects a genome to the contigs that contain the actual genetic
740 :     information.</Notes>
741 :     </Relationship>
742 :     <Relationship name="ComesFrom" from="Genome" to="Source" arity="MM">
743 :     <Notes>This relationship connects a genome to the sources that mapped it. A genome can
744 :     come from a single source or from a cooperation among multiple sources.</Notes>
745 :     </Relationship>
746 :     <Relationship name="IsMadeUpOf" from="Contig" to="Sequence" arity="1M">
747 :     <Notes>A contig is stored in the database as an ordered set of sequences. By splitting the
748 :     contig into sequences, we get a performance boost from only needing to keep small portions
749 :     of a contig in memory at any one time. This relationship connects the contig to its
750 :     constituent sequences.</Notes>
751 :     <Fields>
752 :     <Field name="len" type="int">
753 : parrello 1.15 <Notes>Length of the sequence.</Notes>
754 :     </Field>
755 : parrello 1.1 <Field name="start-position" type="int">
756 : parrello 1.15 <Notes>Index (1-based) of the point in the contig where this
757 :     sequence starts.</Notes>
758 :     </Field>
759 : parrello 1.1 </Fields>
760 :     <FromIndex>
761 :     <Notes>This index enables the application to find all of the sequences in
762 : parrello 1.8 a contig in order, and makes it easier to find a particular residue section.</Notes>
763 : parrello 1.1 <IndexFields>
764 :     <IndexField name="start-position" order="ascending" />
765 :     <IndexField name="len" order="ascending" />
766 :     </IndexFields>
767 :     </FromIndex>
768 :     </Relationship>
769 :     <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
770 : parrello 1.55 <DisplayInfo caption="Targets" theme="seed" />
771 : parrello 1.1 <Notes>This relationship connects a feature to its annotations.</Notes>
772 :     </Relationship>
773 :     <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
774 :     <Notes>This relationship connects an annotation to the user who made it.</Notes>
775 :     </Relationship>
776 :     <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
777 : parrello 1.55 <DisplayInfo caption="\nParticipates\nIn" theme="seed" />
778 : parrello 1.1 <Notes>This relationship connects subsystems to the genomes that use
779 :     it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
780 : parrello 1.52 connected to the genome features through the *SSCell* object.</Notes>
781 : parrello 1.15 <Fields>
782 :     <Field name="variant-code" type="key-string">
783 : parrello 1.20 <Notes>Code indicating the subsystem variant to which this
784 : parrello 1.15 genome belongs. Each subsystem can have multiple variants. A variant
785 : parrello 1.52 code of =-1= indicates that the genome does not have a functional
786 :     variant of the subsystem. A variant code of =0= indicates that
787 : parrello 1.20 the genome's participation is considered iffy.</Notes>
788 : parrello 1.15 </Field>
789 :     </Fields>
790 :     <ToIndex>
791 :     <Notes>This index enables the application to find all of the genomes using
792 :     a subsystem in order by variant code, which is how we wish to display them
793 :     in the spreadsheets.</Notes>
794 :     <IndexFields>
795 :     <IndexField name="variant-code" order="ascending" />
796 :     </IndexFields>
797 :     </ToIndex>
798 : parrello 1.1 </Relationship>
799 :     <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
800 : parrello 1.55 <DisplayInfo caption="Uses" theme="seed" />
801 :     <Notes>This relationship connects roles to the subsystems that implement them.</Notes>
802 : parrello 1.15 <Fields>
803 : parrello 1.50 <Field name="abbr" type="name-string">
804 :     <Notes>Abbreviated name for the role, generally non-unique, but useful
805 :     in column headings for HTML tables.</Notes>
806 :     </Field>
807 : parrello 1.15 <Field name="column-number" type="int">
808 :     <Notes>Column number for this role in the specified subsystem's
809 :     spreadsheet.</Notes>
810 :     </Field>
811 : parrello 1.55 <Field name="auxiliary" type="boolean">
812 :     <Notes>If TRUE, then this role is ancillary to the purpose of the subsystem.
