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

Annotation of /Sprout/SaplingDBD.xml

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (view) (download) (as text)

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 : parrello 1.3 <Issue>We may want to do some compression on the "dna" data type.</Issue>
8 : parrello 1.1 <Issue>Must add back the ability to index a secondary relation. Note that
9 : parrello 1.2 such indexes can only have a single field.</Issue>
10 : parrello 1.1 <Issue>We probably need some type tables that describe things like Identifier(source)
11 : parrello 1.2 or Family(kind).</Issue>
12 : parrello 1.1 <Issue>The ERDB documentation needs to be updated to include DisplayInfo, Asides,
13 : parrello 1.2 the "converse" attribute for relationships, and the Shapes section.</Issue>
14 : parrello 1.1 </Issues>
15 :     <Entities>
16 :     <Entity name="Compound" keyType="name-string">
17 : parrello 1.2 <DisplayInfo theme="web" col="3" row="1"/>
18 : parrello 1.1 <Notes>A compound is a chemical that participates in a reaction.
19 : parrello 1.2 All compounds have a unique ID and may also have one or more names. Both
20 :     ligands and reaction components are treated as compounds.</Notes>
21 : parrello 1.1 <Fields>
22 :     <Field name="label" type="string">
23 :     <Notes>Primary name of the compound. This is the name used in reaction
24 : parrello 1.2 display strings.</Notes>
25 : parrello 1.1 </Field>
26 :     <Field name="name" type="string" relation="CompoundName">
27 :     <Notes>Alternate name for the compound. A compound may have many
28 : parrello 1.2 alternate names. The primary name should also be one of the
29 :     alternate names.</Notes>
30 : parrello 1.1 </Field>
31 :     <Field name="cas-id" type="string" relation="CompoundCAS">
32 :     <Notes>The Chemical Abstract Service ID for the compound. A
33 : parrello 1.2 compound may have at most one CAS ID.</Notes>
34 : parrello 1.1 </Field>
35 :     <Field name="zinc-id" type="string" relation="CompoundZinc">
36 :     <Notes>The ZINC database ID for the compound. A compound may
37 : parrello 1.2 have at most one ZINC ID.</Notes>
38 : parrello 1.1 </Field>
39 :     </Fields>
40 :     <Indexes>
41 :     <Index>
42 :     <Notes>This index allows searching for compounds by name.</Notes>
43 :     <IndexFields>
44 :     <IndexField name="name" order="ascending"/>
45 :     </IndexFields>
46 :     </Index>
47 :     <Index>
48 :     <Notes>This index allows searching for compounds by CAS ID.</Notes>
49 :     <IndexFields>
50 :     <IndexField name="cas-id" order="ascending"/>
51 :     </IndexFields>
52 :     </Index>
53 :     <Index>
54 :     <Notes>This index allows searching for compounds by ZINC ID.</Notes>
55 :     <IndexFields>
56 :     <IndexField name="zinc-id" order="ascending"/>
57 :     </IndexFields>
58 :     </Index>
59 :     </Indexes>
60 :     </Entity>
61 :     <Entity name="Diagram" keyType="name-string">
62 : parrello 1.2 <DisplayInfo theme="web" col="5" row="3"/>
63 : parrello 1.1 <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
64 : parrello 1.2 subsystem. A diagram is identified by a short name and contains a longer descriptive name.</Notes>
65 : parrello 1.1 <Fields>
66 :     <Field name="name" type="text">
67 :     <Notes>Descriptive name of this diagram.</Notes>
68 :     </Field>
69 :     <Field name="content" type="image" relation="DiagramContent">
70 :     <Notes>The content of the diagram, in PNG format encoded as base 64 MIME.</Notes>
71 :     </Field>
72 :     </Fields>
73 :     </Entity>
74 :     <Entity name="Reaction" keyType="key-string">
75 : parrello 1.2 <DisplayInfo theme="web" col="3" row="3"/>
76 : parrello 1.1 <Notes>A reaction is a chemical process that converts one set of compounds (substrate)
77 : parrello 1.2 to another set (products). The reaction ID is generally a small number preceded by a
78 :     letter.</Notes>
79 : parrello 1.1 <Fields>
80 :     <Field name="url" type="string" relation="ReactionURL">
81 :     <Notes>HTML string containing a link to a web location that describes the
82 : parrello 1.2 reaction. This field is optional.</Notes>
83 : parrello 1.1 </Field>
84 :     <Field name="rev" type="boolean">
85 :     <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
86 :     </Field>
87 :     </Fields>
88 :     </Entity>
89 :     <Entity name="Subsystem" keyType="id-string">
90 :     <DisplayInfo theme="seed" col="7" row="3"/>
91 :     <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
92 : parrello 1.2 is an important tool for recognizing parallel genetic features in different organisms. The key
93 :     is an alphanumeric code string.</Notes>
94 : parrello 1.1 <Fields>
95 :     <Field name="name" type="string">
96 :     <Notes>Displayable name of this subsystem.</Notes>
97 :     </Field>
98 :     <Field name="version" type="int">
99 :     <Notes>Version number for the subsystem. This value is incremented each time the subsystem
100 : parrello 1.2 is backed up.</Notes>
101 : parrello 1.1 </Field>
102 :     <Field name="curator" type="string">
103 :     <Notes>Name of the person currently in charge of the subsystem.</Notes>
104 :     </Field>
105 :     <Field name="notes" type="text">
106 :     <Notes>Descriptive notes about the subsystem.</Notes>
107 :     </Field>
108 :     <Field name="description" type="text">
109 :     <Notes>Description of the subsystem's function in the cell.</Notes>
110 :     </Field>
111 :     <Field name="classification" type="string">
112 :     <Notes>Classification string, colon-delimited. This string organizes the
113 : parrello 1.2 subsystems into a hierarchy.</Notes>
114 : parrello 1.1 </Field>
115 :     </Fields>
116 :     <Indexes>
117 :     <Index>
118 :     <Notes>This index is used to get the subsystems in hierarchical order.</Notes>
119 :     <IndexFields>
120 :     <IndexField name="classification" order="ascending"/>
121 :     </IndexFields>
122 :     </Index>
123 :     <Index>
124 :     <Notes>This index is used to get the subsystem by name.</Notes>
125 :     <IndexFields>
126 :     <IndexField name="name" order="ascending"/>
127 :     </IndexFields>
128 :     </Index>
129 :     </Indexes>
130 :     </Entity>
131 :     <Entity name="Publication" keyType="hash-string">
132 : parrello 1.2 <DisplayInfo theme="web" col="1" row="8"/>
133 : parrello 1.1 <Notes>A _publication_ is an article or citation that may be used as evidence for
134 : parrello 1.2 assertions made in the database. The key is a hash code computed from the URL.</Notes>
135 : parrello 1.1 <Fields>
136 :     <Field name="url" type="string">
137 :     <Notes>URL of the article or of its citation.</Notes>
138 :     </Field>
139 :     <Field name="citation" type="text">
140 :     <Notes>Citation string for the article.</Notes>
141 :     </Field>
142 :     </Fields>
143 :     <Indexes>
144 :     <Index>
145 :     <Notes>This index allows searching for the article by the author names and title.</Notes>
146 :     <IndexFields>
147 :     <IndexField name="citation" order="ascending"/>
148 :     </IndexFields>
149 :     </Index>
150 :     </Indexes>
151 :     </Entity>
152 : parrello 1.2 <Entity name="Variant" keyType="name-string">
153 :     <DisplayInfo theme="seed" col="7" row="5"/>
154 :     <Notes>A variant is a functional subset of a subsystem. It indicates the particular
155 :     sequence of roles used to implement a metabolic pathway. Variants are abstract
156 :     concepts used to classify machines. The key of the variant is the subsystem ID followed
157 :     by the variant code (usually a numeric string with zero or more decimal points).</Notes>
158 :     <Fields>
159 :     <Field name="role-rule" type="text">
160 :     <Notes>Boolean expression (encoded as text) that describes the roles in this variant.
