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1 : parrello 1.1 <Database>
2 :     <Title>Sapling Bioinformatics Database</Title>
3 :     <Notes>The Sapling database is a distributable, self-contained copy of the NMPDR data.
4 :     Unlike Sprout, which is optimized for searching, Sapling is designed to be structurally
5 :     simple without sacrificing the ability to find information quickly.</Notes>
6 :     <Issues>
7 :     <Issue>Must add the new "image" data type to ERDB.</Issue>
8 :     <Issue>Must add the new "dna" data type to ERDB.</Issue>
9 :     <Issue>Must add back the ability to index a secondary relation. Note that
10 : parrello 1.2 such indexes can only have a single field.</Issue>
11 : parrello 1.1 <Issue>We probably need some type tables that describe things like Identifier(source)
12 : parrello 1.2 or Family(kind).</Issue>
13 : parrello 1.1 <Issue>The ERDB documentation needs to be updated to include DisplayInfo, Asides,
14 : parrello 1.2 the "converse" attribute for relationships, and the Shapes section.</Issue>
15 :     <Issue>Similarities and pairings are not hooked in correctly.</Issue>
16 : parrello 1.1 </Issues>
17 :     <Entities>
18 :     <Entity name="Compound" keyType="name-string">
19 : parrello 1.2 <DisplayInfo theme="web" col="3" row="1"/>
20 : parrello 1.1 <Notes>A compound is a chemical that participates in a reaction.
21 : parrello 1.2 All compounds have a unique ID and may also have one or more names. Both
22 :     ligands and reaction components are treated as compounds.</Notes>
23 : parrello 1.1 <Fields>
24 :     <Field name="label" type="string">
25 :     <Notes>Primary name of the compound. This is the name used in reaction
26 : parrello 1.2 display strings.</Notes>
27 : parrello 1.1 </Field>
28 :     <Field name="name" type="string" relation="CompoundName">
29 :     <Notes>Alternate name for the compound. A compound may have many
30 : parrello 1.2 alternate names. The primary name should also be one of the
31 :     alternate names.</Notes>
32 : parrello 1.1 </Field>
33 :     <Field name="cas-id" type="string" relation="CompoundCAS">
34 :     <Notes>The Chemical Abstract Service ID for the compound. A
35 : parrello 1.2 compound may have at most one CAS ID.</Notes>
36 : parrello 1.1 </Field>
37 :     <Field name="zinc-id" type="string" relation="CompoundZinc">
38 :     <Notes>The ZINC database ID for the compound. A compound may
39 : parrello 1.2 have at most one ZINC ID.</Notes>
40 : parrello 1.1 </Field>
41 :     </Fields>
42 :     <Indexes>
43 :     <Index>
44 :     <Notes>This index allows searching for compounds by name.</Notes>
45 :     <IndexFields>
46 :     <IndexField name="name" order="ascending"/>
47 :     </IndexFields>
48 :     </Index>
49 :     <Index>
50 :     <Notes>This index allows searching for compounds by CAS ID.</Notes>
51 :     <IndexFields>
52 :     <IndexField name="cas-id" order="ascending"/>
53 :     </IndexFields>
54 :     </Index>
55 :     <Index>
56 :     <Notes>This index allows searching for compounds by ZINC ID.</Notes>
57 :     <IndexFields>
58 :     <IndexField name="zinc-id" order="ascending"/>
59 :     </IndexFields>
60 :     </Index>
61 :     </Indexes>
62 :     </Entity>
63 :     <Entity name="Diagram" keyType="name-string">
64 : parrello 1.2 <DisplayInfo theme="web" col="5" row="3"/>
65 : parrello 1.1 <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
66 : parrello 1.2 subsystem. A diagram is identified by a short name and contains a longer descriptive name.</Notes>
67 : parrello 1.1 <Fields>
68 :     <Field name="name" type="text">
69 :     <Notes>Descriptive name of this diagram.</Notes>
70 :     </Field>
71 :     <Field name="content" type="image" relation="DiagramContent">
72 :     <Notes>The content of the diagram, in PNG format encoded as base 64 MIME.</Notes>
73 :     </Field>
74 :     </Fields>
75 :     </Entity>
76 :     <Entity name="Reaction" keyType="key-string">
77 : parrello 1.2 <DisplayInfo theme="web" col="3" row="3"/>
78 : parrello 1.1 <Notes>A reaction is a chemical process that converts one set of compounds (substrate)
79 : parrello 1.2 to another set (products). The reaction ID is generally a small number preceded by a
80 :     letter.</Notes>
81 : parrello 1.1 <Fields>
82 :     <Field name="url" type="string" relation="ReactionURL">
83 :     <Notes>HTML string containing a link to a web location that describes the
84 : parrello 1.2 reaction. This field is optional.</Notes>
85 : parrello 1.1 </Field>
86 :     <Field name="rev" type="boolean">
87 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
88 :     </Field>
89 :     </Fields>
90 :     </Entity>
91 :     <Entity name="Subsystem" keyType="id-string">
92 :     <DisplayInfo theme="seed" col="7" row="3"/>
93 :     <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
94 : parrello 1.2 is an important tool for recognizing parallel genetic features in different organisms. The key
95 :     is an alphanumeric code string.</Notes>
96 : parrello 1.1 <Fields>
97 :     <Field name="name" type="string">
98 :     <Notes>Displayable name of this subsystem.</Notes>
99 :     </Field>
100 :     <Field name="version" type="int">
101 :     <Notes>Version number for the subsystem. This value is incremented each time the subsystem
102 : parrello 1.2 is backed up.</Notes>
103 : parrello 1.1 </Field>
104 :     <Field name="curator" type="string">
105 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
106 :     </Field>
107 :     <Field name="notes" type="text">
108 :     <Notes>Descriptive notes about the subsystem.</Notes>
109 :     </Field>
110 :     <Field name="description" type="text">
111 :     <Notes>Description of the subsystem's function in the cell.</Notes>
112 :     </Field>
113 :     <Field name="classification" type="string">
114 :     <Notes>Classification string, colon-delimited. This string organizes the
115 : parrello 1.2 subsystems into a hierarchy.</Notes>
116 : parrello 1.1 </Field>
117 :     </Fields>
118 :     <Indexes>
119 :     <Index>
120 :     <Notes>This index is used to get the subsystems in hierarchical order.</Notes>
121 :     <IndexFields>
122 :     <IndexField name="classification" order="ascending"/>
123 :     </IndexFields>
124 :     </Index>
125 :     <Index>
126 :     <Notes>This index is used to get the subsystem by name.</Notes>
127 :     <IndexFields>
128 :     <IndexField name="name" order="ascending"/>
129 :     </IndexFields>
130 :     </Index>
131 :     </Indexes>
132 :     </Entity>
133 :     <Entity name="Publication" keyType="hash-string">
134 : parrello 1.2 <DisplayInfo theme="web" col="1" row="8"/>
135 : parrello 1.1 <Notes>A _publication_ is an article or citation that may be used as evidence for
136 : parrello 1.2 assertions made in the database. The key is a hash code computed from the URL.</Notes>
137 : parrello 1.1 <Fields>
138 :     <Field name="url" type="string">
139 :     <Notes>URL of the article or of its citation.</Notes>
140 :     </Field>
141 :     <Field name="citation" type="text">
142 :     <Notes>Citation string for the article.</Notes>
143 :     </Field>
144 :     </Fields>
145 :     <Indexes>
146 :     <Index>
147 :     <Notes>This index allows searching for the article by the author names and title.</Notes>
148 :     <IndexFields>
149 :     <IndexField name="citation" order="ascending"/>
150 :     </IndexFields>
151 :     </Index>
152 :     </Indexes>
153 :     </Entity>
154 : parrello 1.2 <Entity name="Variant" keyType="name-string">
155 :     <DisplayInfo theme="seed" col="7" row="5"/>
156 :     <Notes>A variant is a functional subset of a subsystem. It indicates the particular
157 :     sequence of roles used to implement a metabolic pathway. Variants are abstract
158 :     concepts used to classify machines. The key of the variant is the subsystem ID followed
159 :     by the variant code (usually a numeric string with zero or more decimal points).</Notes>
160 :     <Fields>
161 :     <Field name="role-rule" type="text">
162 :     <Notes>Boolean expression (encoded as text) that describes the roles in this variant.