813 :     If FALSE, it is essential to its metabolic pathway.</Notes>
814 :     </Field>
815 : parrello 1.57 <Field name="hope-reaction-note" type="text">
816 : parrello 1.55 <Notes>A description of the status of a role in relation to the
817 :     reactions it produces as determined by the scenarios. If present,
818 :     will indicate if the role has been determined to be auxiliary,
819 :     if it has been examined to verify an automatic assignment, and so
820 :     forth.</Notes>
821 :     </Field>
822 : parrello 1.57 <Field name="hope-reaction-link" type="text">
823 : parrello 1.55 <Notes>A description of the mapping between the reactions of
824 :     this role and the scenarios used to validate it.</Notes>
825 :     </Field>
826 : parrello 1.15 </Fields>
827 :     <ToIndex>
828 :     <Notes>This index enables the application to see the subsystem roles
829 :     in column order. The ordering of the roles is usually significant,
830 :     so it is important to preserve it.</Notes>
831 :     <IndexFields>
832 :     <IndexField name="column-number" order="ascending" />
833 :     </IndexFields>
834 :     </ToIndex>
835 : parrello 1.1 </Relationship>
836 :     <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
837 : parrello 1.55 <DisplayInfo caption="Is Row Of" theme="seed" />
838 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
839 :     genome for the spreadsheet column.</Notes>
840 :     </Relationship>
841 :     <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
842 : parrello 1.55 <DisplayInfo caption="Is In\nColumn\nFor" theme="seed" />
843 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
844 :     role for the spreadsheet row.</Notes>
845 :     </Relationship>
846 :     <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
847 : parrello 1.55 <DisplayInfo caption="Is\nContained\nIn" theme="seed" />
848 : parrello 1.1 <Notes>This relationship connects a subsystem's spreadsheet cell to the
849 :     features assigned to it.</Notes>
850 : parrello 1.15 <Fields>
851 :     <Field name="cluster-number" type="int">
852 :     <Notes>ID of this feature's cluster. Clusters represent families of
853 :     related proteins participating in a subsystem.</Notes>
854 :     </Field>
855 :     </Fields>
856 :     </Relationship>
857 :     <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
858 : parrello 1.55 <DisplayInfo caption="Involves" theme="web" />
859 : parrello 1.15 <Notes>This relationship connects a reaction to the compounds that participate
860 :     in it.</Notes>
861 :     <Fields>
862 :     <Field name="product" type="boolean">
863 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
864 :     it is a substrate. When a reaction is written on paper in
865 :     chemical notation, the substrates are left of the arrow and the
866 :     products are to the right. Sorting on this field will cause
867 :     the substrates to appear first, followed by the products. If the
868 :     reaction is reversible, then the notion of substrates and products
869 :     is not at intuitive; however, a value here of FALSE still puts the
870 :     compound left of the arrow and a value of TRUE still puts it to the
871 :     right.</Notes>
872 :     </Field>
873 : parrello 1.19 <Field name="stoichiometry" type="key-string">
874 : parrello 1.15 <Notes>Number of molecules of the compound that participate in a
875 :     single instance of the reaction. For example, if a reaction
876 : parrello 1.19 produces two water molecules, the stoichiometry of water for the
877 : parrello 1.15 reaction would be two. When a reaction is written on paper in
878 : parrello 1.19 chemical notation, the stoichiometry is the number next to the
879 : parrello 1.15 chemical formula of the compound.</Notes>
880 :     </Field>
881 :     <Field name="main" type="boolean">
882 :     <Notes>TRUE if this compound is one of the main participants in
883 :     the reaction, else FALSE. It is permissible for none of the
884 :     compounds in the reaction to be considered main, in which
885 :     case this value would be FALSE for all of the relevant
886 :     compounds.</Notes>
887 :     </Field>
888 :     <Field name="loc" type="key-string">
889 :     <Notes>An optional character string that indicates the relative
890 :     position of this compound in the reaction's chemical formula. The
891 :     location affects the way the compounds present as we cross the
892 :     relationship from the reaction side. The product/substrate flag
893 :     comes first, then the value of this field, then the main flag.
894 :     The default value is an empty string; however, the empty string
895 :     sorts first, so if this field is used, it should probably be
896 :     used for every compound in the reaction.</Notes>
897 :     </Field>
898 : parrello 1.19 <Field name="discriminator" type="int">
899 :     <Notes>A unique ID for this record. The discriminator does not
900 :     provide any useful data, but it prevents identical records from
901 :     being collapsed by the SELECT DISTINCT command used by ERDB to
902 :     retrieve data.</Notes>
903 :     </Field>
904 : parrello 1.15 </Fields>
905 :     <ToIndex>
906 :     <Notes>This index presents the compounds in the reaction in the
907 :     order they should be displayed when writing it in chemical notation.