161 :     The roles themselves are represented by their IDs.</Notes>
162 : parrello 1.1 </Field>
163 :     </Fields>
164 :     </Entity>
165 :     <Entity name="ProteinSequence" keyType="hash-string">
166 :     <DisplayInfo theme="web" col="3" row="7" caption="Protein Sequence"/>
167 :     <Notes>A protein sequence is a specific sequence of amino acids. Unlike a DNA sequence, a
168 : parrello 1.2 protein sequence does not belong to a genome. Identical proteins generated by different
169 :     genomes are generally stored as a single ProteinSequence instance. The key is a
170 :     hash of the protein letter sequence.</Notes>
171 : parrello 1.1 <Fields>
172 :     <Field name="sequence" type="dna">
173 :     <Notes>The sequence contains the letters corresponding to the protein's
174 : parrello 1.2 amino acids.</Notes>
175 : parrello 1.1 </Field>
176 :     <Field name="iedb" type="text" relation="ProteinSequenceIEDB" special="property_search">
177 :     <Notes>A value indicating whether or not the feature can be found in the
178 : parrello 1.2 Immune Epitope Database. If the feature has not been matched to that database,
179 :     this field will have no values. Otherwise, it will have an epitope name and/or
180 :     sequence, hyperlinked to the database.</Notes>
181 : parrello 1.1 </Field>
182 :     <Field name="signal-peptide" type="name-string">
183 :     <Notes>The signal peptide location for this feature. This is expressed as start and end
184 : parrello 1.2 numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
185 :     peptide at the beginning of the feature's protein and extending through 22 amino acid
186 :     positions. An empty string means no signal peptide is present.</Notes>
187 : parrello 1.1 </Field>
188 :     <Field name="transmembrane-map" type="text">
189 :     <Notes>A map indicating which sections of a protein will be embedded in a membrane.
190 : parrello 1.2 This is expressed as a comma-separated list of as start and end numbers with hyphens
191 :     for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
192 :     sections of the protein that become embedded in a membrane: the 10th through 12th
193 :     amino acids, and the 40th through the 60th. An empty string means no
194 :     transmembrane regions are known.</Notes>
195 : parrello 1.1 </Field>
196 :     <Field name="similar-to-human" type="boolean">
197 :     <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
198 : parrello 1.2 else FALSE</Notes>
199 : parrello 1.1 </Field>
200 :     <Field name="isoelectric-point" type="float">
201 :     <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
202 : parrello 1.2 If the pH of the medium is lower than this value, the protein will have a net
203 :     positive charge. If the pH of the medium is higher, then the protein will have a
204 :     net negative charge.</Notes>
205 : parrello 1.1 </Field>
206 :     <Field name="molecular-weight" type="float">
207 :     <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
208 : parrello 1.2 indicates that no protein is created.</Notes>
209 : parrello 1.1 </Field>
210 :     </Fields>
211 :     </Entity>
212 : parrello 1.2 <Entity name="Family" keyType="name-string">
213 :     <DisplayInfo theme="seed" col="4" row="11"/>
214 :     <Notes>A family is a group of features united by a particular determination algorithm.
215 :     The algorithm will frequently-- but not always-- signify a functional role.</Notes>
216 : parrello 1.1 </Entity>
217 : parrello 1.2 <Entity name="MolecularMachine" keyType="key-string">
218 :     <DisplayInfo theme="seed" col="7" row="7" caption="Molecular\nMachine"/>
219 :     <Notes>A molecular machine is a collection of features that implements a metabolic pathway. Machines
220 :     are the physical instances of variants. Each machine corresponds to a row in a subsystem
221 :     spreadsheet. The key is the variant key followed by a colon and the Genome ID.</Notes>
222 : parrello 1.1 <Fields>
223 :     <Field name="type" type="key-string">
224 :     <Notes>The machine type indicates how it relates to the parent variant. A type
225 : parrello 1.2 of "vacant" means that the machine does not appear to actually exist in the
226 :     organism. A type of "incomplete" means that the machine appears to be missing
227 :     many reactions. In all other cases, the type is "normal".</Notes>
228 : parrello 1.1 </Field>
229 :     </Fields>
230 :     </Entity>
231 : parrello 1.2 <Entity name="Scenario" keyType="string">
232 :     <DisplayInfo theme="web" col="5" row="1"/>
233 :     <Notes>A scenario is a partial instance of a subsystem with a defined set of
234 :     reactions.Each scenario converrts input compounds to output compounds using reactions.
235 :     The scenario may use all of the reactions controlled by a subsystem or only
236 :     some, and may also incorporate additional reactions.</Notes>
237 : parrello 1.1 </Entity>
238 : parrello 1.2 <Entity name="Pairing" keyType="name-string">
239 : parrello 1.1 <DisplayInfo theme="seed" col="5" row="11"/>
240 : parrello 1.2 <Notes>A pairing indicates that two protein sequences are found close together on one or
241 :     more DNA sequences. Not all possible pairings are stored in the database; only those that
242 :     are considered for some reason to be significant for annotation purposes.The key of the pairing is the
243 :     concatenation of the protein sequence keys in alphabetical order.</Notes>
244 :     <Asides>Because the protein sequence key is a hash of the sequence letters, the key of a pairing between two
245 :     sequences is computable from the sequences themselves. Theoretically, the pairing
246 :     is unordered: (A,B) and (B,A) are the same pairing. It is frequently the case,
247 :     however, that we need to refer to the "first" or "second" protein in the pairing.
