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1 : parrello 1.1 <Database>
2 : parrello 1.7 <Title>Sapling Bioinformatics Database</Title>
3 : parrello 1.8 <Notes>[p]The Sapling database is a distributable, self-contained copy of the
4 : parrello 1.6 NMPDR data. Unlike Sprout, which is optimized for searching, Sapling is
5 :     designed to be structurally simple without sacrificing the ability to find
6 : parrello 1.8 information quickly.[/p]
7 :     [p]The diagram colors indicate the way the data is loaded: each color indicates
8 :     a different load group.[/p]
9 :     [list]
10 :     [b]Red[/b] Genome group: includes all taxonomy and sequence data.[*]
11 :     [b]Blue[/b] Subsystem group: includes the subsystems themselves
12 :     and all the subsystem spreadsheets.[*]
13 :     [b]Green[/b] Feature group: includes features, feature identifiers,
14 :     protein sequences, and related publications.[*]
15 :     [b]Yellow[/b] Scenario group: includes KEGG diagrams, scenarios,
16 :     and connections to the related chemical reactions.[*]
17 :     [b]Purple[/b] Drug group: includes PDBs and docking data.[*]
18 :     [b]Navy[/b] Model group: includes compounds, reactions,
19 :     structural cues, and models for the cell chemistry.[*]
20 :     [b]Brown[/b] Annotation group: includes feature annotations,
21 :     FIGfams, and functional coupling data.[*]
22 :     [b]Black[/b] Protein group: includes data from the Annotation
23 :     Clearinghouse.
24 :     [/list]
25 :     [p]In this version of Sapling the Red, Blue, Green, Brown, and Yellow objects
26 :     have been loaded. The Purple, Navy, and Black objects are not yet available.[/p]
27 :     </Notes>
28 : parrello 1.7 <Regions>
29 :     <Region name="Chemistry">
30 :     <Notes>The Chemistry region contains data about reactions and subsystem
31 :     scenarios.</Notes>
32 :     </Region>
33 :     <Region name="Annotations">
34 :     <Notes>The Annotations region contains feature annotation history, information
35 :     about functional coupling, and annotation clearinghouse
36 :     assertions.</Notes>
37 :     </Region>
38 :     <Region name="Models">
39 :     <Notes>The Models region contains data related to genome models.</Notes>
40 :     </Region>
41 :     </Regions>
42 : parrello 1.8 <Diagram height="800" ratio="0.7" size="90" fontSize="12" editable="0"/>
43 : parrello 1.7 <Entities>
44 :     <Entity name="Cluster" keyType="int">
45 :     <DisplayInfo theme="brown">
46 : parrello 1.8 <RegionInfo name="Annotations" row="5" col="3"/>
47 : parrello 1.7 </DisplayInfo>
48 :     <Notes>A cluster is a set of features that occur close to each other
49 :     on a genome and are related by a significant degree of functional
50 :     coupling.</Notes>
51 :     </Entity>
52 :     <Entity name="Compound" keyType="string">
53 : parrello 1.8 <DisplayInfo theme="navy">
54 : parrello 1.7 <RegionInfo name="Chemistry" row="1" col="2"/>
55 : parrello 1.8 <RegionInfo name="Models" col="4" row="1"/>
56 : parrello 1.7 </DisplayInfo>
57 :     <Notes>A compound is a chemical that participates in a reaction. All compounds
58 :     have a unique ID and may also have one or more names. Both ligands and reaction
59 :     components are treated as compounds.</Notes>
60 :     <Fields>
61 :     <Field name="label" type="string">
62 :     <Notes>Primary name of the compound. This is the name used
63 :     in reaction display strings.</Notes>
64 :     </Field>
65 :     </Fields>
66 :     <Indexes>
67 :     <Index>
68 :     <Notes>This index allows searching for compounds by name.</Notes>
69 :     <IndexFields>
70 :     <IndexField name="name" order="ascending"/>
71 :     </IndexFields>
72 :     </Index>
73 :     </Indexes>
74 :     </Entity>
75 :     <Entity name="StructuralCue" keyType="string">
76 : parrello 1.8 <DisplayInfo theme="navy" caption="Structural Cue">
77 :     <RegionInfo name="Models" col="2" row="1"/>
78 : parrello 1.7 </DisplayInfo>
79 :     <Notes>A structural cue is a molecular substructure for a compound that
80 :     is useful to known about.</Notes>
81 :     </Entity>
82 :     <Entity name="AliasType" keyType="string">
83 : parrello 1.8 <DisplayInfo theme="navy">
84 :     <RegionInfo name="Models" col="6" row="1"/>
85 : parrello 1.7 </DisplayInfo>
86 :     <Notes>An alias type describes a kind of alternate name for a compound
87 :     or reaction.</Notes>
88 :     </Entity>
89 :     <Entity name="Diagram" keyType="string">
90 :     <DisplayInfo theme="ivory" col="5" row="3">
91 :     <RegionInfo name="Chemistry" row="3" col="4"/>
92 :     </DisplayInfo>
93 :     <Notes>A functional diagram describes a network of chemical
94 :     reactions, often comprising a single subsystem. A diagram is
95 :     identified by a short name and contains a longer descriptive
96 :     name.</Notes>
97 :     <Fields>
98 :     <Field name="name" type="text">
99 :     <Notes>Descriptive name of this diagram.</Notes>
100 :     </Field>
101 :     <Field name="content" type="image" relation="DiagramContent">
102 :     <Notes>The content of the diagram, in PNG format.</Notes>
103 :     </Field>
104 :     </Fields>
105 :     </Entity>
106 :     <Entity name="Reaction" keyType="string">
107 : parrello 1.8 <DisplayInfo theme="navy" col="3" row="3">
108 : parrello 1.7 <RegionInfo name="Chemistry" row="3" col="2"/>
109 : parrello 1.8 <RegionInfo name="Models" row="3" col="4"/>
110 : parrello 1.7 </DisplayInfo>
111 :     <Notes>A reaction is a chemical process that converts one set of
112 :     compounds (substrate) to another set (products). The reaction ID is
113 :     generally a small number preceded by a letter.</Notes>
114 :     <Fields>
115 :     <Field name="url" type="string" relation="ReactionURL">
116 :     <Notes>HTML string containing a link to a web location that
117 :     describes the reaction. This field is optional.</Notes>
118 :     </Field>
119 :     <Field name="rev" type="boolean">
120 :     <Notes>TRUE if this reaction is reversible, else
121 :     FALSE</Notes>
122 :     </Field>
123 :     </Fields>
124 :     </Entity>
125 :     <Entity name="Subsystem" keyType="string">
126 :     <DisplayInfo theme="blue" col="7" row="3">
127 :     <RegionInfo name="" row="1" col="3"/>
128 :     <RegionInfo name="Chemistry" row="3" col="6"/>
129 :     </DisplayInfo>
130 :     <Notes>A subsystem is a collection of roles that work together in a
131 :     cell. Identification of subsystems is an important tool for
132 :     recognizing parallel genetic features in different organisms. The
133 :     key is subsystem name.</Notes>
134 :     <Asides>The subsystem name used to come in two forms-- a natural form
135 :     with spaces and an internal form with underscores. In this database we
136 :     will only have the natural form.</Asides>
137 :     <Fields>
138 :     <Field name="version" type="int">
139 :     <Notes>Version number for the subsystem. This value is
140 :     incremented each time the subsystem is backed up.</Notes>
141 :     </Field>
142 :     <Field name="curator" type="string">
143 :     <Notes>Name of the person currently in charge of the
144 :     subsystem.</Notes>
145 :     </Field>
146 :     <Field name="notes" type="text">
147 :     <Notes>Descriptive notes about the subsystem.</Notes>
148 :     </Field>
149 :     <Field name="description" type="text">
150 :     <Notes>Description of the subsystem's function in the
151 :     cell.</Notes>
152 :     </Field>
153 :     </Fields>
154 :     </Entity>
155 :     <Entity name="SubsystemClass" keyType="string">
156 :     <DisplayInfo theme="blue" caption="Subsystem Class">
157 :     <RegionInfo name="" row="1" col="5"/>
158 :     <RegionInfo name="Chemistry" row="5" col="6"/>
159 :     </DisplayInfo>
160 :     <Notes>Subsystem classes impose a hierarchical organization on the
161 :     subsystems.</Notes>
162 :     </Entity>
163 :     <Entity name="Publication" keyType="hash-string">
164 :     <DisplayInfo theme="green" col="1" row="8">
165 : parrello 1.8 <RegionInfo name="" row="3" col="1"/>
166 : parrello 1.7 </DisplayInfo>
167 :     <Notes>A publication is an article or citation that may be used as
168 :     evidence for assertions made in the database. The key is a hash code
169 :     computed from the original URL. We expect almost all of the articles to
170 :     be in PUBMED, but this object has been implemented in a slightly
171 :     more general fashion just in case.</Notes>
172 :     <Fields>
173 :     <Field name="citation" type="link">
174 :     <Notes>Hyperlink of the article. The text is the article title.</Notes>
175 :     </Field>
176 :     </Fields>
177 :     <Indexes>
178 :     <Index>
179 :     <Notes>This index provides the ability to search by article
180 :     title. It should only be used for LIKE-style searches, since
181 :     the article titles are encoded together with the URLs.</Notes>
182 :     <IndexFields>
183 :     <IndexField name="citation" order="ascending"/>
184 :     </IndexFields>
185 :     </Index>
186 :     </Indexes>
187 :     </Entity>
188 :     <Entity name="Variant" keyType="string">
189 :     <DisplayInfo theme="blue" col="7" row="5">
190 :     <RegionInfo name="" row="3" col="5"/>
191 :     </DisplayInfo>
192 :     <Notes>A variant is a functional subset of a subsystem. It indicates
193 :     the particular sequence of roles used to implement a metabolic
194 :     pathway. Variants are abstract concepts used to classify machines.