908 :     All the substrates appear before all the products, and within that
909 :     ordering, the main compounds appear first.</Notes>
910 : parrello 1.19 <IndexFields>
911 :     <IndexField name="product" order="ascending" />
912 :     <IndexField name="loc" order="ascending" />
913 :     <IndexField name="main" order="descending" />
914 :     </IndexFields>
915 : parrello 1.15 </ToIndex>
916 : parrello 1.1 </Relationship>
917 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
918 : parrello 1.55 <DisplayInfo caption="Is\nLocation\nOf" theme="nmpdr" />
919 : parrello 1.1 <Notes>This relationship connects a feature to the contig segments that work together
920 :     to effect it. The segments are numbered sequentially starting from 1. The database is
921 :     required to place an upper limit on the length of each segment. If a segment is longer
922 : parrello 1.52 than the maximum, it can be broken into smaller bits. The upper limit enables applications
923 :     to locate all features that contain a specific residue. For example, if the upper limit
924 :     is 100 and we are looking for a feature that contains residue 234 of contig *ABC*, we
925 :     can look for features with a begin point between 135 and 333. The results can then be
926 :     filtered by direction and length of the segment.</Notes>
927 : parrello 1.1 <Fields>
928 :     <Field name="locN" type="int">
929 : parrello 1.8 <Notes>Sequence number of this segment.</Notes>
930 :     </Field>
931 : parrello 1.1 <Field name="beg" type="int">
932 : parrello 1.8 <Notes>Index (1-based) of the first residue in the contig that
933 :     belongs to the segment.</Notes>
934 :     </Field>
935 : parrello 1.1 <Field name="len" type="int">
936 : parrello 1.8 <Notes>Number of residues in the segment. A length of 0 identifies
937 :     a specific point between residues. This is the point before the residue if the direction
938 :     is forward and the point after the residue if the direction is backward.</Notes>
939 :     </Field>
940 : parrello 1.1 <Field name="dir" type="char">
941 : parrello 1.52 <Notes>Direction of the segment: =+= if it is forward and
942 :     =-= if it is backward.</Notes>
943 : parrello 1.8 </Field>
944 : parrello 1.1 </Fields>
945 : parrello 1.45 <FromIndex>
946 : parrello 1.1 <Notes>This index allows the application to find all the segments of a feature in
947 : parrello 1.8 the proper order.</Notes>
948 : parrello 1.1 <IndexFields>
949 :     <IndexField name="locN" order="ascending" />
950 :     </IndexFields>
951 :     </FromIndex>
952 :     <ToIndex>
953 :     <Notes>This index is the one used by applications to find all the feature
954 :     segments that contain a specific residue.</Notes>
955 :     <IndexFields>
956 :     <IndexField name="beg" order="ascending" />
957 :     </IndexFields>
958 :     </ToIndex>
959 :     </Relationship>
960 : parrello 1.8 <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
961 :     <Notes>This relationship connects a feature to its known property values.
962 :     The relationship contains text data that indicates the paper or organization
963 :     that discovered evidence that the feature possesses the property. So, for
964 :     example, if two papers presented evidence that a feature is essential,
965 :     there would be an instance of this relationship for both.</Notes>
966 :     <Fields>
967 :     <Field name="evidence" type="text">
968 :     <Notes>URL or citation of the paper or
969 :     institution that reported evidence of the relevant feature possessing
970 :     the specified property value.</Notes>
971 :     </Field>
972 :     </Fields>
973 :     </Relationship>
974 :     <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
975 : parrello 1.55 <DisplayInfo caption="Shows" theme="web" />
976 : parrello 1.8 <Notes>This relationship connects a role to the diagrams on which it
977 :     appears. A role frequently identifies an enzyme, and can appear in many
978 :     diagrams. A diagram generally contains many different roles.</Notes>
979 :     </Relationship>
980 :     <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
981 : parrello 1.55 <DisplayInfo caption="Is Container Of" theme="seed" />
982 : parrello 1.8 <Notes>This relationship connects a subsystem to the spreadsheet cells
983 :     used to analyze and display it. The cells themselves can be thought of
984 :     as a grid with Roles on one axis and Genomes on the other. The
985 :     various features of the subsystem are then assigned to the cells.</Notes>
986 :     </Relationship>
987 :     <Relationship name="IsTrustedBy" from="SproutUser" to="SproutUser" arity="MM">
988 :     <Notes>This relationship identifies the users trusted by each
989 :     particular user. When viewing functional assignments, the
990 :     assignment displayed is the most recent one by a user trusted
991 :     by the current user. The current user implicitly trusts himself.