248 :     When this happens, the first one is always the protein with the alphabetically
249 :     lesser key. The IsInPair relationship automatically shows the proteins in this
250 :     order.</Asides>
251 : parrello 1.1 </Entity>
252 :     <Entity name="Genome" keyType="name-string">
253 :     <DisplayInfo theme="nmpdr" col="7" row="9" caption="Genome Organism"/>
254 : parrello 1.2 <Notes>A genome represents a specific organism with DNA, or a specific meta-genome. All DNA
255 :     sequences in the database belong to genomes.</Notes>
256 : parrello 1.1 <Fields>
257 :     <Field name="full-name" type="name-string">
258 : parrello 1.2 <Notes>Full genus/species/strain name of the genome.</Notes>
259 : parrello 1.1 </Field>
260 :     <Field name="domain" type="name-string">
261 :     <Notes>Domain for this genome or taxonomic classification. The domain is
262 : parrello 1.2 the highest level of the taxonomy tree.</Notes>
263 : parrello 1.1 </Field>
264 :     <Field name="version" type="name-string">
265 :     <Notes>Version string for this genome, generally consisting of the genome ID followed
266 : parrello 1.2 by a period and a string of digits.</Notes>
267 : parrello 1.1 </Field>
268 :     <Field name="complete" type="boolean">
269 :     <Notes>TRUE if the genome is complete, else FALSE</Notes>
270 :     </Field>
271 :     <Field name="dna-size" type="counter">
272 :     <Notes>number of base pairs in the genome</Notes>
273 :     </Field>
274 :     <Field name="primary-group" type="name-string">
275 :     <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR
276 : parrello 1.2 group per organism. An empty string indicates the organism is supporting. In general,
277 :     more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>
278 : parrello 1.1 </Field>
279 :     <Field name="contigs" type="int">
280 :     <Notes>Number of contigs for this organism.</Notes>
281 :     </Field>
282 :     <Field name="pegs" type="int">
283 :     <Notes>Number of protein encoding genes for this organism</Notes>
284 :     </Field>
285 :     <Field name="rnas" type="int">
286 :     <Notes>Number of RNA features found for this organism.</Notes>
287 :     </Field>
288 :     </Fields>
289 :     <Indexes>
290 :     <Index>
291 :     <Notes>This index allows the applications to find all genomes associated with
292 : parrello 1.2 a specific primary (NMPDR) group.</Notes>
293 : parrello 1.1 <IndexFields>
294 :     <IndexField name="primary-group" order="ascending"/>
295 :     <IndexField name="full-name" order="ascending"/>
296 :     </IndexFields>
297 :     </Index>
298 :     <Index>
299 :     <Notes>This index allows the applications to find all genomes in lexical
300 : parrello 1.2 order by name.</Notes>
301 : parrello 1.1 <IndexFields>
302 :     <IndexField name="full-name" order="ascending"/>
303 :     </IndexFields>
304 :     </Index>
305 :     </Indexes>
306 :     </Entity>
307 : parrello 1.2 <Entity name="Feature" keyType="id-string">
308 :     <DisplayInfo theme="seed" col="5" row="9"/>
309 :     <Notes>A feature (sometimes also called a gene) is a part of a genome that is of special
310 :     interest. Features may be spread across multiple DNA sequences (contigs) of a genome, but
311 :     never across more than one genome. Each feature in the database has a unique FIG ID.</Notes>
312 :     <Fields>
313 :     <Field name="feature-type" type="id-string">
314 :     <Notes>Code indicating the type of this feature. Among the codes currently
315 :     supported are "peg" for a protein encoding gene, "bs" for a
316 :     binding site, "opr" for an operon, and so forth.</Notes>
317 :     </Field>
318 :     <Field name="link" type="text" relation="FeatureLink">
319 :     <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
320 :     links are to other websites that have useful about the gene that the feature represents, and
321 :     are coded as raw HTML, using an anchor href tag.</Notes>
322 :     </Field>
323 :     <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
324 :     <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
325 :     cases, this will be a word describing whether the essentiality is confirmed (essential)
326 :     or potential (potential-essential), hyperlinked to the document from which the
327 :     essentiality was curated. If a feature is not essential, this field will have no
328 :     values; otherwise, it may have multiple values.</Notes>
329 :     </Field>
330 :     <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
331 :     <Notes>A value indicating the virulence of the feature, coded as HTML. In most
332 :     cases, this will be a phrase or SA number hyperlinked to the document from which
333 :     the virulence information was curated. If the feature is not virulent, this field
334 :     will have no values; otherwise, it may have multiple values.</Notes>
335 :     </Field>
336 :     <Field name="sequence-length" type="counter">
337 :     <Notes>Number of base pairs in this feature.</Notes>
338 :     </Field>
339 :     <Field name="evidence-code" type="string" relation="FeatureEvidence">
340 :     <Notes>An evidence code describes the possible evidence that exists
341 :     for deciding a feature's functional assignment. A feature may have no evidence,
342 :     a single evidence code, or several.</Notes>
343 :     </Field>
344 :     <Field name="function" type="text">
345 :     <Notes>Functional assignment for this feature. This will often indicate
346 :     the feature's functional role or roles, and may also have comments.</Notes>
347 :     <Asides>It will frequently be the case that a feature is assigned to a single
348 :     role, and it is identical to the function. In some cases, a feature will have
349 :     multiple roles, and all of them will be listed in the function field. In addition,
350 :     the function may have comment text at the end.</Asides>
351 :     </Field>
352 :     </Fields>
353 :     </Entity>
354 :     <Entity name="Annotation" keyType="string">
355 :     <DisplayInfo col="3" row="11" theme="seed"/>
356 :     <Notes>An annotation is a comment attached to a feature. Annotations are used to
357 :     track the history of a feature's functional assignments and any related issues. The
358 :     key is the feature ID followed by a colon and an complemented eight-digit sequence number.</Notes>
359 :     <Asides>The complemented sequence number causes the annotations to sort with the most recent one
360 :     first.</Asides>
361 : parrello 1.1 <Fields>
362 : parrello 1.2 <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 : parrello 1.1 </Field>
371 :     </Fields>
372 :     </Entity>
373 : parrello 1.2 <Entity name="Role" keyType="hash-string">
374 :     <DisplayInfo theme="web" col="5" row="5"/>
375 :     <Notes>A role describes a biological function that may be fulfilled by a feature.