195 :     The key of the variant is the subsystem ID followed by the variant
196 :     code.</Notes>
197 :     <Asides>The variant code is generally a number with zero or more
198 :     decimal points, similar to what it done with software version numbers
199 :     or legal outline numbers.</Asides>
200 :     <Fields>
201 :     <Field name="role-rule" type="text">
202 :     <Notes>Boolean expression (encoded as text) that describes
203 :     the roles in this variant. The roles themselves are
204 :     represented by their IDs.</Notes>
205 :     </Field>
206 :     <Field name="comment" type="text">
207 :     <Notes>Commentary text about the variant.</Notes>
208 :     </Field>
209 :     </Fields>
210 :     </Entity>
211 :     <Entity name="ProteinSequence" keyType="hash-string">
212 :     <DisplayInfo theme="green" col="3" row="7" caption="Protein Sequence">
213 : parrello 1.8 <RegionInfo name="" row="5" col="1"/>
214 : parrello 1.7 <RegionInfo name="Chemistry" row="7" col="2"/>
215 :     <RegionInfo name="Annotations" row="3" col="1"/>
216 :     </DisplayInfo>
217 :     <Notes>A protein sequence is a specific sequence of amino acids.
218 :     Unlike a DNA sequence, a protein sequence does not belong to a
219 :     genome. Identical proteins generated by different genomes are
220 :     generally stored as a single ProteinSequence instance. The key is a
221 :     hash code computed from the protein letter sequence.</Notes>
222 :     <Fields>
223 :     <Field name="sequence" type="text">
224 :     <Notes>The sequence contains the letters corresponding to
225 :     the protein's amino acids.</Notes>
226 :     </Field>
227 :     </Fields>
228 :     </Entity>
229 :     <Entity name="Family" keyType="string">
230 :     <DisplayInfo theme="brown" col="4" row="11">
231 :     <RegionInfo name="Annotations" row="1" col="5"/>
232 :     </DisplayInfo>
233 :     <Notes>A family is a group of features united by a particular
234 :     determination algorithm. The algorithm will frequently-- but not
235 :     always-- signify a functional role. The key is a character code for
236 :     the kind of family (generally two or three letters) followed by
237 :     the family's ID number.</Notes>
238 :     <Fields>
239 :     <Field name="native-name" type="string" relation="FamilyName">
240 :     <Notes>This is an optional common or descriptive name for the
241 :     family. If the family uses a naming scheme that does
242 :     not translate to the standard ID format, the real name
243 :     is put in here.</Notes>
244 :     </Field>
245 :     </Fields>
246 :     <Indexes>
247 :     <Index>
248 :     <Notes>This index enables the user to find a family by its
249 :     native name.</Notes>
250 :     <IndexFields>
251 :     <IndexField name="native-name" order="ascending"/>
252 :     <IndexField name="id" order="ascending"/>
253 :     </IndexFields>
254 :     </Index>
255 :     </Indexes>
256 :     </Entity>
257 :     <Entity name="MolecularMachine" keyType="hash-string">
258 :     <DisplayInfo theme="blue" col="7" row="7" caption="Molecular\nMachine">
259 :     <RegionInfo name="" row="5" col="5"/>
260 :     </DisplayInfo>
261 :     <Notes>A molecular machine is a collection of features that
262 :     implements a metabolic pathway. Machines are the physical instances
263 :     of variants. Each machine corresponds to a row in a subsystem
264 :     spreadsheet. The key is an MD5 hash formed from a comma-separated list
265 :     containing the variant key, the Genome ID, and an optional region
266 :     string.</Notes>
267 :     <Asides>It is possible for a single subsystem to occur multiple times
268 :     in a particular genome. If that is the case, then the subsystem will
269 :     have a molecular machine for each occurrence. The sequence number used
270 :     in forming the key insures that each machine has a unique ID.</Asides>
271 :     <Fields>
272 :     <Field name="type" type="string">
273 :     <Notes>The machine type indicates how the machine relates to
274 :     the parent variant. A type of "vacant" means that the
275 :     machine does not appear to actually exist in the organism. A
276 :     type of "incomplete" means that the machine appears to be
277 :     missing many reactions. In all other cases, the type is
278 :     "normal".</Notes>
279 :     </Field>
280 :     <Field name="curated" type="boolean">
281 :     <Notes>This flag is TRUE if the assignment of the molecular
282 :     machine has been curated, and FALSE if it was made by an
283 :     automated program.</Notes>
284 :     </Field>
285 :     <Field name="region" type="string">
286 :     <Notes>Region in the genome for which the machine is relevant.
287 :     Normally, this is an empty string, indicating that the machine
288 :     covers the whole genome. If a subsystem has multiple machines
289 :     for a genome, this contains a location string describing the
290 :     region occupied by this particular machine.</Notes>
291 :     </Field>
292 :     </Fields>
293 :     </Entity>
294 :     <Entity name="Pairing" keyType="string">
295 :     <DisplayInfo theme="brown" col="5" row="11">
296 :     <RegionInfo name="Annotations" row="3" col="5"/>
297 :     </DisplayInfo>
298 : parrello 1.8 <Notes>A pairing indicates that two features are found
299 :     close together in a genome. Not all possible pairings are stored in
300 :     the database; only those that are considered for some reason to be
301 :     significant for annotation purposes.The key of the pairing is the
302 :     concatenation of the feature IDs in alphabetical order with an
303 :     intervening colon.</Notes>
304 :     <Asides>Theoretically, the pairing is unordered: (A,B) and (B,A) are the
305 :     same pairing. It is frequently the case, however, that we need to refer to
306 :     the "first" or "second" protein in the pairing. When this happens, the
307 :     first one is always the protein with the alphabetically lesser key. The
308 :     IsInPair relationship automatically shows the proteins in this
309 : parrello 1.7 order.</Asides>
310 :     </Entity>
311 :     <Entity name="Genome" keyType="float">
312 : parrello 1.8 <DisplayInfo theme="red">
313 :     <RegionInfo name="Models" col="6" row="7"/>
314 : parrello 1.7 <RegionInfo name="Chemistry" col="6" row="7"/>
315 :     <RegionInfo name="Annotations" row="1" col="3"/>
316 :     <RegionInfo name="" row="7" col="5"/>
317 :     </DisplayInfo>
318 :     <Notes>A genome represents a specific organism with DNA, or a
319 :     specific meta-genome. All DNA sequences in the database belong to
320 :     genomes.</Notes>
321 :     <Fields>
322 :     <Field name="scientific-name" type="string">
323 :     <Notes>Full genus/species/strain name of the genome.</Notes>
324 :     </Field>
325 :     <Field name="complete" type="boolean">
326 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
327 :     </Field>
328 :     <Field name="dna-size" type="counter">
329 :     <Notes>Number of base pairs in the genome.</Notes>
330 :     </Field>
331 :     <Field name="contigs" type="int">
332 :     <Notes>Number of contigs for this genome.</Notes>
333 :     </Field>
334 :     <Field name="pegs" type="int">
335 :     <Notes>Number of protein encoding genes for this genome.</Notes>
336 :     </Field>
337 :     <Field name="rnas" type="int">
338 :     <Notes>Number of RNA features found for this organism.</Notes>
339 :     </Field>
340 :     </Fields>
341 :     <Indexes>
342 :     <Index>
343 :     <Notes>This index allows the applications to find all
344 :     genomes in lexical order by name.</Notes>
345 :     <IndexFields>
346 :     <IndexField name="scientific-name" order="ascending"/>
347 :     </IndexFields>
348 :     </Index>
349 :     </Indexes>
350 :     </Entity>
351 :     <Entity name="Annotation" keyType="string">
352 :     <DisplayInfo col="3" row="11" theme="brown">
353 :     <RegionInfo name="Annotations" row="1" col="1"/>
354 :     </DisplayInfo>
355 :     <Notes>An annotation is a comment attached to a feature. Annotations
356 :     are used to track the history of a feature's functional assignments
357 :     and any related issues. The key is the feature ID followed by a
358 : parrello 1.8 colon and an complemented ten-digit sequence number.</Notes>
359 : parrello 1.7 <Asides>The complemented sequence number causes the annotations to
360 :     sort with the most recent one first.</Asides>
361 :     <Fields>
362 :     <Field name="annotator" type="string">
363 :     <Notes>Name of the annotator who made the comment.</Notes>
364 :     </Field>
365 :     <Field name="comment" type="text">
366 :     <Notes>Text of the annotation.</Notes>
367 :     </Field>
368 :     <Field name="annotation-time" type="date">
369 :     <Notes>Date and time at which the annotation was made.</Notes>
370 :     </Field>
371 :     </Fields>
372 :     </Entity>
373 :     <Entity name="RoleSet" keyType="int">
374 :     <DisplayInfo theme="navy" col="3" row="5" caption="Role Set">
375 :     <RegionInfo name="Chemistry" row="5" col="2"/>
376 : parrello 1.8 <RegionInfo name="Models" row="3" col="2"/>
377 : parrello 1.7 </DisplayInfo>
378 :     <Notes>A role set is a group of roles that work together to
379 :     stimulate a reaction. Most role sets consist of a single role;
380 :     however, some reactions require the presence of multiple roles to
381 :     get them started.</Notes>
382 :     <Asides>A reaction is usually triggered by a single role, but some
383 :     reactions are triggered by a boolean combination of roles (e.g. =(A
384 :     and (B or C) and D) or (E and B and F) or G=). The boolean
385 :     expression can be converted into disjunctive normal form, which is a
386 :     list of alternative sets (e.g. =(A and B and D) or (A and C and D)
387 :     or (E and B and F) or G=). Each alternative is then converted into a
388 :     role set. This allows us to precisely represent the triggering
389 :     conditions of a reaction in the database.</Asides>
390 :     </Entity>
391 :     <Entity name="Contig" keyType="string">
392 :     <DisplayInfo theme="red" col="7" row="11">
393 :     <RegionInfo name="" row="9" col="3"/>
394 :     </DisplayInfo>
395 :     <Notes>A contig is a contiguous sequence of base pairs belonging to
396 :     a single genome. The key of the contig is the genome ID followed
397 :     by a colon and then the contig ID.</Notes>
398 :     <Fields>
399 :     <Field name="length" type="counter">
400 :     <Notes>Number of base pairs in the contig.</Notes>
401 :     </Field>
402 :     </Fields>
403 :     </Entity>
404 :     <Entity name="DNASequence" keyType="string">
405 :     <DisplayInfo theme="red" col="7" row="13">
406 : parrello 1.8 <RegionInfo name="" row="9" col="1"/>
407 : parrello 1.7 </DisplayInfo>
408 :     <Notes>A DNA sequence is a segment of a contig. Contigs are broken
409 :     into multiple DNA sequences in order to prevent problems that might
410 :     arise from loading an entire contig into memory when it consists of
411 :     a billion or more base pairs.</Notes>
412 :     <Asides>The maximum length of a DNA sequence is one million bases.