992 :     If no trusted users are specified in the database, the user
993 : parrello 1.52 also implicitly trusts the user =FIG=.</Notes>
994 : parrello 1.8 </Relationship>
995 : parrello 1.15 <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
996 :     <Notes>This relationship connects a role subset to the roles that it covers.
997 :     A subset is, essentially, a named group of roles belonging to a specific
998 :     subsystem, and this relationship effects that. Note that will a role
999 :     may belong to many subsystems, a subset belongs to only one subsystem,
1000 :     and all roles in the subset must have that subsystem in common.</Notes>
1001 :     </Relationship>
1002 :     <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
1003 :     <Notes>This relationship connects a subset to the genomes that it covers.
1004 :     A subset is, essentially, a named group of genomes participating in a specific
1005 :     subsystem, and this relationship effects that. Note that while a genome
1006 :     may belong to many subsystems, a subset belongs to only one subsystem,
1007 :     and all genomes in the subset must have that subsystem in common.</Notes>
1008 :     </Relationship>
1009 :     <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
1010 :     <Notes>This relationship connects a subsystem to its constituent
1011 :     role subsets. Note that some roles in a subsystem may not belong to a
1012 :     subset, so the relationship between roles and subsystems cannot be
1013 :     derived from the relationships going through the subset.</Notes>
1014 :     </Relationship>
1015 :     <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
1016 :     <Notes>This relationship connects a subsystem to its constituent
1017 :     genome subsets. Note that some genomes in a subsystem may not belong to a
1018 :     subset, so the relationship between genomes and subsystems cannot be
1019 :     derived from the relationships going through the subset.</Notes>
1020 :     </Relationship>
1021 : parrello 1.39 <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
1022 :     <Notes>This relationship connects a feature to the subsystems in which it
1023 :     participates. This is technically redundant information, but it is used
1024 : parrello 1.52 so often that it gets its own table for performance reasons.</Notes>
1025 : parrello 1.40 <Fields>
1026 :     <Field name="genome" type="name-string">
1027 :     <Notes>ID of the genome containing the feature</Notes>
1028 :     </Field>
1029 :     <Field name="type" type="key-string">
1030 :     <Notes>Feature type (eg. peg, rna)</Notes>
1031 :     </Field>
1032 :     </Fields>
1033 :     <ToIndex>
1034 :     <Notes>This index enables the application to view the features of a
1035 :     subsystem sorted by genome and feature type.</Notes>
1036 :     <IndexFields>
1037 :     <IndexField name="genome" order="ascending" />
1038 :     <IndexField name="type" order="ascending" />
1039 :     </IndexFields>
1040 :     </ToIndex>
1041 : parrello 1.39 </Relationship>
1042 : parrello 1.1 </Relationships>
1043 : parrello 1.56 <Shapes>
1044 :     <Shape type="oval" name="Pins">
1045 :     <DisplayInfo theme="nmpdr" col="1" row="4.5" fixed="1" />
1046 :     <Notes>The Pin Server provides information about functional couplings between features.</Notes>
1047 :     </Shape>
1048 :     <Shape type="oval" name="Sims">
1049 :     <DisplayInfo theme="nmpdr" col="1.5" row="5" fixed="1" />
1050 :     <Notes>The Similarity Server contains a high-performance custom database of similarities between features.</Notes>
1051 :     </Shape>
1052 :     <Shape type="oval" name="BBHs">
1053 :     <DisplayInfo theme="nmpdr" col="2" row="5.5" fixed="1" />
1054 :     <Notes>For each feature, the BBH Server has that feature's bidirectional best hits in other genomes.</Notes>
1055 :     </Shape>
1056 :     <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1057 :     <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1058 :     </Shape>
1059 :     </Shapes>
1060 : parrello 1.1 </Database>

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3