376 :     One of the main goals of the database is to assign features to roles. Most
377 :     roles are effected by the construction of proteins. Some, however, deal with
378 :     functional regulation and message transmission.</Notes>
379 :     <Asides>A role represents a single gene function. Many roles are in
380 :     subsystems, but some are not. If a feature has multiple functions, each
381 :     is represented as a separate role.</Asides>
382 : parrello 1.1 <Fields>
383 : parrello 1.2 <Field name="hypothetical" type="boolean">
384 :     <Notes>TRUE if a role is hypothetical, else FALSE</Notes>
385 :     </Field>
386 :     <Field name="name" type="string">
387 :     <Notes>English name of this role. The actual role ID is computed from this field.</Notes>
388 : parrello 1.1 </Field>
389 :     </Fields>
390 :     </Entity>
391 : parrello 1.2 <Entity name="RoleSet" keyType="int">
392 :     <DisplayInfo theme="web" col="3" row="5" caption="Role Set"/>
393 :     <Notes>A role set is a group of roles that work together to stimulate a reaction. Most role sets consist of a single
394 :     role; however, some reactions require the presence of multiple roles to get them started.</Notes>
395 :     <Asides>A reaction is usually triggered by a single role, but some reactions are triggered
396 :     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
397 :     expression can be converted into disjunctive normal form, which is a list of alternative sets
398 :     (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
399 :     into a role set. This allows us to precisely represent the triggering conditions of a reaction in the database.</Asides>
400 :     </Entity>
401 : parrello 1.1 <Entity name="DnaSequence" keyType="name-string">
402 :     <DisplayInfo theme="nmpdr" col="7" row="11" caption="DNA Sequence"/>
403 :     <Notes>A DNA sequence (sometimes called a "contig") is a contiguous sequence of base pairs
404 : parrello 1.2 belonging to a single genome. The key of the DNA sequence is the genome ID followed by
405 :     the contig ID.</Notes>
406 : parrello 1.1 <Fields>
407 :     <Field name="length" type="counter">
408 :     <Notes>Number of base pairs in the DNA sequence.</Notes>
409 :     </Field>
410 :     <Field name="bases" type="text" relation="DnaSequenceBases">
411 :     <Notes>A string of letters representing the nucleotides of the sequence.</Notes>
412 :     </Field>
413 :     </Fields>
414 :     </Entity>
415 : parrello 1.2 <Entity name="TaxonomicGrouping" keyType="string">
416 :     <DisplayInfo row="10" col="8" caption="Taxonomic\nGrouping" theme="nmpdr"/>
417 :     <Notes>A taxonomic grouping is a segment of the classification for an organism.
418 :     Taxonomic groupings are organized into a strict hierarchy by the IsClassOf
419 :     relationship.</Notes>
420 : parrello 1.1 <Fields>
421 : parrello 1.2 <Field name="level" type="int">
422 :     <Notes>Taxonomic classification level. A level of 0 indicates that this is
423 :     a specific strain with DNA attached. Higher levels indicate progressively
424 :     larger classifications. Each level number represents a specific type of
425 :     classification. Sub-species is always 1, species is always 2, genus is always
426 :     3, and so forth, up to 99 for domain. This means that as you travel up the
427 :     taxonomy tree, the ranks will be non-sequential.</Notes>
428 : parrello 1.1 </Field>
429 : parrello 1.2 </Fields>
430 :     <Indexes>
431 :     <Index>
432 :     <Notes>This index allows the applications to find all groupings by level.
433 :     lower (less inclusive) levels will occur first.</Notes>
434 :     <IndexFields>
435 :     <IndexField name="level" order="ascending"/>
436 :     </IndexFields>
437 :     </Index>
438 :     </Indexes>
439 :     </Entity>
440 :     <Entity name="Structure" keyType="name-string">
441 :     <DisplayInfo theme="web" col="2" row="5"/>
442 :     <Notes>A structure is the geometrical representation of a protein sequence. A single protein sequence may
443 :     have multiple structural representations, either because it is folded in different ways or because there
444 :     are alternative representation formats. The key field is the representation type (e.g. PDB, SCOPE)
445 :     followed by the ID, with an intervening vertical bar.</Notes>
446 :     </Entity>
447 :     <Entity name="FcEvidenceSet" keyType="int">
448 :     <DisplayInfo theme="seed" col="5" row="13" caption="Functional Coupling Evidence Set"/>
449 :     <Notes>A functional coupling evidence set indicates evidence for a functional connection between protein
450 :     sequence pairs. The protein sequences possessing the connection are the ones that
451 :     participate in the evidence set's pairings.</Notes>
452 :     <Asides>The pairings for a particular evidence set
453 :     will contain protein sequences that are significantly similar. In other words, if
454 :     (A,B) and (X,Y) are both pairings in a single evidence set, then (A =~ X) and
455 :     (B =~ Y) or (A =~ Y) and (B =~ X), depending on the value of the "inverted" attribute of
456 :     the IsDeterminedBy relationship. Essentially, a pairing in its own right is unordered.
457 :     If (A,B) is a pair, then so is (B,A). However, the evidence set maintains a correspondence
458 :     between its pairs that _is_ ordered, because the constituent pairs must match. The
459 :     direction in which a pair matches others in the set is an attribute of the relationship from the pairs
460 :     to the sets.</Asides>
461 :     <Fields>
462 :     <Field name="score" type="int">
463 :     <Notes>Score for this evidence set. The score indicates the number of
464 :     significantly different genomes represented by the pairings.</Notes>
465 : parrello 1.1 </Field>
466 :     </Fields>
467 : parrello 1.2 </Entity>
468 :     <Entity name="MachineRole" keyType="name-string">
469 :     <DisplayInfo row="7" col="5" caption="Machine Role" theme="seed"/>
470 :     <Notes>A machine role represents a role as it occurs in a molecular machine. The key
471 :     is the machine key plus the role abbreviation.</Notes>
472 :     <Asides>The machine role corresponds to a cell on the subsystem spreadsheet. Features
473 :     in the subsystem are assigned directly to the machine role.</Asides>
474 :     </Entity>
475 :     <Entity name="IdentifierSet" keyType="name-string">
476 :     <DisplayInfo row="9" col="1" theme="seed"/>
477 :     <Notes>The identifier set is a group of identifiers that mean the same thing, usually either a Feature
478 :     or a Protein Sequence. The identifiers in a set will frequently belong to different genomic databases.
479 :     Thus, if a specific protein sequence has one name in the NMPDR and another name in RefSeq, both of
480 :     the names would be in the same identifier set.</Notes>
481 :     </Entity>
482 :     <Entity name="Identifier" keyType="string">
483 :     <DisplayInfo theme="seed" col="3" row="9"/>
484 :     <Notes>An identifier is an alternate name for a feature or protein sequence.</Notes>
485 :     <Asides>Some identifiers name features or protein sequences that do not exist in the database. In this case,
486 :     the feature or protein sequence is considered _external_; that is, it belongs to another database.</Asides>
487 :     <Fields>
488 :     <Field name="source" type="key-string">
489 :     <Notes>Specific type of the identifier, such as its source database or category.