413 :     The key is the contigID followed by a 7-digit ordinal number. So,
414 :     the first sequence will have an ordinal of 0000000 and contain the base
415 :     pairs from position 1 to position 1,000,000, the second will have an
416 :     ordinal of 0000001 and contain the pairs from position 1,000,001 to
417 :     2,000,000, and so forth. This will allow us to store 10 trillion
418 :     base pairs per contig.</Asides>
419 :     <Fields>
420 :     <Field name="sequence" type="dna">
421 :     <Notes>Base pairs that make up this sequence.</Notes>
422 :     </Field>
423 :     </Fields>
424 :     </Entity>
425 :     <Entity name="Structure" keyType="string">
426 : parrello 1.8 <DisplayInfo theme="purple" col="2" row="5">
427 : parrello 1.7 <RegionInfo name="Chemistry" row="5" col="1"/>
428 :     </DisplayInfo>
429 :     <Notes>A structure is the geometrical representation of a protein
430 :     sequence. A single protein sequence may have multiple structural
431 :     representations, either because it is folded in different ways or
432 :     because there are alternative representation formats. The key field
433 : parrello 1.8 is the representation type (currently only PDB) followed by
434 : parrello 1.7 a colon and the ID.</Notes>
435 :     </Entity>
436 :     <Entity name="EcNumber" keyType="string">
437 :     <DisplayInfo theme="navy" col="3" row="7" caption="EC\nNumber">
438 : parrello 1.8 <RegionInfo name="Models" row="5" col="2"/>
439 : parrello 1.7 </DisplayInfo>
440 :     <Notes>EC numbers are assigned by the Enzyme Commission, and consist
441 :     of four numbers separated by periods, each indicating a successively
442 :     smaller cateogry of enzymes.</Notes>
443 :     </Entity>
444 :     <Entity name="MachineRole" keyType="string">
445 :     <DisplayInfo row="7" col="5" caption="Machine Role" theme="blue">
446 :     <RegionInfo name="" row="5" col="3"/>
447 :     </DisplayInfo>
448 :     <Notes>A machine role represents a role as it occurs in a molecular
449 :     machine. The key is the machine key plus the role
450 :     abbreviation.</Notes>
451 :     <Asides>The machine role corresponds to a cell on the subsystem
452 :     spreadsheet. Features in the subsystem are assigned directly to the
453 :     machine role.</Asides>
454 :     </Entity>
455 :     <Entity name="Model" keyType="string">
456 :     <DisplayInfo col="7" row="7" theme="navy">
457 : parrello 1.8 <RegionInfo name="Models" row="5" col="6"/>
458 : parrello 1.7 </DisplayInfo>
459 :     <Notes>A model specifies a relationship between sets of features and
460 :     reactions in a cell. It is used to simulate cell growth and gene
461 :     knockouts to validate annotations.</Notes>
462 :     </Entity>
463 :     <Entity name="FeatureSet" keyType="hash-string">
464 :     <DisplayInfo theme="navy" col="5" row="7">
465 : parrello 1.8 <RegionInfo name="Models" row="5" col="4"/>
466 : parrello 1.7 </DisplayInfo>
467 :     <Notes>A feature set is a group of features that implement a reaction
468 :     in a particular model.</Notes>
469 :     <Asides>The key is a hash string computed from the model name and a
470 :     sorted list of the initial features in the set.</Asides>
471 :     </Entity>
472 :     <Entity name="GenomeSet" keyType="string">
473 :     <DisplayInfo theme="red">
474 : parrello 1.8 <RegionInfo name="" row="5" col="6"/>
475 : parrello 1.7 </DisplayInfo>
476 :     <Notes>A genome set is a named group of related genomes.</Notes>
477 :     </Entity>
478 :     <Entity name="Source" keyType="string">
479 : parrello 1.8 <DisplayInfo theme="black">
480 : parrello 1.7 <RegionInfo name="Annotations" row="7" col="1"/>
481 :     </DisplayInfo>
482 :     <Notes>A source is a user or organization that is permitted to make assertions
483 :     about identifiers.</Notes>
484 :     </Entity>
485 :     <Entity name="PairSet" keyType="int">
486 :     <DisplayInfo theme="brown" col="5" row="13" caption="Pair Set">
487 :     <RegionInfo name="Annotations" row="5" col="5"/>
488 :     </DisplayInfo>
489 :     <Notes>A pair set indicates evidence for a functional connection between
490 :     protein sequence pairs. The protein sequences possessing the connection
491 :     are the ones that participate in the evidence set's pairings.</Notes>
492 :     <Asides>The pairings for a particular evidence set will contain
493 :     protein sequences that are significantly similar. In other words, if
494 :     (A,B) and (X,Y) are both pairings in a single evidence set, then (A
495 :     =~ X) and (B =~ Y) or (A =~ Y) and (B =~ X), depending on the value
496 :     of the "inverted" attribute of the IsDeterminedBy relationship.