163 :     The roles themselves are represented by their IDs.</Notes>
164 : parrello 1.1 </Field>
165 :     </Fields>
166 :     </Entity>
167 :     <Entity name="ProteinSequence" keyType="hash-string">
168 :     <DisplayInfo theme="web" col="3" row="7" caption="Protein Sequence"/>
169 :     <Notes>A protein sequence is a specific sequence of amino acids. Unlike a DNA sequence, a
170 : parrello 1.2 protein sequence does not belong to a genome. Identical proteins generated by different
171 :     genomes are generally stored as a single ProteinSequence instance. The key is a
172 :     hash of the protein letter sequence.</Notes>
173 : parrello 1.1 <Fields>
174 :     <Field name="sequence" type="dna">
175 :     <Notes>The sequence contains the letters corresponding to the protein's
176 : parrello 1.2 amino acids.</Notes>
177 : parrello 1.1 </Field>
178 :     <Field name="iedb" type="text" relation="ProteinSequenceIEDB" special="property_search">
179 :     <Notes>A value indicating whether or not the feature can be found in the
180 : parrello 1.2 Immune Epitope Database. If the feature has not been matched to that database,
181 :     this field will have no values. Otherwise, it will have an epitope name and/or
182 :     sequence, hyperlinked to the database.</Notes>
183 : parrello 1.1 </Field>
184 :     <Field name="signal-peptide" type="name-string">
185 :     <Notes>The signal peptide location for this feature. This is expressed as start and end
186 : parrello 1.2 numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
187 :     peptide at the beginning of the feature's protein and extending through 22 amino acid
188 :     positions. An empty string means no signal peptide is present.</Notes>
189 : parrello 1.1 </Field>
190 :     <Field name="transmembrane-map" type="text">
191 :     <Notes>A map indicating which sections of a protein will be embedded in a membrane.
192 : parrello 1.2 This is expressed as a comma-separated list of as start and end numbers with hyphens
193 :     for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
194 :     sections of the protein that become embedded in a membrane: the 10th through 12th
195 :     amino acids, and the 40th through the 60th. An empty string means no
196 :     transmembrane regions are known.</Notes>
197 : parrello 1.1 </Field>
198 :     <Field name="similar-to-human" type="boolean">
199 :     <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
200 : parrello 1.2 else FALSE</Notes>
201 : parrello 1.1 </Field>
202 :     <Field name="isoelectric-point" type="float">
203 :     <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
204 : parrello 1.2 If the pH of the medium is lower than this value, the protein will have a net
205 :     positive charge. If the pH of the medium is higher, then the protein will have a
206 :     net negative charge.</Notes>
207 : parrello 1.1 </Field>
208 :     <Field name="molecular-weight" type="float">
209 :     <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
210 : parrello 1.2 indicates that no protein is created.</Notes>
211 : parrello 1.1 </Field>
212 :     </Fields>
213 :     </Entity>
214 : parrello 1.2 <Entity name="Family" keyType="name-string">
215 :     <DisplayInfo theme="seed" col="4" row="11"/>
216 :     <Notes>A family is a group of features united by a particular determination algorithm.
217 :     The algorithm will frequently-- but not always-- signify a functional role.</Notes>
218 : parrello 1.1 </Entity>
219 : parrello 1.2 <Entity name="MolecularMachine" keyType="key-string">
220 :     <DisplayInfo theme="seed" col="7" row="7" caption="Molecular\nMachine"/>
221 :     <Notes>A molecular machine is a collection of features that implements a metabolic pathway. Machines
222 :     are the physical instances of variants. Each machine corresponds to a row in a subsystem
223 :     spreadsheet. The key is the variant key followed by a colon and the Genome ID.</Notes>
224 : parrello 1.1 <Fields>
225 :     <Field name="type" type="key-string">
226 :     <Notes>The machine type indicates how it relates to the parent variant. A type
227 : parrello 1.2 of "vacant" means that the machine does not appear to actually exist in the
228 :     organism. A type of "incomplete" means that the machine appears to be missing
229 :     many reactions. In all other cases, the type is "normal".</Notes>
230 : parrello 1.1 </Field>
231 :     </Fields>
232 :     </Entity>
233 : parrello 1.2 <Entity name="Scenario" keyType="string">
234 :     <DisplayInfo theme="web" col="5" row="1"/>
235 :     <Notes>A scenario is a partial instance of a subsystem with a defined set of
236 :     reactions.Each scenario converrts input compounds to output compounds using reactions.
237 :     The scenario may use all of the reactions controlled by a subsystem or only
238 :     some, and may also incorporate additional reactions.</Notes>
239 : parrello 1.1 </Entity>
240 : parrello 1.2 <Entity name="Pairing" keyType="name-string">
241 : parrello 1.1 <DisplayInfo theme="seed" col="5" row="11"/>
242 : parrello 1.2 <Notes>A pairing indicates that two protein sequences are found close together on one or
243 :     more DNA sequences. Not all possible pairings are stored in the database; only those that
244 :     are considered for some reason to be significant for annotation purposes.The key of the pairing is the
245 :     concatenation of the protein sequence keys in alphabetical order.</Notes>
246 :     <Asides>Because the protein sequence key is a hash of the sequence letters, the key of a pairing between two
247 :     sequences is computable from the sequences themselves. Theoretically, the pairing
248 :     is unordered: (A,B) and (B,A) are the same pairing. It is frequently the case,
249 :     however, that we need to refer to the "first" or "second" protein in the pairing.