490 :     The type can usually be decoded to convert the identifier to a URL.</Notes>
491 : parrello 1.1 </Field>
492 :     </Fields>
493 : parrello 1.2 <Indexes>
494 :     <Index>
495 :     <Notes>This index allows all the identifiers of a specified type to be located.</Notes>
496 :     <IndexFields>
497 :     <IndexField name="source" order="ascending"/>
498 :     </IndexFields>
499 :     </Index>
500 :     </Indexes>
501 :     </Entity>
502 :     </Entities>
503 :     <Relationships>
504 : parrello 1.1 <Relationship name="IsTerminusFor" from="Compound" to="Scenario" arity="MM" converse="HasAsTerminus">
505 :     <DisplayInfo caption="Has As\nTerminus"/>
506 :     <Notes>A terminus for a scenario is a compound that acts as its input or output. A compound
507 : parrello 1.2 can be the terminus for many scenarios, and a scenario will have many termini. The relationship
508 :     attributes indicate whether the compound is an input to the scenario or an output. In some
509 :     cases, there may be multiple alternative output groups. This is also indicated by the
510 :     attributes.</Notes>
511 : parrello 1.1 <Fields>
512 :     <Field name="group-number" type="int">
513 :     <Notes>If zero, then the compound is an input. Otherwise, this is the index number
514 : parrello 1.2 of the output group. Each output group represents an alternative set of output
515 :     compounds.</Notes>
516 : parrello 1.1 </Field>
517 :     </Fields>
518 :     <ToIndex>
519 :     <Notes>This index allows the application to view a scenario's compounds by group.</Notes>
520 :     <IndexFields>
521 : parrello 1.3 <IndexField name="group-number" order="ascending"/>
522 : parrello 1.1 </IndexFields>
523 :     </ToIndex>
524 :     </Relationship>
525 : parrello 1.2 <Relationship name="IsRelevantFor" from="Diagram" to="Subsystem" arity="MM" converse="IsRelevantTo">
526 :     <DisplayInfo theme="seed" caption="Is\nRelevant\nFor"/>
527 :     <Notes>Thie relationship connects each subsystem to the diagrams that are useful in curating
528 :     and understanding the subsystem. A subsystem may overlap many diagrams, but only those considered
529 :     crucial are connected via this relationship. The relationship is many-to-many.</Notes>
530 : parrello 1.1 </Relationship>
531 :     <Relationship name="Describes" from="Subsystem" to="Variant" arity="1M" converse="IsDescribedBy">
532 :     <DisplayInfo theme="seed"/>
533 :     <Notes>This relationship connects a subsystem to the individual variants used
534 :     to implement it. Each variant contains a slightly different subset of the
535 :     roles in the parent subsystem.</Notes>
536 :     </Relationship>
537 : parrello 1.3 <Relationship name="Displays" from="Diagram" to="Reaction" arity="MM" converse="IsDisplayedOn">
538 : parrello 1.1 <DisplayInfo theme="web"/>
539 :     <Notes>This relationship connects a diagram to its reactions. A diagram shows multiple
540 :     reactions, and a reaction can be on many diagrams.</Notes>
541 :     </Relationship>
542 : parrello 1.2 <Relationship name="IsOwnerOf" from="Genome" to="Feature" arity="1M" converse="IsOwnedBy">
543 :     <DisplayInfo caption="Is\nOwned\nBy" theme="seed"/>
544 :     <Notes>This relationship connects each feature to its parent genome.</Notes>
545 : parrello 1.1 </Relationship>
546 : parrello 1.2 <Relationship name="IsImplementedBy" from="Variant" to="MolecularMachine" arity="1M" converse="Implements">
547 :     <DisplayInfo theme="seed" caption="Is\nImplemented\nBy" row="6" col="7"/>
548 : parrello 1.1 <Notes>This relationship connects a variant to the physical machines that implement
549 :     it in the genomes. A variant is implemented by many machines, but a machine belongs to
550 :     only one variant.</Notes>
551 :     </Relationship>
552 : parrello 1.2 <Relationship name="Uses" theme="seed" from="Genome" to="MolecularMachine" arity="1M" converse="IsUsedBy">
553 :     <DisplayInfo theme="seed" caption="Is\nUsed\nBy"/>
554 :     <Notes>This relationship connects a genome to the machines that form its
555 :     metabolic pathways. A genome can use many machines, but a machine is used by exactly
556 :     one genome.</Notes>
557 :     </Relationship>
558 :     <Relationship name="Includes" from="Subsystem" to="Role" arity="MM" converse="IsIncludedIn">
559 :     <DisplayInfo theme="seed" caption="Includes"/>
560 :     <Notes>A subsystem is defined by its roles. The subsystem's variants contain slightly
561 :     different sets of roles, but all of the roles in a variant must be connected to the
562 :     parent subsystem by this relationship. A subsystem always has at least one
563 :     role, and a role always belongs to at least one subsystem.</Notes>
564 : parrello 1.1 <Fields>
565 : parrello 1.2 <Field name="sequence" type="counter">
566 :     <Notes>Sequence number of the role within the subsystem. When the roles
567 :     are formed into a variant, they will generally appear in sequence order.</Notes>
568 : parrello 1.1 </Field>
569 : parrello 1.2 <Field name="abbreviation" type="key-string">
570 :     <Notes>Abbreviation for this role in this subsystem. The abbreviations are
571 :     used in columnar displays, and they also appear on diagrams.</Notes>
572 : parrello 1.1 </Field>
573 :     </Fields>
574 : parrello 1.2 <FromIndex>
575 :     <Notes>This index insures that the roles of the subsystem are presented in sequence
576 :     order.</Notes>
577 : parrello 1.1 <IndexFields>
578 : parrello 1.2 <IndexField name="sequence" order="ascending"/>
579 : parrello 1.1 </IndexFields>
580 : parrello 1.2 </FromIndex>
581 : parrello 1.1 </Relationship>
582 : parrello 1.3 <Relationship name="Catalyzes" from="ProteinSequence" to="Role" arity="MM" converse="IsCatalyzedBy">
583 :     <DisplayInfo theme="web" caption="Is\nCatalyzed\nBy"/>
584 : parrello 1.1 <Notes>This relationship connects a protein sequence to the functional roles it
585 : parrello 1.2 implements in the cell. A protein sequence can implement many roles, and a role can
586 :     be implemented by many protein sequences. Roles that perform regulatory or message
587 : parrello 1.1 transmission functions do not participate in this relationship.</Notes>
588 :     </Relationship>
589 : parrello 1.2 <Relationship name="IsCombinationOf" from="RoleSet" to="Role" arity="MM" converse="IsInCombination">