497 :     Essentially, a pairing in its own right is unordered. If (A,B) is a
498 :     pair, then so is (B,A). However, the evidence set maintains a
499 :     correspondence between its pairs that _is_ ordered, because the
500 :     constituent pairs must match. The direction in which a pair matches
501 :     others in the set is an attribute of the relationship from the pairs
502 :     to the sets.</Asides>
503 :     <Fields>
504 :     <Field name="score" type="int">
505 :     <Notes>Score for this evidence set. The score indicates the
506 :     number of significantly different genomes represented by the
507 :     pairings.</Notes>
508 :     </Field>
509 :     </Fields>
510 :     </Entity>
511 :     <Entity name="Role" keyType="string">
512 :     <DisplayInfo theme="blue" col="5" row="5">
513 :     <RegionInfo name="" row="3" col="3"/>
514 :     <RegionInfo name="Chemistry" row="5" col="4"/>
515 : parrello 1.8 <RegionInfo name="Models" col="2" row="7"/>
516 : parrello 1.7 </DisplayInfo>
517 :     <Notes>A role describes a biological function that may be fulfilled
518 :     by a feature. One of the main goals of the database is to assign
519 :     features to roles. Most roles are effected by the construction of
520 :     proteins. Some, however, deal with functional regulation and message
521 :     transmission.</Notes>
522 :     <Asides>A role represents a single gene function. Only roles in
523 :     subsystems are represented in this way. The key of the role
524 :     is a hash code computed from the name.</Asides>
525 :     <Fields>
526 :     <Field name="hypothetical" type="boolean">
527 :     <Notes>TRUE if a role is hypothetical, else FALSE</Notes>
528 :     </Field>
529 :     </Fields>
530 :     </Entity>
531 :     <Entity name="Feature" keyType="string">
532 :     <DisplayInfo theme="green">
533 : parrello 1.8 <RegionInfo name="Models" col="4" row="7"/>
534 : parrello 1.7 <RegionInfo name="Chemistry" col="4" row="7"/>
535 :     <RegionInfo name="" col="3" row="7"/>
536 :     <RegionInfo name="Annotations" col="3" row="3"/>
537 :     </DisplayInfo>
538 :     <Notes>A feature (sometimes also called a gene) is a part of a
539 :     genome that is of special interest. Features may be spread across
540 :     multiple DNA sequences (contigs) of a genome, but never across more
541 :     than one genome. Each feature in the database has a unique FIG
542 :     ID that functions as its ID in this table.</Notes>
543 :     <Fields>
544 :     <Field name="feature-type" type="string">
545 :     <Notes>Code indicating the type of this feature. Among the
546 :     codes currently supported are "peg" for a protein encoding
547 :     gene, "bs" for a binding site, "opr" for an operon, and so
548 :     forth.</Notes>
549 :     </Field>
550 :     <Field name="link" type="text" relation="FeatureLink">
551 :     <Notes>Web hyperlink for this feature. A feature can have no
552 :     hyperlinks or it can have many. The links are to other
553 :     websites that have useful about the gene that the feature
554 :     represents, and are coded as raw HTML, using an anchor href
555 :     tag.</Notes>
556 :     </Field>
557 :     <Field name="essential" type="link" relation="FeatureEssential" special="property_search">
558 :     <Notes>A value indicating the essentiality of the feature,
559 :     In most cases, this will be a word describing whether the
560 :     essentiality is confirmed (essential) or potential
561 :     (potential-essential), hyperlinked to the document
562 :     from which the essentiality was curated. If a feature is not
563 :     essential, this field will have no values; otherwise, it may
564 :     have multiple values.</Notes>
565 :     </Field>
566 :     <Field name="virulent" type="link" relation="FeatureVirulent" special="property_search">
567 :     <Notes>A value indicating the virulence of the feature,
568 :     coded as HTML. In most cases, this will be a phrase or SA
569 :     number hyperlinked to the document from which the virulence
570 :     information was curated. If the feature is not virulent,
571 :     this field will have no values; otherwise, it may have
572 :     multiple values.</Notes>
573 :     </Field>
574 :     <Field name="sequence-length" type="counter">
575 :     <Notes>Number of base pairs in this feature.</Notes>
576 :     </Field>
577 :     <Field name="evidence-code" type="string" relation="FeatureEvidence">
578 :     <Notes>An evidence code describes the possible evidence that
579 :     exists for deciding a feature's functional assignment. A
580 :     feature may have no evidence, a single evidence code, or
581 :     several.</Notes>
582 :     </Field>
583 :     <Field name="locked" type="boolean">
584 :     <Notes>If TRUE, then this feature is locked and its functional
585 :     role assignment cannot be changed.</Notes>
586 :     </Field>
587 :     <Field name="function" type="text">
588 :     <Notes>Functional assignment for this feature. This will
589 :     often indicate the feature's functional role or roles, and
590 :     may also have comments.</Notes>
591 :     <Asides>It will frequently be the case that a feature is
592 :     assigned to a single role, and it is identical to the
593 :     function. In some cases, a feature will have multiple roles,
594 :     and all of them will be listed in the function field. In
595 :     addition, the function may have comment text at the
596 :     end.</Asides>
597 :     </Field>
598 :     </Fields>
599 :     </Entity>
600 :     <Entity name="Identifier" keyType="string">
601 :     <DisplayInfo theme="green" col="3" row="9">
602 : parrello 1.8 <RegionInfo name="" row="7" col="1"/>
603 : parrello 1.7 <RegionInfo name="Annotations" row="5" col="1"/>
604 :     </DisplayInfo>
605 :     <Notes>An identifier is an alternate name for a feature or a protein
606 :     sequence.</Notes>
607 :     <Asides>Identifiers are preferentially associated with features; however, in
608 :     some cases the precise feature named by an external identifier cannot be
609 :     computed; in this case, the identifier is associated with the protein
610 :     sequence. Identifiers are stored in a prefixed format that insures identifiers
611 :     from different sources have different IDs.</Asides>
612 :     <Fields>
613 :     <Field name="source" type="string">
614 :     <Notes>Specific type of the identifier, such as its source
615 :     database or category. The type can usually be decoded to
616 :     convert the identifier to a URL.</Notes>
617 :     </Field>
618 :     <Field name="natural-form" type="string">
619 :     <Notes>Natural form of the identifier. This is how the identifier looks
620 :     without the identifying prefix (if one is present).</Notes>
621 :     </Field>
622 :     </Fields>
623 :     <Indexes>
624 :     <Index>
625 :     <Notes>This index allows all the identifiers of a specified
626 :     type to be located.</Notes>
627 :     <IndexFields>
628 :     <IndexField name="source" order="ascending"/>
629 :     <IndexField name="id" order="ascending"/>
630 :     </IndexFields>
631 :     </Index>
632 :     <Index>
633 :     <Notes>This index allows looking up a natural identifier (that is,
634 :     one without the identifying prefix..</Notes>
635 :     <IndexFields>
636 :     <IndexField name="natural-form" order="ascending"/>
637 :     </IndexFields>
638 :     </Index>
639 :     </Indexes>
640 :     </Entity>
641 :     <Entity name="Scenario" keyType="string">
642 :     <DisplayInfo theme="ivory" col="5" row="1">
643 :     <RegionInfo name="Chemistry" row="1" col="4"/>
644 :     </DisplayInfo>
645 :     <Notes>A scenario is a partial instance of a subsystem with a
646 :     defined set of reactions. Each scenario converrts input compounds to
647 :     output compounds using reactions. The scenario may use all of the
648 :     reactions controlled by a subsystem or only some, and may also
649 :     incorporate additional reactions.</Notes>
650 :     </Entity>
651 :     <Entity name="TaxonomicGrouping" keyType="float">
652 :     <DisplayInfo row="8" col="7" caption="Taxonomic\nGrouping" theme="red">
653 :     <RegionInfo name="" row="9" col="5"/>
654 :     </DisplayInfo>
655 :     <Notes>A taxonomic grouping is a segment of the classification for
656 :     an organism. Taxonomic groupings are organized into a strict
657 :     hierarchy by the IsGroupContaining relationship.</Notes>
658 :     <Fields>
659 :     <Field name="domain" type="boolean">
660 :     <Notes>TRUE if this is a domain grouping, else FALSE.</Notes>
661 :     </Field>
662 :     <Field name="hidden" type="boolean">
663 :     <Notes>TRUE if this is a hidden grouping, else FALSE. Hidden groupings
664 :     are not typically shown in a lineage list.</Notes>
665 :     </Field>
666 :     <Field name="scientific-name" type="string">
667 :     <Notes>Primary scientific name for this grouping. This is the name used
668 :     when displaying a taxonomy.</Notes>
669 :     </Field>
670 :     <Field name="alias" type="string" relation="TaxonomicGroupingAlias">
671 :     <Notes>Alternate name for this grouping. A grouping
672 :     may have many alternate names. The scientific name should also
673 :     be in this list.</Notes>
674 :     </Field>
675 :     </Fields>
676 :     <Indexes>
677 :     <Index>
678 :     <Notes>This index allows the user to find a particular
679 :     taxonomic grouping by name. Because the scientifc name is
680 :     also an alias, there is no index on scientific name.</Notes>
681 :     <IndexFields>
682 :     <IndexField name="alias" order="ascending"/>
683 :     </IndexFields>
684 :     </Index>
685 :     </Indexes>
686 :     </Entity>
687 :     </Entities>
688 :     <Relationships>
689 :     <Relationship name="IsFoundIn" arity="MM" from="StructuralCue" to="Compound" converse="IsComprisedOf">
690 : parrello 1.8 <DisplayInfo theme="navy" caption="Is\nFound\nIn">
691 :     <RegionInfo name="Models"/>
692 : parrello 1.7 </DisplayInfo>
693 :     <Notes>This relationship connects a compound to the known structural cues.