250 :     When this happens, the first one is always the protein with the alphabetically
251 :     lesser key. The IsInPair relationship automatically shows the proteins in this
252 :     order.</Asides>
253 : parrello 1.1 </Entity>
254 :     <Entity name="Genome" keyType="name-string">
255 :     <DisplayInfo theme="nmpdr" col="7" row="9" caption="Genome Organism"/>
256 : parrello 1.2 <Notes>A genome represents a specific organism with DNA, or a specific meta-genome. All DNA
257 :     sequences in the database belong to genomes.</Notes>
258 : parrello 1.1 <Fields>
259 :     <Field name="full-name" type="name-string">
260 : parrello 1.2 <Notes>Full genus/species/strain name of the genome.</Notes>
261 : parrello 1.1 </Field>
262 :     <Field name="domain" type="name-string">
263 :     <Notes>Domain for this genome or taxonomic classification. The domain is
264 : parrello 1.2 the highest level of the taxonomy tree.</Notes>
265 : parrello 1.1 </Field>
266 :     <Field name="version" type="name-string">
267 :     <Notes>Version string for this genome, generally consisting of the genome ID followed
268 : parrello 1.2 by a period and a string of digits.</Notes>
269 : parrello 1.1 </Field>
270 :     <Field name="complete" type="boolean">
271 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
272 :     </Field>
273 :     <Field name="dna-size" type="counter">
274 :     <Notes>number of base pairs in the genome</Notes>
275 :     </Field>
276 :     <Field name="primary-group" type="name-string">
277 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR
278 : parrello 1.2 group per organism. An empty string indicates the organism is supporting. In general,
279 :     more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>
280 : parrello 1.1 </Field>
281 :     <Field name="contigs" type="int">
282 :     <Notes>Number of contigs for this organism.</Notes>
283 :     </Field>
284 :     <Field name="pegs" type="int">
285 :     <Notes>Number of protein encoding genes for this organism</Notes>
286 :     </Field>
287 :     <Field name="rnas" type="int">
288 :     <Notes>Number of RNA features found for this organism.</Notes>
289 :     </Field>
290 :     </Fields>
291 :     <Indexes>
292 :     <Index>
293 :     <Notes>This index allows the applications to find all genomes associated with
294 : parrello 1.2 a specific primary (NMPDR) group.</Notes>
295 : parrello 1.1 <IndexFields>
296 :     <IndexField name="primary-group" order="ascending"/>
297 :     <IndexField name="full-name" order="ascending"/>
298 :     </IndexFields>
299 :     </Index>
300 :     <Index>
301 :     <Notes>This index allows the applications to find all genomes in lexical
302 : parrello 1.2 order by name.</Notes>
303 : parrello 1.1 <IndexFields>
304 :     <IndexField name="full-name" order="ascending"/>
305 :     </IndexFields>
306 :     </Index>
307 :     </Indexes>
308 :     </Entity>
309 : parrello 1.2 <Entity name="Feature" keyType="id-string">
310 :     <DisplayInfo theme="seed" col="5" row="9"/>
311 :     <Notes>A feature (sometimes also called a gene) is a part of a genome that is of special
312 :     interest. Features may be spread across multiple DNA sequences (contigs) of a genome, but
313 :     never across more than one genome. Each feature in the database has a unique FIG ID.</Notes>
314 :     <Fields>
315 :     <Field name="feature-type" type="id-string">
316 :     <Notes>Code indicating the type of this feature. Among the codes currently
317 :     supported are "peg" for a protein encoding gene, "bs" for a
318 :     binding site, "opr" for an operon, and so forth.</Notes>
319 :     </Field>
320 :     <Field name="link" type="text" relation="FeatureLink">
321 :     <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
322 :     links are to other websites that have useful about the gene that the feature represents, and
323 :     are coded as raw HTML, using an anchor href tag.</Notes>
324 :     </Field>
325 :     <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
326 :     <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
327 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
328 :     or potential (potential-essential), hyperlinked to the document from which the
329 :     essentiality was curated. If a feature is not essential, this field will have no
330 :     values; otherwise, it may have multiple values.</Notes>
331 :     </Field>
332 :     <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
333 :     <Notes>A value indicating the virulence of the feature, coded as HTML. In most
334 :     cases, this will be a phrase or SA number hyperlinked to the document from which
335 :     the virulence information was curated. If the feature is not virulent, this field
336 :     will have no values; otherwise, it may have multiple values.</Notes>
337 :     </Field>
338 :     <Field name="sequence-length" type="counter">
339 :     <Notes>Number of base pairs in this feature.</Notes>
340 :     </Field>
341 :     <Field name="evidence-code" type="string" relation="FeatureEvidence">
342 :     <Notes>An evidence code describes the possible evidence that exists
343 :     for deciding a feature's functional assignment. A feature may have no evidence,
344 :     a single evidence code, or several.</Notes>
345 :     </Field>
346 :     <Field name="function" type="text">
347 :     <Notes>Functional assignment for this feature. This will often indicate
348 :     the feature's functional role or roles, and may also have comments.</Notes>
349 :     <Asides>It will frequently be the case that a feature is assigned to a single
350 :     role, and it is identical to the function. In some cases, a feature will have
351 :     multiple roles, and all of them will be listed in the function field. In addition,
352 :     the function may have comment text at the end.</Asides>
353 :     </Field>
354 :     </Fields>
355 :     </Entity>
356 :     <Entity name="Annotation" keyType="string">
357 :     <DisplayInfo col="3" row="11" theme="seed"/>
358 :     <Notes>An annotation is a comment attached to a feature. Annotations are used to
359 :     track the history of a feature's functional assignments and any related issues. The
360 :     key is the feature ID followed by a colon and an complemented eight-digit sequence number.</Notes>
361 :     <Asides>The complemented sequence number causes the annotations to sort with the most recent one
362 :     first.</Asides>
363 : parrello 1.1 <Fields>
364 : parrello 1.2 <Field name="annotator" type="string">
365 :     <Notes>Name of the annotator who made the comment.</Notes>
366 :     </Field>
367 :     <Field name="comment" type="text">
368 :     <Notes>Text of the annotation.</Notes>
369 :     </Field>
370 :     <Field name="annotation-time" type="date">
371 :     <Notes>Date and time at which the annotation was made.</Notes>
372 : parrello 1.1 </Field>
373 :     </Fields>
374 :     </Entity>
375 : parrello 1.2 <Entity name="Role" keyType="hash-string">
376 :     <DisplayInfo theme="web" col="5" row="5"/>
377 :     <Notes>A role describes a biological function that may be fulfilled by a feature.