590 :     <DisplayInfo theme="web" caption="Is\nCombination\nOf"/>
591 :     <Notes>This relationship combines roles into role sets. Each role set is a combination of roles that can
592 :     trigger a reaction.</Notes>
593 :     </Relationship>
594 :     <Relationship name="IsTriggeredBy" from="Reaction" to="RoleSet" arity="MM" converse="Triggers">
595 :     <DisplayInfo theme="web" caption="Is\nTriggered\nBy"/>
596 :     <Notes>A reaction can be triggered by many role sets. A role set can trigger many reactions.</Notes>
597 :     </Relationship>
598 :     <Relationship name="IsClassOf" from="TaxonomicGrouping" to="TaxonomicGrouping" arity="1M" converse="IsClassifiedAs">
599 :     <DisplayInfo theme="nmpdr" col="8" row="11" fixed="1" caption="Is\nClass\nOf"/>
600 :     <Notes>The recursive IsClassOf relationship organizes taxonomic groupings into a hierarchy
601 :     based on the standard organism taxonomy.</Notes>
602 :     </Relationship>
603 :     <Relationship name="IsFoundOn" from="Role" to="Diagram" arity="MM" converse="IsLocationOf">
604 :     <DisplayInfo theme="web" caption="Is\nLocation\nOf"/>
605 :     <Notes>This relationship connects a role to the diagrams on which it appears. A diagram
606 :     always contains many roles. A role may appear on multiple diagrams.</Notes>
607 : parrello 1.1 </Relationship>
608 :     <Relationship name="IsLocatedIn" from="Feature" to="DnaSequence" arity="MM" converse="IsLocusFor">
609 : parrello 1.2 <DisplayInfo theme="seed" caption="Is\nLocated\nIn" fixed="1" row="10" col="6"/>
610 : parrello 1.1 <Notes>A feature is a set of DNA sequence fragments. Most features are a single contiquous
611 :     fragment, so they are located in only one DNA sequence; however, fragments have a maximum
612 :     length, so even a single contiguous feature may participate in this relationship multiple
613 :     times. A few features belong to multiple DNA sequences. In that case, however, all the
614 :     DNA sequences belong to the same genome. A DNA sequence itself will frequently have
615 :     thousands of features connected to it.</Notes>
616 :     <Fields>
617 :     <Field name="locN" type="int">
618 :     <Notes>Sequence number of this segment.</Notes>
619 :     </Field>
620 :     <Field name="beg" type="int">
621 :     <Notes>Index (1-based) of the first residue in the contig that
622 :     belongs to the segment.</Notes>
623 :     </Field>
624 :     <Field name="len" type="int">
625 :     <Notes>Number of residues in the segment. A length of 0 identifies
626 :     a specific point between residues. This is the point before the residue if the direction
627 :     is forward and the point after the residue if the direction is backward.</Notes>
628 :     </Field>
629 :     <Field name="dir" type="char">
630 :     <Notes>Direction of the segment: "+" if it is forward and
631 :     "-" if it is backward.</Notes>
632 :     </Field>
633 :     </Fields>
634 :     <FromIndex>
635 :     <Notes>This index allows the application to find all the segments of a feature in
636 :     the proper order.</Notes>
637 :     <IndexFields>
638 :     <IndexField name="locN" order="ascending"/>
639 :     </IndexFields>
640 :     </FromIndex>
641 :     <ToIndex>
642 :     <Notes>This index is the one used by applications to find all the feature
643 :     segments that contain a specific residue.</Notes>
644 :     <IndexFields>
645 :     <IndexField name="beg" order="ascending"/>
646 :     </IndexFields>
647 :     </ToIndex>
648 :     </Relationship>
649 : parrello 1.2 <Relationship name="IsDeterminedBy" from="FcEvidenceSet" to="Pairing" arity="MM" converse="Determines">
650 :     <DisplayInfo theme="seed" caption="Determines"/>
651 :     <Notes>A functional coupling evidence set exists because it has pairings in it, and this relationship
652 :     connects the evidence set to its constituent pairings. A pairing cam belong to
653 :     multiple evidence sets.</Notes>
654 :     <Fields>
655 :     <Field name="inverted" type="boolean">
656 :     <Notes>A pairing is an unordered pair of protein sequences, but its
657 :     similarity to other pairings in an evidence set is ordered. Let (A,B) be
658 :     a pairing and (X,Y) be another pairing in the same set. If this flag is
659 :     FALSE, then (A =~ X) and (B =~ Y). If this flag is TRUE, then (A =~ Y) and
660 :     (B =~ X).</Notes>
661 :     </Field>
662 :     </Fields>
663 :     </Relationship>
664 :     <Relationship name="IsFunctionOf" from="Role" to="Feature" arity="MM" converse="Targets">
665 :     <DisplayInfo theme="seed" fixed="1" row="7" col="4" caption="Is\nFunction\nOf"/>
666 :     <Notes>This relationship connects a role to the features that facilitate the role.
667 :     A role can be the function of multiple features, and a single feature may have
668 :     multiple roles.</Notes>
669 : parrello 1.1 </Relationship>
670 :     <Relationship name="IsMadeUpOf" from="Genome" to="DnaSequence" arity="1M" converse="MakesUp">
671 :     <DisplayInfo theme="nmpdr" caption="Is\nMade Up\nOf"/>
672 :     <Notes>This relationship connects each genome to the DNA sequences that make it up.</Notes>
673 :     </Relationship>
674 : parrello 1.2 <Relationship name="IsAnnotatedBy" from="Feature" to="Annotation" arity="1M" converse="Annotates">
675 :     <DisplayInfo theme="seed" caption="Is\nAnnotated\nBy" fixed="1" col="3" row="10"/>
676 :     <Notes>This relationship connects a feature to its annotations. A feature may have
677 :     multiple annotations, but an annotation belongs to only one feature.</Notes>
678 :     </Relationship>
679 :     <Relationship name="HasMember" from="Family" to="Feature" arity="1M" converse="IsMemberOf">
680 :     <DisplayInfo theme="seed" caption="Is\nMember\nOf" row="10" col="4" fixed="1"/>
681 :     <Notes>This relationship connects each feature family to its constituent
682 :     features. A family always has many features, but a single feature can
683 :     be found in at most one family.</Notes>
684 : parrello 1.1 </Relationship>
685 :     <Relationship name="Attracts" from="Structure" to="Compound" arity="MM" converse="IsAttractedTo">
686 : parrello 1.2 <DisplayInfo theme="web" row="1" col="2" fixed="1" caption="Is\nAttracted\nTo"/>
687 : parrello 1.1 <Notes>This relationship connects a compound to the protein structures that attract it.