694 :     The structural cues enable the application to query compounds by molecular
695 :     structure.</Notes>
696 :     <Fields>
697 :     <Field name="count" type="int">
698 :     <Notes>Number of times the cue occurs in the compound.</Notes>
699 :     </Field>
700 :     </Fields>
701 :     </Relationship>
702 :     <Relationship name="HasAliasOf" arity="MM" from="Compound" to="AliasType" converse="IsAliasOf">
703 : parrello 1.8 <DisplayInfo theme="navy">
704 :     <RegionInfo name="Models" caption="Has\nAlias\nOf"/>
705 : parrello 1.7 </DisplayInfo>
706 :     <Notes>This relationship is used to find all the alternate names for a
707 :     compound.</Notes>
708 :     <Fields>
709 :     <Field name="alias" type="string">
710 :     <Notes>This is the actual alias used, and is frequently the main point of
711 :     access for this relationship.</Notes>
712 :     </Field>
713 :     </Fields>
714 :     <FromIndex>
715 :     <Notes>This index allows the application to find a particular alias if the
716 :     type is known.</Notes>
717 :     <IndexFields>
718 : parrello 1.8 <IndexField name="alias" order="ascending"/>
719 : parrello 1.7 </IndexFields>
720 :     </FromIndex>
721 :     <Indexes>
722 :     <Index>
723 :     <Notes>This index can be used to find a particular alias when the type is
724 :     not known.</Notes>
725 :     <IndexFields>
726 : parrello 1.8 <IndexField name="alias" order="ascending"/>
727 : parrello 1.7 </IndexFields>
728 :     </Index>
729 :     </Indexes>
730 :     </Relationship>
731 :     <Relationship name="HasReactionAliasOf" arity="MM" from="Reaction" to="AliasType" converse="IsAliasOfReaction">
732 : parrello 1.8 <DisplayInfo theme="navy">
733 :     <RegionInfo name="Models" caption="Has\nReaction\nAlias Of"/>
734 : parrello 1.7 </DisplayInfo>
735 :     <Notes>This relationship is used to find all the alternate names for a
736 :     reaction.</Notes>
737 :     <Fields>
738 :     <Field name="alias" type="string">
739 :     <Notes>This is the actual alias used, and is frequently the main point of
740 :     access for this relationship.</Notes>
741 :     </Field>
742 :     </Fields>
743 :     <FromIndex>
744 :     <Notes>This index allows the application to find a particular alias if the
745 :     type is known.</Notes>
746 :     <IndexFields>
747 : parrello 1.8 <IndexField name="alias" order="ascending"/>
748 : parrello 1.7 </IndexFields>
749 :     </FromIndex>
750 :     <Indexes>
751 :     <Index>
752 :     <Notes>This index can be used to find a particular alias when the type is
753 :     not known.</Notes>
754 :     <IndexFields>
755 : parrello 1.8 <IndexField name="alias" order="ascending"/>
756 : parrello 1.7 </IndexFields>
757 :     </Index>
758 :     </Indexes>
759 :     </Relationship>
760 :     <Relationship name="OccursIn" arity="MM" from="Feature" to="Cluster" converse="IsOccurrenceOf">
761 :     <DisplayInfo theme="brown" caption="Occurs In">
762 : parrello 1.8 <RegionInfo name="Annotations"/>
763 : parrello 1.7 </DisplayInfo>
764 :     <Notes>This relationship connects features to clusters. It is generally expected
765 :     that the presence of features in a cluster indicates a functional relationship.</Notes>
766 :     </Relationship>
767 :     <Relationship name="IsCategorizedInto" arity="MM" from="Reaction" to="EcNumber" converse="Categorizes">
768 :     <DisplayInfo theme="navy" caption="Is\nCategorized\nInto">
769 :     <RegionInfo name="Models"/>
770 :     </DisplayInfo>
771 :     <Notes>This relationship connects an EC number to reactions that are consistent
772 :     with the chemistry described by the EC class.</Notes>
773 :     </Relationship>
774 :     <Relationship name="IsConsistentWith" arity="MM" from="EcNumber" to="Role">
775 :     <DisplayInfo theme="navy" caption="Is\nConsistent\nWith">
776 :     <RegionInfo name="Models"/>
777 :     </DisplayInfo>
778 :     <Notes>This relationship connects a functional role to the EC numbers consistent
779 :     with the chemistry described in the role.</Notes>
780 :     </Relationship>
781 :     <Relationship name="IsSetOf" from="FeatureSet" to="Feature" arity="MM" converse="IsInSet">
782 :     <DisplayInfo theme="navy" caption="Is\nSet\nOf">
783 :     <RegionInfo name="Models"/>
784 :     </DisplayInfo>
785 :     <Notes>This relationship connects a feature set to its constituent features.
786 :     All of the features in a set must be present for a set to stimulate a
787 :     reaction.</Notes>
788 :     </Relationship>
789 :     <Relationship name="IsStimulatedBy" from="Reaction" to="FeatureSet" arity="MM" converse="Stimulates">
790 :     <DisplayInfo theme="navy" caption="Is\nStimulated\nBy">
791 : parrello 1.8 <RegionInfo name="Models"/>
792 : parrello 1.7 </DisplayInfo>
793 :     <Notes>In the context of a model, a reaction is stimulated when all features
794 :     in a feature set are present. By comparing feature sets to role sets we
795 :     can determine whether a model is consistent with annotations.</Notes>
796 :     </Relationship>
797 :     <Relationship name="IsModeledBy" arity="1M" from="Genome" to="Model" converse="Models">
798 :     <DisplayInfo theme="navy" caption="Models">
799 :     <RegionInfo name="Models"/>
800 :     </DisplayInfo>
801 :     <Notes>A genome can be modeled by many different models, but a model belongs
802 :     to only one genome.</Notes>
803 :     </Relationship>
804 :     <Relationship name="IsRequiredBy" arity="MM" from="Reaction" to="Model" converse="Requires">
805 :     <DisplayInfo theme="navy" caption="Is\nRequired\nBy">
806 :     <RegionInfo name="Models"/>
807 :     </DisplayInfo>
808 :     <Notes>This relationship specifies the reactions that occur in the model.
809 :     The direction is an attribute of this relationship.</Notes>
810 :     <Fields>
811 :     <Field name="direction" type="char">
812 :     <Notes>This field indicates the direction in which the reaction
813 :     operates in the context of the model. The values are 'F' (forward),
814 :     'R' (reverse) and 'B' (both).</Notes>
815 :     </Field>
816 :     </Fields>
817 :     </Relationship>
818 :     <Relationship name="IsTerminusFor" from="Compound" to="Scenario" arity="MM" converse="HasAsTerminus">
819 :     <DisplayInfo caption="Has As\nTerminus" theme="ivory">
820 :     <RegionInfo name="Chemistry"/>
821 :     </DisplayInfo>
822 :     <Notes>A terminus for a scenario is a compound that acts as its
823 :     input or output. A compound can be the terminus for many scenarios,
824 :     and a scenario will have many termini. The relationship attributes
825 :     indicate whether the compound is an input to the scenario or an
826 :     output. In some cases, there may be multiple alternative output
827 :     groups. This is also indicated by the attributes.</Notes>
828 :     <Fields>
829 :     <Field name="group-number" type="int">
830 :     <Notes>If zero, then the compound is an input. If one, the compound is
831 :     an output. If two, the compound is an auxiliary output.</Notes>
832 :     </Field>
833 :     </Fields>
834 :     <ToIndex>
835 :     <Notes>This index allows the application to view a scenario's
836 :     compounds by group.</Notes>
837 :     <IndexFields>
838 :     <IndexField name="group-number" order="ascending"/>
839 :     </IndexFields>
840 :     </ToIndex>
841 :     </Relationship>
842 :     <Relationship name="IsSuperclassOf" arity="1M" from="SubsystemClass" to="SubsystemClass" converse="IsSubclassOf">
843 :     <DisplayInfo caption="Is\nSuperclass\nOf" theme="blue" col="7" row="1" fixed="1">
844 :     <RegionInfo name="" row="1" col="6"/>
845 : parrello 1.8 <RegionInfo name="Chemistry" row="6" col="6" caption="Is\nSubclass\nOf" />
846 : parrello 1.7 </DisplayInfo>
847 :     <Notes>This is a recursive relationship that imposes a hierarchy on
848 :     the subsystem classes.</Notes>
849 :     </Relationship>
850 :     <Relationship name="Describes" from="Subsystem" to="Variant" arity="1M" converse="IsDescribedBy">
851 :     <DisplayInfo theme="blue">
852 :     <RegionInfo name=""/>
853 :     </DisplayInfo>
854 :     <Notes>This relationship connects a subsystem to the individual
855 :     variants used to implement it. Each variant contains a slightly
856 :     different subset of the roles in the parent subsystem.</Notes>
857 :     </Relationship>
858 :     <Relationship name="Displays" from="Diagram" to="Reaction" arity="MM" converse="IsDisplayedOn">
859 : parrello 1.8 <DisplayInfo theme="ivory" caption="Is\nDisplayed\nOn">
860 : parrello 1.7 <RegionInfo name="Chemistry"/>
861 :     </DisplayInfo>
862 :     <Notes>This relationship connects a diagram to its reactions. A
863 :     diagram shows multiple reactions, and a reaction can be on many
864 :     diagrams.</Notes>
865 : parrello 1.8 <Fields>
866 :     <Field name="location" type="rectangle">
867 :     <Notes>Location of the reaction's node on the diagram.</Notes>
868 :     </Field>
869 :     </Fields>
870 :     </Relationship>
871 :     <Relationship name="IsRelevantFor" from="Diagram" to="Subsystem" arity="MM" converse="IsRelevantTo">
872 :     <DisplayInfo theme="ivory" caption="Is\nRelevant\nFor">
873 :     <RegionInfo name="Chemistry" />
874 :     </DisplayInfo>
875 :     <Notes>This relationship connects a diagram to the subsystems that are depicted on
876 :     it. Only diagrams which are useful in curating or annotation the subsystem are
877 :     specified in this relationship.</Notes>
878 : parrello 1.7 </Relationship>
879 :     <Relationship name="IsImplementedBy" from="Variant" to="MolecularMachine" arity="1M" converse="Implements">
880 :     <DisplayInfo theme="blue" caption="Is\nImplemented\nBy" row="6" col="7">
881 :     <RegionInfo name=""/>
882 :     </DisplayInfo>
883 :     <Notes>This relationship connects a variant to the physical machines
884 :     that implement it in the genomes. A variant is implemented by many
885 :     machines, but a machine belongs to only one variant.</Notes>
886 :     </Relationship>
887 :     <Relationship name="Uses" from="Genome" to="MolecularMachine" arity="1M" converse="IsUsedBy">
888 :     <DisplayInfo theme="blue" caption="Is\nUsed\nBy">
889 :     <RegionInfo name=""/>
890 :     </DisplayInfo>
891 :     <Notes>This relationship connects a genome to the machines that form
892 :     its metabolic pathways. A genome can use many machines, but a
893 :     machine is used by exactly one genome.</Notes>
894 :     </Relationship>
895 :     <Relationship name="Includes" from="Subsystem" to="Role" arity="MM" converse="IsIncludedIn">
896 :     <DisplayInfo theme="blue" caption="Includes">
897 : parrello 1.8 <RegionInfo name="" />
898 :     <RegionInfo name="Chemistry" />
899 : parrello 1.7 </DisplayInfo>
900 :     <Notes>A subsystem is defined by its roles. The subsystem's variants
901 :     contain slightly different sets of roles, but all of the roles in a
902 :     variant must be connected to the parent subsystem by this
903 :     relationship. A subsystem always has at least one role, and a role
904 :     always belongs to at least one subsystem.</Notes>
905 :     <Fields>
906 :     <Field name="sequence" type="counter">
907 :     <Notes>Sequence number of the role within the subsystem.