378 :     One of the main goals of the database is to assign features to roles. Most
379 :     roles are effected by the construction of proteins. Some, however, deal with
380 :     functional regulation and message transmission.</Notes>
381 :     <Asides>A role represents a single gene function. Many roles are in
382 :     subsystems, but some are not. If a feature has multiple functions, each
383 :     is represented as a separate role.</Asides>
384 : parrello 1.1 <Fields>
385 : parrello 1.2 <Field name="hypothetical" type="boolean">
386 :     <Notes>TRUE if a role is hypothetical, else FALSE</Notes>
387 :     </Field>
388 :     <Field name="name" type="string">
389 :     <Notes>English name of this role. The actual role ID is computed from this field.</Notes>
390 : parrello 1.1 </Field>
391 :     </Fields>
392 :     </Entity>
393 : parrello 1.2 <Entity name="RoleSet" keyType="int">
394 :     <DisplayInfo theme="web" col="3" row="5" caption="Role Set"/>
395 :     <Notes>A role set is a group of roles that work together to stimulate a reaction. Most role sets consist of a single
396 :     role; however, some reactions require the presence of multiple roles to get them started.</Notes>
397 :     <Asides>A reaction is usually triggered by a single role, but some reactions are triggered
398 :     by a boolean combination of roles (e.g. =(A and (B or C) and D) or (E and B and F) or G=). The boolean
399 :     expression can be converted into disjunctive normal form, which is a list of alternative sets
400 :     (e.g. =(A and B and D) or (A and C and D) or (E and B and F) or G=). Each alternative is then converted
401 :     into a role set. This allows us to precisely represent the triggering conditions of a reaction in the database.</Asides>
402 :     </Entity>
403 : parrello 1.1 <Entity name="DnaSequence" keyType="name-string">
404 :     <DisplayInfo theme="nmpdr" col="7" row="11" caption="DNA Sequence"/>
405 :     <Notes>A DNA sequence (sometimes called a "contig") is a contiguous sequence of base pairs
406 : parrello 1.2 belonging to a single genome. The key of the DNA sequence is the genome ID followed by
407 :     the contig ID.</Notes>
408 : parrello 1.1 <Fields>
409 :     <Field name="length" type="counter">
410 :     <Notes>Number of base pairs in the DNA sequence.</Notes>
411 :     </Field>
412 :     <Field name="bases" type="text" relation="DnaSequenceBases">
413 :     <Notes>A string of letters representing the nucleotides of the sequence.</Notes>
414 :     </Field>
415 :     </Fields>
416 :     </Entity>
417 : parrello 1.2 <Entity name="TaxonomicGrouping" keyType="string">
418 :     <DisplayInfo row="10" col="8" caption="Taxonomic\nGrouping" theme="nmpdr"/>
419 :     <Notes>A taxonomic grouping is a segment of the classification for an organism.
420 :     Taxonomic groupings are organized into a strict hierarchy by the IsClassOf
421 :     relationship.</Notes>
422 : parrello 1.1 <Fields>
423 : parrello 1.2 <Field name="level" type="int">
424 :     <Notes>Taxonomic classification level. A level of 0 indicates that this is
425 :     a specific strain with DNA attached. Higher levels indicate progressively
426 :     larger classifications. Each level number represents a specific type of
427 :     classification. Sub-species is always 1, species is always 2, genus is always
428 :     3, and so forth, up to 99 for domain. This means that as you travel up the
429 :     taxonomy tree, the ranks will be non-sequential.</Notes>
430 : parrello 1.1 </Field>
431 : parrello 1.2 </Fields>
432 :     <Indexes>
433 :     <Index>
434 :     <Notes>This index allows the applications to find all groupings by level.
435 :     lower (less inclusive) levels will occur first.</Notes>
436 :     <IndexFields>
437 :     <IndexField name="level" order="ascending"/>
438 :     </IndexFields>
439 :     </Index>
440 :     </Indexes>
441 :     </Entity>
442 :     <Entity name="Structure" keyType="name-string">
443 :     <DisplayInfo theme="web" col="2" row="5"/>
444 :     <Notes>A structure is the geometrical representation of a protein sequence. A single protein sequence may
445 :     have multiple structural representations, either because it is folded in different ways or because there
446 :     are alternative representation formats. The key field is the representation type (e.g. PDB, SCOPE)
447 :     followed by the ID, with an intervening vertical bar.</Notes>
448 :     </Entity>
449 :     <Entity name="FcEvidenceSet" keyType="int">
450 :     <DisplayInfo theme="seed" col="5" row="13" caption="Functional Coupling Evidence Set"/>
451 :     <Notes>A functional coupling evidence set indicates evidence for a functional connection between protein
452 :     sequence pairs. The protein sequences possessing the connection are the ones that
453 :     participate in the evidence set's pairings.</Notes>
454 :     <Asides>The pairings for a particular evidence set
455 :     will contain protein sequences that are significantly similar. In other words, if
456 :     (A,B) and (X,Y) are both pairings in a single evidence set, then (A =~ X) and
457 :     (B =~ Y) or (A =~ Y) and (B =~ X), depending on the value of the "inverted" attribute of
458 :     the IsDeterminedBy relationship. Essentially, a pairing in its own right is unordered.
459 :     If (A,B) is a pair, then so is (B,A). However, the evidence set maintains a correspondence
460 :     between its pairs that _is_ ordered, because the constituent pairs must match. The
461 :     direction in which a pair matches others in the set is an attribute of the relationship from the pairs
462 :     to the sets.</Asides>
463 :     <Fields>
464 :     <Field name="score" type="int">
465 :     <Notes>Score for this evidence set. The score indicates the number of
466 :     significantly different genomes represented by the pairings.</Notes>
467 : parrello 1.1 </Field>
468 :     </Fields>
469 : parrello 1.2 </Entity>
470 :     <Entity name="MachineRole" keyType="name-string">
471 :     <DisplayInfo row="7" col="5" caption="Machine Role" theme="seed"/>
472 :     <Notes>A machine role represents a role as it occurs in a molecular machine. The key
473 :     is the machine key plus the role abbreviation.</Notes>
474 :     <Asides>The machine role corresponds to a cell on the subsystem spreadsheet. Features
475 :     in the subsystem are assigned directly to the machine role.</Asides>
476 :     </Entity>
477 :     <Entity name="IdentifierSet" keyType="name-string">
478 :     <DisplayInfo row="9" col="1" theme="seed"/>
479 :     <Notes>The identifier set is a group of identifiers that mean the same thing, usually either a Feature
480 :     or a Protein Sequence. The identifiers in a set will frequently belong to different genomic databases.
481 :     Thus, if a specific protein sequence has one name in the NMPDR and another name in RefSeq, both of
482 :     the names would be in the same identifier set.</Notes>
483 :     </Entity>
484 :     <Entity name="Identifier" keyType="string">
485 :     <DisplayInfo theme="seed" col="3" row="9"/>
486 :     <Notes>An identifier is an alternate name for a feature or protein sequence.</Notes>
487 :     <Asides>Some identifiers name features or protein sequences that do not exist in the database. In this case,
488 :     the feature or protein sequence is considered _external_; that is, it belongs to another database.</Asides>
489 :     <Fields>
490 :     <Field name="source" type="key-string">
491 :     <Notes>Specific type of the identifier, such as its source database or category.