688 :     This is an incomplete relationship that exists to service drug targeting queries. Only
689 :     the attractions whose parameters have been determined through modeling or
690 :     experimentation are included. The goal is to determine the docking energy between
691 :     the compound and the protein structure.</Notes>
692 :     <Fields>
693 :     <Field name="reason" type="id-string">
694 :     <Notes>Indication of the reason for determining the docking energy.
695 :     A value of "Random" indicates the docking was attempted as a part
696 :     of a random survey used to determine the docking characteristics of a
697 :     protein structure. A value of "Rich" indicates the docking was attempted
698 :     because a low-energy docking result was predicted for the compound.</Notes>
699 :     </Field>
700 :     <Field name="tool" type="id-string">
701 :     <Notes>Name of the tool used to compute the docking energy.</Notes>
702 :     </Field>
703 :     <Field name="total-energy" type="float">
704 :     <Notes>Total energy required for the compound to dock with the structure,
705 :     in kcal/mol. A negative value means energy is released.</Notes>
706 :     </Field>
707 :     <Field name="vanderwalls-energy" type="float">
708 :     <Notes>Docking energy in kcal/mol that results from the geometric fit
709 :     (Van der Waals force) between the structure and the compound.</Notes>
710 :     </Field>
711 :     <Field name="electrostatic-energy" type="float">
712 :     <Notes>Docking energy in kcal/mol that results from the movement of
713 :     electrons (electrostatic force) between the structure and the
714 :     compound.</Notes>
715 :     </Field>
716 :     </Fields>
717 :     <FromIndex>
718 :     <Notes>This index enables the application to view a structure's docking results from
719 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
720 :     <IndexFields>
721 :     <IndexField name="total-energy" order="ascending"/>
722 :     </IndexFields>
723 :     </FromIndex>
724 :     <ToIndex>
725 :     <Notes>This index enables the application to view a compound's docking results from
726 :     the lowest energy (best docking) to highest energy (worst docking).</Notes>
727 :     <IndexFields>
728 :     <IndexField name="total-energy" order="ascending"/>
729 :     </IndexFields>
730 :     </ToIndex>
731 :     </Relationship>
732 : parrello 1.2 <Relationship name="Involves" from="Reaction" to="Compound" arity="MM" converse="IsInvolvedIn">
733 :     <DisplayInfo theme="web" caption="Is\nInvolved\nIn" fixed="1" row="2" col="2.5"/>
734 :     <Notes>This relationship connects a reaction to the compounds that participate in
735 :     it. A reaction involves many compounds, and a compound can be involved in many reactions.
736 :     The relationship attributes indicate whether a compound is a product or substrate of the
737 :     reaction, as well as its stoichiometry.</Notes>
738 :     <Fields>
739 :     <Field name="product" type="boolean">
740 :     <Notes>TRUE if the compound is a product of the reaction, FALSE if
741 :     it is a substrate. When a reaction is written on paper in
742 :     chemical notation, the substrates are left of the arrow and the
743 :     products are to the right. Sorting on this field will cause
744 :     the substrates to appear first, followed by the products. If the
745 :     reaction is reversible, then the notion of substrates and products
746 :     is not intuitive; however, a value here of FALSE still puts the
747 :     compound left of the arrow and a value of TRUE still puts it to the
748 :     right.</Notes>
749 :     </Field>
750 :     <Field name="stoichiometry" type="key-string">
751 :     <Notes>Number of molecules of the compound that participate in a
752 :     single instance of the reaction. For example, if a reaction
753 :     produces two water molecules, the stoichiometry of water for the
754 :     reaction would be two. When a reaction is written on paper in
755 :     chemical notation, the stoichiometry is the number next to the
756 :     chemical formula of the compound.</Notes>
757 :     </Field>
758 :     <Field name="main" type="boolean">
759 :     <Notes>TRUE if this compound is one of the main participants in
760 :     the reaction, else FALSE. It is permissible for none of the
761 :     compounds in the reaction to be considered main, in which
762 :     case this value would be FALSE for all of the relevant
763 :     compounds.</Notes>
764 :     </Field>
765 :     <Field name="loc" type="key-string">
766 :     <Notes>An optional character string that indicates the relative
767 :     position of this compound in the reaction's chemical formula. The
768 :     location affects the way the compounds present as we cross the
769 :     relationship from the reaction side. The product/substrate flag
770 :     comes first, then the value of this field, then the main flag.
771 :     The default value is an empty string; however, the empty string
772 :     sorts first, so if this field is used, it should probably be
773 :     used for every compound in the reaction.</Notes>
774 :     </Field>
775 :     <Field name="discriminator" type="int">
776 :     <Notes>A unique ID for this record. The discriminator does not
777 :     provide any useful data, but it prevents identical records from
778 :     being collapsed by the SELECT DISTINCT command used by ERDB to
779 :     retrieve data.</Notes>
780 :     </Field>
781 :     </Fields>
782 :     <ToIndex>
783 :     <Notes>This index presents the compounds in the reaction in the
784 :     order they should be displayed when writing it in chemical notation.
785 :     All the substrates appear before all the products, and within that
786 :     ordering, the main compounds appear first.</Notes>
787 :     <IndexFields>
788 :     <IndexField name="product" order="ascending"/>
789 :     <IndexField name="loc" order="ascending"/>
790 :     <IndexField name="main" order="descending"/>
791 :     </IndexFields>
792 :     </ToIndex>
793 :     </Relationship>
794 : parrello 1.3 <Relationship name="Shows" from="Diagram" to="Compound" arity="MM" converse="IsShownOn">
795 :     <DisplayInfo theme="web" fixed="1" caption="Is\nShown\nOn" row="2" col="3.5"/>
796 : parrello 1.2 <Notes>This relationship indicates that a compound appears on a particular diagram.