908 :     When the roles are formed into a variant, they will
909 :     generally appear in sequence order.</Notes>
910 :     </Field>
911 :     <Field name="abbreviation" type="string">
912 :     <Notes>Abbreviation for this role in this subsystem. The
913 :     abbreviations are used in columnar displays, and they also
914 :     appear on diagrams.</Notes>
915 :     </Field>
916 :     </Fields>
917 :     <FromIndex>
918 :     <Notes>This index insures that the roles of the subsystem are
919 :     presented in sequence order.</Notes>
920 :     <IndexFields>
921 :     <IndexField name="sequence" order="ascending"/>
922 :     </IndexFields>
923 :     </FromIndex>
924 :     </Relationship>
925 :     <Relationship name="IsCombinationOf" from="RoleSet" to="Role" arity="MM" converse="IsInCombination">
926 :     <DisplayInfo theme="navy" caption="Is\nCombination\nOf">
927 :     <RegionInfo name="Chemistry"/>
928 : parrello 1.8 <RegionInfo name="Models" fixed="1" col="1" row="5"/>
929 : parrello 1.7 </DisplayInfo>
930 :     <Notes>This relationship combines roles into role sets. Each role
931 :     set is a combination of roles that can trigger a reaction.</Notes>
932 :     </Relationship>
933 :     <Relationship name="IsTriggeredBy" from="Reaction" to="RoleSet" arity="MM" converse="Triggers">
934 :     <DisplayInfo theme="navy" caption="Is\nTriggered\nBy">
935 :     <RegionInfo name="Chemistry"/>
936 :     <RegionInfo name="Models"/>
937 :     </DisplayInfo>
938 :     <Notes>A reaction can be triggered by many role sets. A role set can
939 :     trigger many reactions.</Notes>
940 :     </Relationship>
941 :     <Relationship name="IsMadeUpOf" from="Genome" to="Contig" arity="1M" converse="MakesUp">
942 :     <DisplayInfo theme="red" caption="Is\nMade Up\nOf">
943 :     <RegionInfo name=""/>
944 :     </DisplayInfo>
945 :     <Notes>This relationship connects each genome to the DNA sequences
946 :     that make it up.</Notes>
947 :     </Relationship>
948 :     <Relationship name="Attracts" from="Structure" to="Compound" arity="MM" converse="IsAttractedTo">
949 : parrello 1.8 <DisplayInfo theme="purple" row="1" col="2" fixed="1" caption="Is\nAttracted\nTo">
950 : parrello 1.7 <RegionInfo name="Chemistry" row="1" col="1"/>
951 :     </DisplayInfo>
952 :     <Notes>This relationship connects a compound to the protein
953 :     structures that attract it. This is an incomplete relationship that
954 :     exists to service drug targeting queries. Only the attractions whose
955 :     parameters have been determined through modeling or experimentation
956 :     are included. The goal is to determine the docking energy between
957 :     the compound and the protein structure.</Notes>
958 :     <Fields>
959 :     <Field name="reason" type="string">
960 :     <Notes>Indication of the reason for determining the docking
961 :     energy. A value of "Random" indicates the docking was
962 :     attempted as a part of a random survey used to determine the
963 :     docking characteristics of a protein structure. A value of
964 :     "Rich" indicates the docking was attempted because a
965 :     low-energy docking result was predicted for the
966 :     compound.</Notes>
967 :     </Field>
968 :     <Field name="tool" type="string">
969 :     <Notes>Name of the tool used to compute the docking
970 :     energy.</Notes>
971 :     </Field>
972 :     <Field name="total-energy" type="float">
973 :     <Notes>Total energy required for the compound to dock with
974 :     the structure, in kcal/mol. A negative value means energy is
975 :     released.</Notes>
976 :     </Field>
977 :     <Field name="vanderwaals-energy" type="float">
978 :     <Notes>Docking energy in kcal/mol that results from the
979 :     geometric fit (Van der Waals force) between the structure
980 :     and the compound.</Notes>
981 :     </Field>
982 :     <Field name="electrostatic-energy" type="float">
983 :     <Notes>Docking energy in kcal/mol that results from the
984 :     movement of electrons (electrostatic force) between the
985 :     structure and the compound.</Notes>
986 :     </Field>
987 :     </Fields>
988 :     <FromIndex>
989 :     <Notes>This index enables the application to view a structure's
990 :     docking results from the lowest energy (best docking) to highest
991 :     energy (worst docking).</Notes>
992 :     <IndexFields>
993 :     <IndexField name="total-energy" order="ascending"/>
994 :     </IndexFields>
995 :     </FromIndex>
996 :     <ToIndex>
997 :     <Notes>This index enables the application to view a compound's
998 :     docking results from the lowest energy (best docking) to highest
999 :     energy (worst docking).</Notes>
1000 :     <IndexFields>
1001 :     <IndexField name="total-energy" order="ascending"/>
1002 :     </IndexFields>
1003 :     </ToIndex>
1004 :     </Relationship>
1005 :     <Relationship name="Involves" from="Reaction" to="Compound" arity="MM" converse="IsInvolvedIn">
1006 : parrello 1.8 <DisplayInfo theme="navy" caption="Is\nInvolved\nIn">
1007 :     <RegionInfo name="Chemistry" row="2" col="1.5" fixed="1"/>
1008 :     <RegionInfo name="Models"/>
1009 : parrello 1.7 </DisplayInfo>
1010 :     <Notes>This relationship connects a reaction to the compounds that
1011 :     participate in it. A reaction involves many compounds, and a
1012 :     compound can be involved in many reactions. The relationship
1013 :     attributes indicate whether a compound is a product or substrate of
1014 :     the reaction, as well as its stoichiometry.</Notes>
1015 :     <Fields>
1016 :     <Field name="product" type="boolean">
1017 :     <Notes>TRUE if the compound is a product of the reaction,
1018 :     FALSE if it is a substrate. When a reaction is written on
1019 :     paper in chemical notation, the substrates are left of the
1020 :     arrow and the products are to the right. Sorting on this
1021 :     field will cause the substrates to appear first, followed by
1022 :     the products. If the reaction is reversible, then the notion
1023 :     of substrates and products is not intuitive; however, a
1024 :     value here of FALSE still puts the compound left of the
1025 :     arrow and a value of TRUE still puts it to the
1026 :     right.</Notes>
1027 :     </Field>
1028 :     <Field name="stoichiometry" type="string">
1029 :     <Notes>Number of molecules of the compound that participate
1030 :     in a single instance of the reaction. For example, if a
1031 :     reaction produces two water molecules, the stoichiometry of
1032 :     water for the reaction would be two. When a reaction is
1033 :     written on paper in chemical notation, the stoichiometry is
1034 :     the number next to the chemical formula of the
1035 :     compound.</Notes>
1036 :     </Field>
1037 :     <Field name="main" type="boolean">
1038 :     <Notes>TRUE if this compound is one of the main participants
1039 :     in the reaction, else FALSE. It is permissible for none of
1040 :     the compounds in the reaction to be considered main, in
1041 :     which case this value would be FALSE for all of the relevant
1042 :     compounds.</Notes>
1043 :     </Field>
1044 :     <Field name="loc" type="string">
1045 :     <Notes>An optional character string that indicates the
1046 :     relative position of this compound in the reaction's
1047 :     chemical formula. The location affects the way the compounds
1048 :     present as we cross the relationship from the reaction side.