492 :     The type can usually be decoded to convert the identifier to a URL.</Notes>
493 : parrello 1.1 </Field>
494 :     </Fields>
495 : parrello 1.2 <Indexes>
496 :     <Index>
497 :     <Notes>This index allows all the identifiers of a specified type to be located.</Notes>
498 :     <IndexFields>
499 :     <IndexField name="source" order="ascending"/>
500 :     </IndexFields>
501 :     </Index>
502 :     </Indexes>
503 :     </Entity>
504 :     </Entities>
505 :     <Relationships>
506 : parrello 1.1 <Relationship name="IsTerminusFor" from="Compound" to="Scenario" arity="MM" converse="HasAsTerminus">
507 :     <DisplayInfo caption="Has As\nTerminus"/>
508 :     <Notes>A terminus for a scenario is a compound that acts as its input or output. A compound
509 : parrello 1.2 can be the terminus for many scenarios, and a scenario will have many termini. The relationship
510 :     attributes indicate whether the compound is an input to the scenario or an output. In some
511 :     cases, there may be multiple alternative output groups. This is also indicated by the
512 :     attributes.</Notes>
513 : parrello 1.1 <Fields>
514 :     <Field name="group-number" type="int">
515 :     <Notes>If zero, then the compound is an input. Otherwise, this is the index number
516 : parrello 1.2 of the output group. Each output group represents an alternative set of output
517 :     compounds.</Notes>
518 : parrello 1.1 </Field>
519 :     </Fields>
520 :     <ToIndex>
521 :     <Notes>This index allows the application to view a scenario's compounds by group.</Notes>
522 :     <IndexFields>
523 :     <IndexField name="group-number" type="int"/>
524 :     </IndexFields>
525 :     </ToIndex>
526 :     </Relationship>
527 : parrello 1.2 <Relationship name="IsRelevantFor" from="Diagram" to="Subsystem" arity="MM" converse="IsRelevantTo">
528 :     <DisplayInfo theme="seed" caption="Is\nRelevant\nFor"/>
529 :     <Notes>Thie relationship connects each subsystem to the diagrams that are useful in curating
530 :     and understanding the subsystem. A subsystem may overlap many diagrams, but only those considered
531 :     crucial are connected via this relationship. The relationship is many-to-many.</Notes>
532 : parrello 1.1 </Relationship>
533 :     <Relationship name="Describes" from="Subsystem" to="Variant" arity="1M" converse="IsDescribedBy">
534 :     <DisplayInfo theme="seed"/>
535 :     <Notes>This relationship connects a subsystem to the individual variants used
536 :     to implement it. Each variant contains a slightly different subset of the
537 :     roles in the parent subsystem.</Notes>
538 :     </Relationship>
539 :     <Relationship name="Shows" from="Diagram" to="Reaction" arity="MM" converse="IsShowedOn">
540 :     <DisplayInfo theme="web"/>
541 :     <Notes>This relationship connects a diagram to its reactions. A diagram shows multiple
542 :     reactions, and a reaction can be on many diagrams.</Notes>
543 :     </Relationship>
544 : parrello 1.2 <Relationship name="IsOwnerOf" from="Genome" to="Feature" arity="1M" converse="IsOwnedBy">
545 :     <DisplayInfo caption="Is\nOwned\nBy" theme="seed"/>
546 :     <Notes>This relationship connects each feature to its parent genome.</Notes>
547 : parrello 1.1 </Relationship>
548 : parrello 1.2 <Relationship name="IsImplementedBy" from="Variant" to="MolecularMachine" arity="1M" converse="Implements">
549 :     <DisplayInfo theme="seed" caption="Is\nImplemented\nBy" row="6" col="7"/>
550 : parrello 1.1 <Notes>This relationship connects a variant to the physical machines that implement
551 :     it in the genomes. A variant is implemented by many machines, but a machine belongs to
552 :     only one variant.</Notes>
553 :     </Relationship>
554 : parrello 1.2 <Relationship name="Uses" theme="seed" from="Genome" to="MolecularMachine" arity="1M" converse="IsUsedBy">
555 :     <DisplayInfo theme="seed" caption="Is\nUsed\nBy"/>
556 :     <Notes>This relationship connects a genome to the machines that form its
557 :     metabolic pathways. A genome can use many machines, but a machine is used by exactly
558 :     one genome.</Notes>
559 :     </Relationship>
560 :     <Relationship name="Includes" from="Subsystem" to="Role" arity="MM" converse="IsIncludedIn">
561 :     <DisplayInfo theme="seed" caption="Includes"/>
562 :     <Notes>A subsystem is defined by its roles. The subsystem's variants contain slightly
563 :     different sets of roles, but all of the roles in a variant must be connected to the
564 :     parent subsystem by this relationship. A subsystem always has at least one
565 :     role, and a role always belongs to at least one subsystem.</Notes>
566 : parrello 1.1 <Fields>
567 : parrello 1.2 <Field name="sequence" type="counter">
568 :     <Notes>Sequence number of the role within the subsystem. When the roles
569 :     are formed into a variant, they will generally appear in sequence order.</Notes>
570 : parrello 1.1 </Field>
571 : parrello 1.2 <Field name="abbreviation" type="key-string">
572 :     <Notes>Abbreviation for this role in this subsystem. The abbreviations are
573 :     used in columnar displays, and they also appear on diagrams.</Notes>
574 : parrello 1.1 </Field>
575 :     </Fields>
576 : parrello 1.2 <FromIndex>
577 :     <Notes>This index insures that the roles of the subsystem are presented in sequence
578 :     order.</Notes>
579 : parrello 1.1 <IndexFields>
580 : parrello 1.2 <IndexField name="sequence" order="ascending"/>
581 : parrello 1.1 </IndexFields>
582 : parrello 1.2 </FromIndex>
583 : parrello 1.1 </Relationship>
584 : parrello 1.2 <Relationship name="Implements" from="ProteinSequence" to="Role" arity="MM" converse="IsCatalyzedBy">
585 :     <DisplayInfo theme="web" caption="Is\nImplemented\nBy"/>
586 : parrello 1.1 <Notes>This relationship connects a protein sequence to the functional roles it
587 : parrello 1.2 implements in the cell. A protein sequence can implement many roles, and a role can
588 :     be implemented by many protein sequences. Roles that perform regulatory or message
589 : parrello 1.1 transmission functions do not participate in this relationship.</Notes>
590 :     </Relationship>
591 : parrello 1.2 <Relationship name="IsCombinationOf" from="RoleSet" to="Role" arity="MM" converse="IsInCombination">
592 :     <DisplayInfo theme="web" caption="Is\nCombination\nOf"/>
593 :     <Notes>This relationship combines roles into role sets. Each role set is a combination of roles that can
594 :     trigger a reaction.</Notes>
595 :     </Relationship>