797 :     The same compound can appear on many diagrams, and a diagram always contains many
798 :     compounds.</Notes>
799 :     </Relationship>
800 :     <Relationship name="IsContainedIn" from="Feature" to="MachineRole" arity="MM" converse="Contains">
801 :     <DisplayInfo theme="seed" caption="Is\nContained\nIn" row="8" col="5"/>
802 :     <Notes>This relationship connects a machine role to the features that occur in it. A feature
803 :     may occur in many machine roles and a machine role may contain many features. The subsystem
804 :     annotation process is essentially the maintenance of this relationship.</Notes>
805 :     </Relationship>
806 :     <Relationship name="IsRoleOf" from="Role" to="MachineRole" arity="1M" converse="HasRole">
807 :     <DisplayInfo caption="Is\nRole\nOf" theme="seed"/>
808 :     <Notes>This relationship connects a role to the machine roles that represent its
809 :     appearance in a molecular machine. A machine role has exactly one associated role,
810 :     but a role may be represented by many machine roles.</Notes>
811 :     </Relationship>
812 :     <Relationship name="Exposes" from="ProteinSequence" to="Structure" arity="MM" converse="IsExposedBy">
813 :     <DisplayInfo theme="web" fixed="1" row="7" col="2" caption="Is\nExposed\nBy"/>
814 :     <Notes>This relationship connects a protein sequence to its structural representations. It is a
815 :     many-to-many relationship. Note that only some protein sequences have known structural representations.</Notes>
816 :     </Relationship>
817 :     <Relationship name="IsSubInstanceOf" from="Subsystem" to="Scenario" arity="1M" converse="Validates">
818 :     <DisplayInfo theme="seed" caption="Is Part\nInstance\nOf" fixed="1" row="1" col="7"/>
819 :     <Notes>This relationship connects a scenario to its subsystem it validates. A scenario
820 :     belongs to exactly one subsystem, but a subsystem may have multiple scenarios.</Notes>
821 :     </Relationship>
822 : parrello 1.1 <Relationship name="Overlaps" from="Scenario" to="Diagram" arity="MM" converse="IncludesPartOf">
823 : parrello 1.2 <DisplayInfo theme="web" fixed="1" row="2" col="5.5"/>
824 : parrello 1.1 <Notes>A Scenario overlaps a diagram when the diagram displays a portion of the reactions
825 :     that make up the scenario. A scenario may overlap many diagrams, and a diagram may
826 :     be include portions of many scenarios.</Notes>
827 :     </Relationship>
828 :     <Relationship name="HasParticipant" from="Scenario" to="Reaction" arity="MM" converse="ParticipatesIn">
829 : parrello 1.2 <DisplayInfo theme="web" caption="Has\nParticipant" row="2" col="4.5" fixed="1"/>
830 : parrello 1.1 <Notes>A scenario consists of many participant reactions that convert the input compounds
831 :     to output compounds. A single reaction may participate in many scenarios.</Notes>
832 : parrello 1.2 <Fields>
833 :     <Field name="type" type="int">
834 :     <Notes>Indicates the type of participaton. If 0, the reaction is in the main pathway of
835 :     the scenario. If 1, the reaction is necessary to make the model work but is not in the
836 :     subsystem. If 2, the reaction is part of the subsystem but should not be included in
837 :     the modelling process.</Notes>
838 :     </Field>
839 :     </Fields>
840 :     <FromIndex>
841 :     <Notes>This index presents the reactions in the scenario in order from
842 :     most important to least important.</Notes>
843 :     <IndexFields>
844 :     <IndexField name="type" order="ascending"/>
845 :     </IndexFields>
846 :     </FromIndex>
847 : parrello 1.1 </Relationship>
848 : parrello 1.3 <Relationship name="IsInPair" from="Feature" to="Pairing" arity="MM" converse="IsPairOf">
849 : parrello 1.2 <DisplayInfo theme="seed" caption="Is In\nPair"/>
850 :     <Notes>A pairing contains exactly two protein sequences. A protein sequence can
851 :     belong to multiple pairings. When going from a protein sequence to its pairings,
852 :     they are presented in alphabetical order by sequence key.</Notes>
853 : parrello 1.1 </Relationship>
854 :     <Relationship name="Concerns" from="Publication" to="ProteinSequence" arity="MM" converse="IsATopicOf">
855 : parrello 1.2 <DisplayInfo theme="web" row="8" col="2" caption="Is A\nTopic\nOf" fixed="1"/>
856 : parrello 1.1 <Notes>This relationship connects a publication to the protein sequences it
857 :     describes.</Notes>
858 :     </Relationship>
859 : parrello 1.2 <Relationship name="IsTaxonomyOf" to="Genome" from="TaxonomicGrouping" arity="1M" converse="IsInTaxa">
860 :     <DisplayInfo theme="nmpdr" fixed="1" caption="Is In\nTaxa" row="9" col="8"/>
861 :     <Notes>A genome belongs to exactly one taxonomic grouping. A taxonomic grouping
862 :     contains many genomes. Some taxonomic groupings do not contain any genomes. These
863 :     in fact contain other taxonomic groups.</Notes>
864 :     </Relationship>
865 :     <Relationship name="IsSequenceFor" from="ProteinSequence" to="Identifier" arity="1M" converse="IsFeatureFor">
866 :     <DisplayInfo caption="Is\nSequence\nFor" theme="seed"/>
867 :     <Notes>This relationship connects a peg identifier to the protein sequence it produces (if any).
868 :     Only peg identifiers participate in this relationship. Identifiers that name RNAs,
869 :     operons, or other non-protein feature do not connect to protein sequences. A single
870 :     protein sequence will frequently have many identifiers.</Notes>
871 :     </Relationship>
872 :     <Relationship name="IncludesIdentifier" from="IdentifierSet" to="Identifier" arity="1M" converse="IsIncludedInSet">
873 :     <DisplayInfo theme="seed" caption="Includes" row="9.5" col="1.5"/>
874 :     <Notes>An identifier set contains many identifiers. If the set identifies a feature, then one of the identifiers
875 :     will be a feature ID. If the set identifies a protein sequence, then one of the identifiers will be the
876 :     MD5 hash key for the protein sequence.</Notes>
877 : parrello 1.1 </Relationship>
878 : parrello 1.4 <Relationship name="IsMachineOf" from="MolecularMachine" to="MachineRole" arity="1M" converse="IsRoleFor">
879 :     <DisplayInfo caption="Is\nRole\nFor" theme="seed" row="7" col="6"/>
880 :     <Notes>This relationship connects a molecular machine to its various machine roles.
881 :     Each machine has many machine roles, but each machine role belongs to only one machine.</Notes>
882 :     </Relationship>
883 : parrello 1.1 </Relationships>
884 :     <Shapes>
885 : parrello 1.2 <Shape type="diamond" name="ConsistsOf" from="Variant" to="Role">
886 :     <DisplayInfo theme="neutral" caption="Belongs To" connected="1"/>
887 :     <Notes>This relationship is not physically implemented in the database. It is
888 :     implicit in the data for a variant. A variant contains a boolean expression that
889 :     describes the various combinations of roles it can contain.</Notes>
890 :     </Shape>
891 :     <Shape type="diamond" name="IsIdentifiedBy" from="Feature" to="Identifier">
892 :     <DisplayInfo theme="neutral" caption="Identifies" connected="1"/>
893 :     <Notes>This relationship is not physically implemented in the database. It is
894 : parrello 1.3 implicit in the data for an identifier. If the identifier is a FIG feature
895 : parrello 1.2 ID, then it identifies that feature, as do all other identifiers in the same
896 :     identifier set.</Notes>
897 :     </Shape>
898 : parrello 1.1 </Shapes>
899 :     </Database>

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3