1049 :     The product/substrate flag comes first, then the value of
1050 :     this field, then the main flag. The default value is an
1051 :     empty string; however, the empty string sorts first, so if
1052 :     this field is used, it should probably be used for every
1053 :     compound in the reaction.</Notes>
1054 :     </Field>
1055 :     <Field name="discriminator" type="int">
1056 :     <Notes>A unique ID for this record. The discriminator does
1057 :     not provide any useful data, but it prevents identical
1058 :     records from being collapsed by sort process used to
1059 :     load the database from constituent files.</Notes>
1060 :     </Field>
1061 :     </Fields>
1062 :     <ToIndex>
1063 :     <Notes>This index presents the compounds in the reaction in the
1064 :     order they should be displayed when writing it in chemical
1065 :     notation. All the substrates appear before all the products, and
1066 :     within that ordering, the main compounds appear first.</Notes>
1067 :     <IndexFields>
1068 :     <IndexField name="product" order="ascending"/>
1069 :     <IndexField name="loc" order="ascending"/>
1070 :     <IndexField name="main" order="descending"/>
1071 :     </IndexFields>
1072 :     </ToIndex>
1073 :     </Relationship>
1074 :     <Relationship name="Shows" from="Diagram" to="Compound" arity="MM" converse="IsShownOn">
1075 :     <DisplayInfo theme="ivory" fixed="1" caption="Is\nShown\nOn" row="2" col="3.5">
1076 :     <RegionInfo name="Chemistry" row="2" col="2.5"/>
1077 :     </DisplayInfo>
1078 :     <Notes>This relationship indicates that a compound appears on a
1079 :     particular diagram. The same compound can appear on many diagrams,
1080 :     and a diagram always contains many compounds.</Notes>
1081 : parrello 1.8 <Fields>
1082 :     <Field name="location" type="rectangle">
1083 :     <Notes>Location of the compound's node on the diagram.</Notes>
1084 :     </Field>
1085 :     </Fields>
1086 : parrello 1.7 </Relationship>
1087 :     <Relationship name="IsRoleOf" from="Role" to="MachineRole" arity="1M" converse="HasRole">
1088 :     <DisplayInfo caption="Is\nRole\nOf" theme="blue">
1089 :     <RegionInfo name=""/>
1090 :     </DisplayInfo>
1091 :     <Notes>This relationship connects a role to the machine roles that
1092 :     represent its appearance in a molecular machine. A machine role has
1093 :     exactly one associated role, but a role may be represented by many
1094 :     machine roles.</Notes>
1095 :     </Relationship>
1096 :     <Relationship name="Exposes" from="ProteinSequence" to="Structure" arity="MM" converse="IsExposedBy">
1097 : parrello 1.8 <DisplayInfo theme="purple" fixed="1" row="7" col="2" caption="Is\nExposed\nBy">
1098 : parrello 1.7 <RegionInfo name="Chemistry" row="7" col="1"/>
1099 :     </DisplayInfo>
1100 :     <Notes>This relationship connects a protein sequence to its
1101 :     structural representations. It is a many-to-many relationship. Note
1102 :     that only some protein sequences have known structural
1103 :     representations.</Notes>
1104 :     </Relationship>
1105 :     <Relationship name="IsSubInstanceOf" from="Subsystem" to="Scenario" arity="1M" converse="Validates">
1106 :     <DisplayInfo theme="ivory" caption="Is Sub-\nInstance\nOf" fixed="1" row="1" col="7">
1107 :     <RegionInfo name="Chemistry" row="1" col="6"/>
1108 :     </DisplayInfo>
1109 :     <Notes>This relationship connects a scenario to its subsystem it
1110 :     validates. A scenario belongs to exactly one subsystem, but a
1111 :     subsystem may have multiple scenarios.</Notes>
1112 :     </Relationship>
1113 :     <Relationship name="Overlaps" from="Scenario" to="Diagram" arity="MM" converse="IncludesPartOf">
1114 :     <DisplayInfo theme="ivory" fixed="1" row="2" col="5.5">
1115 :     <RegionInfo name="Chemistry" row="2" col="4.5"/>
1116 :     </DisplayInfo>
1117 :     <Notes>A Scenario overlaps a diagram when the diagram displays a
1118 :     portion of the reactions that make up the scenario. A scenario may
1119 :     overlap many diagrams, and a diagram may be include portions of many
1120 :     scenarios.</Notes>
1121 :     </Relationship>
1122 :     <Relationship name="HasParticipant" from="Scenario" to="Reaction" arity="MM" converse="ParticipatesIn">
1123 :     <DisplayInfo theme="ivory" caption="Has\nParticipant" row="2" col="4.5" fixed="1">
1124 :     <RegionInfo name="Chemistry" row="2" col="3.5"/>
1125 :     </DisplayInfo>
1126 :     <Notes>A scenario consists of many participant reactions that
1127 :     convert the input compounds to output compounds. A single reaction
1128 :     may participate in many scenarios.</Notes>
1129 :     <Fields>
1130 :     <Field name="type" type="int">
1131 :     <Notes>Indicates the type of participaton. If 0, the
1132 :     reaction is in the main pathway of the scenario. If 1, the
1133 :     reaction is necessary to make the model work but is not in
1134 :     the subsystem. If 2, the reaction is part of the subsystem
1135 :     but should not be included in the modelling process.</Notes>
1136 :     </Field>
1137 :     </Fields>
1138 :     <FromIndex>
1139 :     <Notes>This index presents the reactions in the scenario in
1140 :     order from most important to least important.</Notes>
1141 :     <IndexFields>
1142 :     <IndexField name="type" order="ascending"/>
1143 :     </IndexFields>
1144 :     </FromIndex>
1145 :     </Relationship>
1146 :     <Relationship name="IsInPair" from="Feature" to="Pairing" arity="MM" converse="IsPairOf">
1147 :     <DisplayInfo theme="brown" caption="Is In\nPair">
1148 :     <RegionInfo name="Annotations"/>
1149 :     </DisplayInfo>
1150 :     <Notes>A pairing contains exactly two protein sequences. A protein
1151 :     sequence can belong to multiple pairings. When going from a protein
1152 :     sequence to its pairings, they are presented in alphabetical order
1153 :     by sequence key.</Notes>
1154 :     </Relationship>
1155 :     <Relationship name="IsTaxonomyOf" from="TaxonomicGrouping" to="Genome" arity="1M" converse="IsInTaxa">
1156 :     <DisplayInfo theme="red" fixed="1" caption="Is In\nTaxa" row="9" col="6">
1157 :     <RegionInfo name="" row="8" col="5"/>
1158 :     </DisplayInfo>
1159 :     <Notes>A genome is assigned to a particular point in the taxonomy tree, but not
1160 :     necessarily to a leaf node. In some cases, the exact species and strain is
1161 :     not available when inserting the genome, so it is placed at the lowest node
1162 :     that probably contains the actual genome.</Notes>
1163 :     </Relationship>
1164 :     <Relationship name="IsMachineOf" from="MolecularMachine" to="MachineRole" arity="1M" converse="IsRoleFor">
1165 :     <DisplayInfo caption="Is\nRole\nFor" theme="blue" row="7" col="6">
1166 :     <RegionInfo name=""/>
1167 :     </DisplayInfo>
1168 :     <Notes>This relationship connects a molecular machine to its various
1169 :     machine roles. Each machine has many machine roles, but each machine
1170 :     role belongs to only one machine.</Notes>
1171 :     </Relationship>
1172 :     <Relationship name="Encompasses" from="Model" to="FeatureSet" arity="1M" converse="IsEncompassedIn">
1173 :     <DisplayInfo theme="navy" caption="Is\nEncompassed\nIn">
1174 :     <RegionInfo name="Models"/>
1175 :     </DisplayInfo>
1176 :     <Notes>This relationship connects a model to its feature sets. A feature set
1177 :     can only be in a single model. The model can be said to be identified by its
1178 :     feature sets.</Notes>
1179 :     </Relationship>
1180 :     <Relationship name="IsClassFor" arity="1M" from="SubsystemClass" to="Subsystem" converse="IsInClass">
1181 :     <DisplayInfo caption="Is In\nClass" theme="blue">
1182 :     <RegionInfo name=""/>
1183 :     <RegionInfo name="Chemistry"/>
1184 :     </DisplayInfo>
1185 :     <Notes>This relationship connects each subsystem class with the
1186 :     subsystems that belong to it. A class can contain many subsystems,
1187 :     but a subsystem is only in one class. Some subsystems are not in any
1188 :     class, but this is usually a temporary condition.</Notes>
1189 :     </Relationship>
1190 :     <Relationship name="IsAnnotatedBy" from="Feature" to="Annotation" arity="1M" converse="Annotates">
1191 :     <DisplayInfo theme="brown" caption="Is\nAnnotated\nBy">
1192 :     <RegionInfo name="Annotations"/>
1193 :     </DisplayInfo>
1194 :     <Notes>This relationship connects a feature to its annotations. A
1195 :     feature may have multiple annotations, but an annotation belongs to
1196 :     only one feature.</Notes>
1197 :     </Relationship>
1198 :     <Relationship name="HasMember" from="Family" to="Feature" arity="MM" converse="IsMemberOf">
1199 :     <DisplayInfo theme="brown" caption="Is\nMember\nOf">
1200 :     <RegionInfo name="Annotations"/>
1201 :     </DisplayInfo>
1202 :     <Notes>This relationship connects each feature family to its
1203 :     constituent features. A family always has many features, and a
1204 :     single feature can be found in many families.</Notes>
1205 :     </Relationship>
1206 :     <Relationship name="Concerns" from="Publication" to="ProteinSequence" arity="MM" converse="IsATopicOf">
1207 :     <DisplayInfo theme="green">
1208 :     <RegionInfo name=""/>
1209 :     </DisplayInfo>
1210 :     <Notes>This relationship connects a publication to the protein
1211 :     sequences it describes.</Notes>
1212 :     </Relationship>
1213 :     <Relationship name="IsCollectionOf" from="GenomeSet" to="Genome" arity="1M" converse="IsCollectedInto">
1214 :     <DisplayInfo theme="red" caption="Is\nCollection\nOf">
1215 : parrello 1.8 <RegionInfo name="" row="6" col="6" fixed="1"/>
1216 : parrello 1.7 </DisplayInfo>
1217 :     <Notes>A genome belongs to only one genome set. For each set, this relationship marks the genome to be used as its representative.</Notes>
1218 :     <Fields>
1219 :     <Field name="representative" type="boolean">
1220 :     <Notes>TRUE for the representative genome of the set, else FALSE.</Notes>
1221 :     </Field>
1222 :     </Fields>
1223 :     </Relationship>
1224 :     <Relationship name="HasAssertionFrom" from="Identifier" to="Source" converse="Asserts" arity="MM">
1225 : parrello 1.8 <DisplayInfo theme="black" caption="Has\nAssertion\nFrom">
1226 : parrello 1.7 <RegionInfo name="Annotations"/>
1227 :     </DisplayInfo>
1228 :     <Notes>Sources (users) can make assertions about identifiers using the annotation clearinghouse.