596 :     <Relationship name="IsTriggeredBy" from="Reaction" to="RoleSet" arity="MM" converse="Triggers">
597 :     <DisplayInfo theme="web" caption="Is\nTriggered\nBy"/>
598 :     <Notes>A reaction can be triggered by many role sets. A role set can trigger many reactions.</Notes>
599 :     </Relationship>
600 :     <Relationship name="IsClassOf" from="TaxonomicGrouping" to="TaxonomicGrouping" arity="1M" converse="IsClassifiedAs">
601 :     <DisplayInfo theme="nmpdr" col="8" row="11" fixed="1" caption="Is\nClass\nOf"/>
602 :     <Notes>The recursive IsClassOf relationship organizes taxonomic groupings into a hierarchy
603 :     based on the standard organism taxonomy.</Notes>
604 :     </Relationship>
605 :     <Relationship name="IsFoundOn" from="Role" to="Diagram" arity="MM" converse="IsLocationOf">
606 :     <DisplayInfo theme="web" caption="Is\nLocation\nOf"/>
607 :     <Notes>This relationship connects a role to the diagrams on which it appears. A diagram
608 :     always contains many roles. A role may appear on multiple diagrams.</Notes>
609 : parrello 1.1 </Relationship>
610 :     <Relationship name="IsLocatedIn" from="Feature" to="DnaSequence" arity="MM" converse="IsLocusFor">
611 : parrello 1.2 <DisplayInfo theme="seed" caption="Is\nLocated\nIn" fixed="1" row="10" col="6"/>
612 : parrello 1.1 <Notes>A feature is a set of DNA sequence fragments. Most features are a single contiquous
613 :     fragment, so they are located in only one DNA sequence; however, fragments have a maximum
614 :     length, so even a single contiguous feature may participate in this relationship multiple
615 :     times. A few features belong to multiple DNA sequences. In that case, however, all the
616 :     DNA sequences belong to the same genome. A DNA sequence itself will frequently have
617 :     thousands of features connected to it.</Notes>
618 :     <Fields>
619 :     <Field name="locN" type="int">
620 :     <Notes>Sequence number of this segment.</Notes>
621 :     </Field>
622 :     <Field name="beg" type="int">
623 :     <Notes>Index (1-based) of the first residue in the contig that
624 :     belongs to the segment.</Notes>
625 :     </Field>
626 :     <Field name="len" type="int">
627 :     <Notes>Number of residues in the segment. A length of 0 identifies
628 :     a specific point between residues. This is the point before the residue if the direction
629 :     is forward and the point after the residue if the direction is backward.</Notes>
630 :     </Field>
631 :     <Field name="dir" type="char">
632 :     <Notes>Direction of the segment: "+" if it is forward and
633 :     "-" if it is backward.</Notes>
634 :     </Field>
635 :     </Fields>
636 :     <FromIndex>
637 :     <Notes>This index allows the application to find all the segments of a feature in
638 :     the proper order.</Notes>
639 :     <IndexFields>
640 :     <IndexField name="locN" order="ascending"/>
641 :     </IndexFields>
642 :     </FromIndex>
643 :     <ToIndex>
644 :     <Notes>This index is the one used by applications to find all the feature
645 :     segments that contain a specific residue.</Notes>
646 :     <IndexFields>
647 :     <IndexField name="beg" order="ascending"/>
648 :     </IndexFields>
649 :     </ToIndex>
650 :     </Relationship>
651 : parrello 1.2 <Relationship name="IsDeterminedBy" from="FcEvidenceSet" to="Pairing" arity="MM" converse="Determines">
652 :     <DisplayInfo theme="seed" caption="Determines"/>
653 :     <Notes>A functional coupling evidence set exists because it has pairings in it, and this relationship
654 :     connects the evidence set to its constituent pairings. A pairing cam belong to
655 :     multiple evidence sets.</Notes>
656 :     <Fields>
657 :     <Field name="inverted" type="boolean">
658 :     <Notes>A pairing is an unordered pair of protein sequences, but its
659 :     similarity to other pairings in an evidence set is ordered. Let (A,B) be
660 :     a pairing and (X,Y) be another pairing in the same set. If this flag is
661 :     FALSE, then (A =~ X) and (B =~ Y). If this flag is TRUE, then (A =~ Y) and
662 :     (B =~ X).</Notes>
663 :     </Field>
664 :     </Fields>
665 :     </Relationship>
666 :     <Relationship name="IsFunctionOf" from="Role" to="Feature" arity="MM" converse="Targets">
667 :     <DisplayInfo theme="seed" fixed="1" row="7" col="4" caption="Is\nFunction\nOf"/>
668 :     <Notes>This relationship connects a role to the features that facilitate the role.
669 :     A role can be the function of multiple features, and a single feature may have
670 :     multiple roles.</Notes>
671 : parrello 1.1 </Relationship>
672 :     <Relationship name="IsMadeUpOf" from="Genome" to="DnaSequence" arity="1M" converse="MakesUp">
673 :     <DisplayInfo theme="nmpdr" caption="Is\nMade Up\nOf"/>
674 :     <Notes>This relationship connects each genome to the DNA sequences that make it up.</Notes>
675 :     </Relationship>
676 : parrello 1.2 <Relationship name="IsAnnotatedBy" from="Feature" to="Annotation" arity="1M" converse="Annotates">
677 :     <DisplayInfo theme="seed" caption="Is\nAnnotated\nBy" fixed="1" col="3" row="10"/>
678 :     <Notes>This relationship connects a feature to its annotations. A feature may have
679 :     multiple annotations, but an annotation belongs to only one feature.</Notes>
680 :     </Relationship>
681 :     <Relationship name="HasMember" from="Family" to="Feature" arity="1M" converse="IsMemberOf">
682 :     <DisplayInfo theme="seed" caption="Is\nMember\nOf" row="10" col="4" fixed="1"/>
683 :     <Notes>This relationship connects each feature family to its constituent
684 :     features. A family always has many features, but a single feature can
685 :     be found in at most one family.</Notes>
686 : parrello 1.1 </Relationship>
687 :     <Relationship name="Attracts" from="Structure" to="Compound" arity="MM" converse="IsAttractedTo">
688 : parrello 1.2 <DisplayInfo theme="web" row="1" col="2" fixed="1" caption="Is\nAttracted\nTo"/>
689 : parrello 1.1 <Notes>This relationship connects a compound to the protein structures that attract it.
690 :     This is an incomplete relationship that exists to service drug targeting queries. Only
691 :     the attractions whose parameters have been determined through modeling or
692 :     experimentation are included. The goal is to determine the docking energy between
693 :     the compound and the protein structure.</Notes>
694 :     <Fields>
695 :     <Field name="reason" type="id-string">
696 :     <Notes>Indication of the reason for determining the docking energy.
697 :     A value of "Random" indicates the docking was attempted as a part
698 :     of a random survey used to determine the docking characteristics of a
699 :     protein structure. A value of "Rich" indicates the docking was attempted
700 :     because a low-energy docking result was predicted for the compound.</Notes>
701 :     </Field>
702 :     <Field name="tool" type="id-string">
703 :     <Notes>Name of the tool used to compute the docking energy.</Notes>
704 :     </Field>
705 :     <Field name="total-energy" type="float">
706 :     <Notes>Total energy required for the compound to dock with the structure,
707 :     in kcal/mol. A negative value means energy is released.</Notes>
708 :     </Field>
709 :     <Field name="vanderwalls-energy" type="float">
710 :     <Notes>Docking energy in kcal/mol that results from the geometric fit
711 :     (Van der Waals force) between the structure and the compound.</Notes>
712 :     </Field>
713 :     <Field name="electrostatic-energy" type="float">
714 :     <Notes>Docking energy in kcal/mol that results from the movement of
715 :     electrons (electrostatic force) between the structure and the
716 :     compound.</Notes>
717 :     </Field>
718 :     </Fields>
719 :     <FromIndex>
720 :     <Notes>This index enables the application to view a structure's docking results from
721 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
722 :     <IndexFields>
723 :     <IndexField name="total-energy" order="ascending"/>
724 :     </IndexFields>
725 :     </FromIndex>
726 :     <ToIndex>
727 :     <Notes>This index enables the application to view a compound's docking results from
728 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
729 :     <IndexFields>
730 :     <IndexField name="total-energy" order="ascending"/>
731 :     </IndexFields>
732 :     </ToIndex>
733 :     </Relationship>
734 : parrello 1.2 <Relationship name="Involves" from="Reaction" to="Compound" arity="MM" converse="IsInvolvedIn">
735 :     <DisplayInfo theme="web" caption="Is\nInvolved\nIn" fixed="1" row="2" col="2.5"/>
736 :     <Notes>This relationship connects a reaction to the compounds that participate in
737 :     it. A reaction involves many compounds, and a compound can be involved in many reactions.
738 :     The relationship attributes indicate whether a compound is a product or substrate of the
739 :     reaction, as well as its stoichiometry.</Notes>
740 :     <Fields>
741 :     <Field name="product" type="boolean">
742 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
743 :     it is a substrate. When a reaction is written on paper in
744 :     chemical notation, the substrates are left of the arrow and the
745 :     products are to the right. Sorting on this field will cause
746 :     the substrates to appear first, followed by the products. If the
747 :     reaction is reversible, then the notion of substrates and products
748 :     is not intuitive; however, a value here of FALSE still puts the
749 :     compound left of the arrow and a value of TRUE still puts it to the
750 :     right.</Notes>
751 :     </Field>
752 :     <Field name="stoichiometry" type="key-string">
753 :     <Notes>Number of molecules of the compound that participate in a
754 :     single instance of the reaction. For example, if a reaction
755 :     produces two water molecules, the stoichiometry of water for the
756 :     reaction would be two. When a reaction is written on paper in
757 :     chemical notation, the stoichiometry is the number next to the
758 :     chemical formula of the compound.</Notes>
759 :     </Field>
760 :     <Field name="main" type="boolean">
761 :     <Notes>TRUE if this compound is one of the main participants in
762 :     the reaction, else FALSE. It is permissible for none of the
763 :     compounds in the reaction to be considered main, in which
764 :     case this value would be FALSE for all of the relevant
765 :     compounds.</Notes>
766 :     </Field>
767 :     <Field name="loc" type="key-string">
768 :     <Notes>An optional character string that indicates the relative
769 :     position of this compound in the reaction's chemical formula. The
770 :     location affects the way the compounds present as we cross the
771 :     relationship from the reaction side. The product/substrate flag
772 :     comes first, then the value of this field, then the main flag.
773 :     The default value is an empty string; however, the empty string
774 :     sorts first, so if this field is used, it should probably be
775 :     used for every compound in the reaction.</Notes>
776 :     </Field>
777 :     <Field name="discriminator" type="int">
778 :     <Notes>A unique ID for this record. The discriminator does not
779 :     provide any useful data, but it prevents identical records from
780 :     being collapsed by the SELECT DISTINCT command used by ERDB to
781 :     retrieve data.</Notes>
782 :     </Field>
783 :     </Fields>
784 :     <ToIndex>
785 :     <Notes>This index presents the compounds in the reaction in the
786 :     order they should be displayed when writing it in chemical notation.
787 :     All the substrates appear before all the products, and within that
788 :     ordering, the main compounds appear first.</Notes>
789 :     <IndexFields>
790 :     <IndexField name="product" order="ascending"/>
791 :     <IndexField name="loc" order="ascending"/>
792 :     <IndexField name="main" order="descending"/>
793 :     </IndexFields>
794 :     </ToIndex>
795 :     </Relationship>
796 :     <Relationship name="Contains" from="Diagram" to="Compound" arity="MM" converse="IsContainedIn">
797 :     <DisplayInfo theme="web" fixed="1" caption="Is\nContained\nIn" row="2" col="3.5"/>
798 :     <Notes>This relationship indicates that a compound appears on a particular diagram.
799 :     The same compound can appear on many diagrams, and a diagram always contains many
800 :     compounds.</Notes>
801 :     </Relationship>
802 :     <Relationship name="IsContainedIn" from="Feature" to="MachineRole" arity="MM" converse="Contains">
803 :     <DisplayInfo theme="seed" caption="Is\nContained\nIn" row="8" col="5"/>
804 :     <Notes>This relationship connects a machine role to the features that occur in it. A feature
805 :     may occur in many machine roles and a machine role may contain many features. The subsystem
806 :     annotation process is essentially the maintenance of this relationship.</Notes>
807 :     </Relationship>
808 :     <Relationship name="IsRoleOf" from="Role" to="MachineRole" arity="1M" converse="HasRole">
809 :     <DisplayInfo caption="Is\nRole\nOf" theme="seed"/>
810 :     <Notes>This relationship connects a role to the machine roles that represent its
811 :     appearance in a molecular machine. A machine role has exactly one associated role,
812 :     but a role may be represented by many machine roles.</Notes>
813 :     </Relationship>
814 : parrello 1.1 <Relationship name="IsTerminusFor" from="Compound" to="Scenario" arity="MM" converse="HasAsTerminus">
815 : parrello 1.2 <DisplayInfo theme="web" caption="Is\nTerminus\nFor"/>
816 : parrello 1.1 <Notes>A terminus for a scenario is a compound that acts as its input or output. A
817 :     compound can be the terminus for many scenarios, and a scenario will have many termini.