1229 :     When a user makes a new assertion about an identifier, it erases the old one.</Notes>
1230 :     <Fields>
1231 :     <Field name="time-stamp" type="date">
1232 :     <Notes>This is the date and time the assertion was made.</Notes>
1233 :     </Field>
1234 :     <Field name="function" type="text">
1235 :     <Notes>The function is the text of the assertion made about the identifier.</Notes>
1236 :     </Field>
1237 :     <Field name="expert" type="boolean">
1238 :     <Notes>TRUE if this is an expert assertion, else FALSE</Notes>
1239 :     </Field>
1240 :     </Fields>
1241 :     </Relationship>
1242 :     <Relationship name="IsDeterminedBy" from="PairSet" to="Pairing" arity="1M" converse="Determines">
1243 :     <DisplayInfo theme="brown" caption="Determines">
1244 :     <RegionInfo name="Annotations"/>
1245 :     </DisplayInfo>
1246 :     <Notes>A functional coupling evidence set exists because it has
1247 :     pairings in it, and this relationship connects the evidence set to
1248 :     its constituent pairings. A pairing cam belong to multiple evidence
1249 :     sets.</Notes>
1250 :     <Fields>
1251 :     <Field name="inverted" type="boolean">
1252 :     <Notes>A pairing is an unordered pair of protein sequences,
1253 :     but its similarity to other pairings in a pair set is
1254 :     ordered. Let (A,B) be a pairing and (X,Y) be another pairing
1255 :     in the same set. If this flag is FALSE, then (A =~ X) and (B
1256 :     =~ Y). If this flag is TRUE, then (A =~ Y) and (B =~
1257 :     X).</Notes>
1258 :     </Field>
1259 :     </Fields>
1260 :     </Relationship>
1261 :     <Relationship name="IsContainedIn" from="Feature" to="MachineRole" arity="MM" converse="Contains">
1262 :     <DisplayInfo theme="blue" caption="Contains" row="8" col="5">
1263 :     <RegionInfo name=""/>
1264 :     </DisplayInfo>
1265 :     <Notes>This relationship connects a machine role to the features
1266 :     that occur in it. A feature may occur in many machine roles and a
1267 :     machine role may contain many features. The subsystem annotation
1268 :     process is essentially the maintenance of this relationship.</Notes>
1269 :     </Relationship>
1270 :     <Relationship name="IsOwnerOf" from="Genome" to="Feature" arity="1M" converse="IsOwnedBy">
1271 :     <DisplayInfo caption="Is\nOwned\nBy" theme="green"/>
1272 :     <Notes>This relationship connects each feature to its parent genome.</Notes>
1273 :     </Relationship>
1274 :     <Relationship name="IsProteinFor" from="ProteinSequence" to="Feature" arity="1M" converse="Produces">
1275 :     <DisplayInfo caption="Is\nProtein\nFor" theme="green">
1276 :     <RegionInfo name=""/>
1277 :     <RegionInfo name="Annotations"/>
1278 : parrello 1.8 <RegionInfo name="Chemistry"/>
1279 : parrello 1.7 </DisplayInfo>
1280 :     <Notes>This relationship connects a peg feature to the protein
1281 :     sequence it produces (if any). Only peg features participate in this
1282 :     relationship. A single protein sequence will frequently be produced
1283 :     by many features.</Notes>
1284 :     </Relationship>
1285 :     <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM" converse="IsLocusFor">
1286 :     <DisplayInfo theme="green" caption="Is\nLocated\nIn" fixed="1" row="10" col="6">
1287 :     <RegionInfo name="" row="8" col="3"/>
1288 :     </DisplayInfo>
1289 :     <Notes>A feature is a set of DNA sequence fragments. Most features
1290 :     are a single contiquous fragment, so they are located in only one
1291 :     DNA sequence; however, fragments have a maximum length, so even a
1292 :     single contiguous feature may participate in this relationship
1293 :     multiple times. A few features belong to multiple DNA sequences. In
1294 :     that case, however, all the DNA sequences belong to the same genome.
1295 :     A DNA sequence itself will frequently have thousands of features
1296 :     connected to it.</Notes>
1297 :     <Fields>
1298 :     <Field name="ordinal" type="int">
1299 :     <Notes>Sequence number of this segment, starting from 1
1300 :     and proceeding sequentially forward from there.</Notes>
1301 :     </Field>
1302 :     <Field name="begin" type="int">
1303 :     <Notes>Index (1-based) of the first residue in the contig
1304 :     that belongs to the segment.</Notes>
1305 :     <Asides>The begin value is not the start residue, it is the
1306 :     leftmost residue. If the direction is backward, it will
1307 :     actually be the end residue.</Asides>
1308 :     </Field>
1309 :     <Field name="len" type="int">
1310 :     <Notes>Length of this segment.</Notes>
1311 :     </Field>
1312 :     <Field name="dir" type="char">
1313 :     <Notes>Direction (strand) of the segment: "+" if it is
1314 :     forward and "-" if it is backward.</Notes>
1315 :     </Field>
1316 :     </Fields>
1317 :     <FromIndex>
1318 :     <Notes>This index allows the application to find all the
1319 :     segments of a feature in the proper order.</Notes>
1320 :     <IndexFields>
1321 :     <IndexField name="ordinal" order="ascending"/>
1322 :     </IndexFields>
1323 :     </FromIndex>
1324 :     <ToIndex>
1325 :     <Notes>This index is the one used by applications to find all
1326 :     the feature segments that contain a specific residue.</Notes>
1327 :     <IndexFields>
1328 :     <IndexField name="begin" order="ascending"/>
1329 :     </IndexFields>
1330 :     </ToIndex>
1331 :     </Relationship>
1332 :     <Relationship name="Identifies" from="Identifier" to="Feature" arity="MM" converse="IsIdentifiedByF">
1333 :     <DisplayInfo theme="green">
1334 : parrello 1.8 <RegionInfo name="" caption="Is\nIdentified\nBy"/>
1335 : parrello 1.7 <RegionInfo name="Annotations"/>
1336 :     </DisplayInfo>
1337 :     <Notes>The normal case is that an identifier identifies a single
1338 :     feature, while a feature can have many identifiers. Some identifiers,
1339 :     however, are ambiguous and will connect to many features.</Notes>
1340 :     </Relationship>
1341 :     <Relationship name="IsNamedBy" from="ProteinSequence" to="Identifier" arity="MM" converse="Names">
1342 : parrello 1.8 <DisplayInfo theme="black" caption="Is\nNamed\nBy">
1343 :     <RegionInfo name="Annotations"/>
1344 : parrello 1.7 </DisplayInfo>
1345 :     <Notes>The normal case is that an identifier names a single
1346 :     protein sequence, while a protein sequence can have many identifiers,
1347 :     but some identifiers name multiple sequences.</Notes>
1348 :     <Asides>This relationship is populated with data submitted to the annotation
1349 :     clearinghouse as well as external IDs in the non-redundant database.</Asides>
1350 :     </Relationship>
1351 : parrello 1.8 <Relationship name="HasSection" from="Contig" to="DNASequence" arity="1M" converse="IsSectionOf">
1352 :     <DisplayInfo caption="Is\nSection\Of" theme="red">
1353 :     <RegionInfo name=""/>
1354 :     </DisplayInfo>
1355 :     <Notes>This relationship connects a contig to its actual DNA
1356 :     sequences.</Notes>
1357 :     </Relationship>
1358 :     <Relationship name="IsGroupFor" from="TaxonomicGrouping" to="TaxonomicGrouping" arity="1M" converse="IsInGroup">
1359 :     <DisplayInfo theme="red" caption="Is\nGroup\nFor">
1360 :     <RegionInfo name="" row="9" col="6" fixed="1"/>
1361 :     </DisplayInfo>
1362 :     <Notes>The recursive IsGroupContaining relationship organizes
1363 :     taxonomic groupings into a hierarchy based on the standard organism
1364 :     taxonomy.</Notes>
1365 :     </Relationship>
1366 : parrello 1.7 </Relationships>
1367 :     <Shapes>
1368 :     <Shape type="diamond" name="ConsistsOf" from="Variant" to="Role">
1369 :     <DisplayInfo theme="neutral" caption="Belongs To" connected="1">
1370 :     <RegionInfo name=""/>
1371 :     </DisplayInfo>
1372 :     <Notes>This relationship is not physically implemented in the
1373 :     database. It is implicit in the data for a variant. A variant
1374 :     contains a boolean expression that describes the various
1375 :     combinations of roles it can contain.</Notes>
1376 :     </Shape>
1377 :     </Shapes>
1378 : parrello 1.1 </Database>

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