818 :     The relationship attributes indicate whether the compound is an input to the scenario or
819 : parrello 1.2 an output.</Notes>
820 : parrello 1.1 <Fields>
821 :     <Field name="group-number" type="int">
822 : parrello 1.2 <Notes>The group number is 0 for an input compound; 1, for an output compound, and 2 for
823 :     an auxiliary compound. An ancillary compound is one that is produced by the
824 :     scenario, but is not the primary output.</Notes>
825 : parrello 1.1 </Field>
826 :     </Fields>
827 :     <ToIndex>
828 :     <Notes>This index presents the terminal compounds for a scenario in group
829 :     order.</Notes>
830 :     <IndexFields>
831 :     <IndexField name="group-number" order="ascending"/>
832 :     </IndexFields>
833 :     </ToIndex>
834 :     </Relationship>
835 : parrello 1.2 <Relationship name="Exposes" from="ProteinSequence" to="Structure" arity="MM" converse="IsExposedBy">
836 :     <DisplayInfo theme="web" fixed="1" row="7" col="2" caption="Is\nExposed\nBy"/>
837 :     <Notes>This relationship connects a protein sequence to its structural representations. It is a
838 :     many-to-many relationship. Note that only some protein sequences have known structural representations.</Notes>
839 :     </Relationship>
840 :     <Relationship name="IsSubInstanceOf" from="Subsystem" to="Scenario" arity="1M" converse="Validates">
841 :     <DisplayInfo theme="seed" caption="Is Part\nInstance\nOf" fixed="1" row="1" col="7"/>
842 :     <Notes>This relationship connects a scenario to its subsystem it validates. A scenario
843 :     belongs to exactly one subsystem, but a subsystem may have multiple scenarios.</Notes>
844 :     </Relationship>
845 : parrello 1.1 <Relationship name="Overlaps" from="Scenario" to="Diagram" arity="MM" converse="IncludesPartOf">
846 : parrello 1.2 <DisplayInfo theme="web" fixed="1" row="2" col="5.5"/>
847 : parrello 1.1 <Notes>A Scenario overlaps a diagram when the diagram displays a portion of the reactions
848 :     that make up the scenario. A scenario may overlap many diagrams, and a diagram may
849 :     be include portions of many scenarios.</Notes>
850 :     </Relationship>
851 :     <Relationship name="HasParticipant" from="Scenario" to="Reaction" arity="MM" converse="ParticipatesIn">
852 : parrello 1.2 <DisplayInfo theme="web" caption="Has\nParticipant" row="2" col="4.5" fixed="1"/>
853 : parrello 1.1 <Notes>A scenario consists of many participant reactions that convert the input compounds
854 :     to output compounds. A single reaction may participate in many scenarios.</Notes>
855 : parrello 1.2 <Fields>
856 :     <Field name="type" type="int">
857 :     <Notes>Indicates the type of participaton. If 0, the reaction is in the main pathway of
858 :     the scenario. If 1, the reaction is necessary to make the model work but is not in the
859 :     subsystem. If 2, the reaction is part of the subsystem but should not be included in
860 :     the modelling process.</Notes>
861 :     </Field>
862 :     </Fields>
863 :     <FromIndex>
864 :     <Notes>This index presents the reactions in the scenario in order from
865 :     most important to least important.</Notes>
866 :     <IndexFields>
867 :     <IndexField name="type" order="ascending"/>
868 :     </IndexFields>
869 :     </FromIndex>
870 : parrello 1.1 </Relationship>
871 : parrello 1.2 <Relationship name="IsInPair" from="Feature" to="Pairing" arity="MM" converse="Contains">
872 :     <DisplayInfo theme="seed" caption="Is In\nPair"/>
873 :     <Notes>A pairing contains exactly two protein sequences. A protein sequence can
874 :     belong to multiple pairings. When going from a protein sequence to its pairings,
875 :     they are presented in alphabetical order by sequence key.</Notes>
876 : parrello 1.1 </Relationship>
877 :     <Relationship name="Concerns" from="Publication" to="ProteinSequence" arity="MM" converse="IsATopicOf">
878 : parrello 1.2 <DisplayInfo theme="web" row="8" col="2" caption="Is A\nTopic\nOf" fixed="1"/>
879 : parrello 1.1 <Notes>This relationship connects a publication to the protein sequences it
880 :     describes.</Notes>
881 :     </Relationship>
882 : parrello 1.2 <Relationship name="IsTaxonomyOf" to="Genome" from="TaxonomicGrouping" arity="1M" converse="IsInTaxa">
883 :     <DisplayInfo theme="nmpdr" fixed="1" caption="Is In\nTaxa" row="9" col="8"/>
884 :     <Notes>A genome belongs to exactly one taxonomic grouping. A taxonomic grouping
885 :     contains many genomes. Some taxonomic groupings do not contain any genomes. These
886 :     in fact contain other taxonomic groups.</Notes>
887 :     </Relationship>
888 :     <Relationship name="IsMachineOf" from="MolecularMachine" to="MachineRole" arity="1M" converse="IsRoleOf">
889 :     <DisplayInfo caption="Is\nMachine\nOf" theme="seed"/>
890 :     <Notes>This relationship connects a molecular machine to its various machine roles.
891 :     Each machine has many machine roles, but each machine role belongs to only one machine.</Notes>
892 :     </Relationship>
893 :     <Relationship name="IsSequenceFor" from="ProteinSequence" to="Identifier" arity="1M" converse="IsFeatureFor">
894 :     <DisplayInfo caption="Is\nSequence\nFor" theme="seed"/>
895 :     <Notes>This relationship connects a peg identifier to the protein sequence it produces (if any).
896 :     Only peg identifiers participate in this relationship. Identifiers that name RNAs,
897 :     operons, or other non-protein feature do not connect to protein sequences. A single
898 :     protein sequence will frequently have many identifiers.</Notes>
899 :     </Relationship>
900 :     <Relationship name="IncludesIdentifier" from="IdentifierSet" to="Identifier" arity="1M" converse="IsIncludedInSet">
901 :     <DisplayInfo theme="seed" caption="Includes" row="9.5" col="1.5"/>
902 :     <Notes>An identifier set contains many identifiers. If the set identifies a feature, then one of the identifiers
903 :     will be a feature ID. If the set identifies a protein sequence, then one of the identifiers will be the
904 :     MD5 hash key for the protein sequence.</Notes>
905 : parrello 1.1 </Relationship>
906 :     </Relationships>
907 :     <Shapes>
908 : parrello 1.2 <Shape type="diamond" name="ConsistsOf" from="Variant" to="Role">
909 :     <DisplayInfo theme="neutral" caption="Belongs To" connected="1"/>
910 :     <Notes>This relationship is not physically implemented in the database. It is
911 :     implicit in the data for a variant. A variant contains a boolean expression that
912 :     describes the various combinations of roles it can contain.</Notes>
913 :     </Shape>
914 :     <Shape type="diamond" name="IsIdentifiedBy" from="Feature" to="Identifier">
915 :     <DisplayInfo theme="neutral" caption="Identifies" connected="1"/>
916 :     <Notes>This relationship is not physically implemented in the database. It is
917 :     implicit in the data for an identifier. If the identifiers is a FIG feature
918 :     ID, then it identifies that feature, as do all other identifiers in the same
919 :     identifier set.</Notes>
920 :     </Shape>
921 : parrello 1.1 </Shapes>
922 :     </Database>

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