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revision 1.10, Mon Aug 15 18:43:49 2005 UTC revision 1.56, Tue Sep 9 21:02:10 2008 UTC
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1  <?xml version="1.0" encoding="utf-8" ?>  <?xml version="1.0" encoding="utf-8" ?>
2  <Database>  <Database>
3      <Title>Sprout Genome and Subsystem Database</Title>      <Title>Sprout Genome and Subsystem Database</Title>
4        <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.
5        The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external
6        servers available to the Sprout software. The Sprout database is reloaded approximately once
7        per month. There is significant redundancy in the Sprout database because it has been
8        optimized for searching. In particular, the Feature table contains an extra copy of the
9        feature's functional role and a list of possible search terms.</Notes>
10      <Entities>      <Entities>
11          <Entity name="Genome" keyType="name-string">          <Entity name="Genome" keyType="name-string">
12              <Notes>A [i]genome[/i] contains the sequence data for a particular individual organism.</Notes>              <DisplayInfo theme="nmpdr" col="3" row="1" />
13                <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
14              <Fields>              <Fields>
15                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
16                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
                     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>  
17                  </Field>                  </Field>
18                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
19                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
20                  </Field>                  </Field>
21                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
22                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
23                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
24                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
25                      <DataGen>StringGen('PKVKVK999')</DataGen>                  </Field>
26                    <Field name="version" type="name-string">
27                        <Notes>version string for this genome, generally consisting of the genome ID followed
28                        by a period and a string of digits.</Notes>
29                  </Field>                  </Field>
30                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
31                      <Notes>The access code determines which users can look at the data relating to this genome.                      <Notes>The access code field is deprecated. Its function has been replaced by
32                      Each user is associated with a set of access codes. In order to view a genome, one of                      the account management system developed for the [[RapidAnnotationServer]].</Notes>
33                      the user's access codes must match this value.</Notes>                  </Field>
34                      <DataGen>RandParam('low','medium','high')</DataGen>                  <Field name="complete" type="boolean">
35                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
36                    </Field>
37                    <Field name="dna-size" type="counter">
38                        <Notes>number of base pairs in the genome</Notes>
39                  </Field>                  </Field>
40                  <Field name="taxonomy" type="text">                  <Field name="taxonomy" type="text">
41                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                      <Notes>The taxonomy string contains the full [[Wikipedia:taxonomy]] of the organism, while individual elements
42                      separated by semi-colons (and optional white space), starting with the domain and ending with                      separated by semi-colons (and optional white space), starting with the domain and ending with
43                      the disambiguated genus and species (which is the organism's scientific name plus an                      the disambiguated genus and species (which is the organism's scientific name plus an
44                      identifying string).</Notes>                      identifying string).</Notes>
                     <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),  
                                                   ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>  
45                  </Field>                  </Field>
46                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="primary-group" type="name-string">
47                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
48                      page or of particular interest to a research group or web site. A single genome can belong to multiple                      per organism (either based on the organism name or the default value =Supporting=). In general,
49                      such groups or none at all.</Notes>                      more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>
50                    </Field>
51                    <Field name="contigs" type="int">
52                        <Notes>Number of contigs for this organism.</Notes>
53                    </Field>
54                    <Field name="pegs" type="int">
55                        <Notes>Number of [[protein encoding genes]] for this organism</Notes>
56                    </Field>
57                    <Field name="rnas" type="int">
58                        <Notes>Number of RNA features found for this organism.</Notes>
59                  </Field>                  </Field>
60              </Fields>              </Fields>
61              <Indexes>              <Indexes>
# Line 51  Line 70 
70                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
71                      </IndexFields>                      </IndexFields>
72                  </Index>                  </Index>
73                  <Index Unique="false">                  <Index>
74                        <Notes>This index allows the applications to find all genomes associated with
75                        a specific primary (NMPDR) group.</Notes>
76                        <IndexFields>
77                            <IndexField name="primary-group" order="ascending" />
78                            <IndexField name="genus" order="ascending" />
79                            <IndexField name="species" order="ascending" />
80                            <IndexField name="unique-characterization" order="ascending" />
81                        </IndexFields>
82                    </Index>
83                    <Index>
84                      <Notes>This index allows the applications to find all genomes for a particular                      <Notes>This index allows the applications to find all genomes for a particular
85                      species.</Notes>                      species.</Notes>
86                      <IndexFields>                      <IndexFields>
# Line 62  Line 91 
91                  </Index>                  </Index>
92              </Indexes>              </Indexes>
93          </Entity>          </Entity>
94            <Entity name="CDD" keyType="key-string">
95                <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
96                on a feature's protein. The ID is six-digit string assigned by the public
97                Conserved Domain Database. A CDD
98                can occur on multiple features and a feature generally has multiple CDDs.</Notes>
99            </Entity>
100          <Entity name="Source" keyType="medium-string">          <Entity name="Source" keyType="medium-string">
101              <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization              <Notes>A source describes a place from which genome data was taken. This can be an organization
102              or a paper citation.</Notes>              or a paper citation.</Notes>
103              <Fields>              <Fields>
104                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
105                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>  
106                  </Field>                  </Field>
107                  <Field name="description" type="text">                  <Field name="description" type="text">
108                      <Notes>Description the source. The description can be a street address or a citation.</Notes>                      <Notes>Description of the source. The description can be a street address or a citation.</Notes>
                     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
109                  </Field>                  </Field>
110              </Fields>              </Fields>
111          </Entity>          </Entity>
112          <Entity name="Contig" keyType="name-string">          <Entity name="Contig" keyType="name-string">
113              <Notes>A [i]contig[/i] is a contiguous run of residues. The contig's ID consists of the              <DisplayInfo theme="nmpdr" col="1" row="1" />
114                <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
115              genome ID followed by a name that identifies which contig this is for the parent genome. As              genome ID followed by a name that identifies which contig this is for the parent genome. As
116              is the case with all keys in this database, the individual components are separated by a              is the case with all keys in this database, the individual components are separated by a
117              period.              period. A contig can contain over a million residues. For performance reasons, therefore,
118              [p]A contig can contain over a million residues. For performance reasons, therefore,              the contig is split into multiple pieces called sequences. The sequences
             the contig is split into multiple pieces called [i]sequences[/i]. The sequences  
119              contain the characters that represent the residues as well as data on the quality of              contain the characters that represent the residues as well as data on the quality of
120              the residue identification.</Notes>              the residue identification.</Notes>
121          </Entity>          </Entity>
122          <Entity name="Sequence" keyType="name-string">          <Entity name="Sequence" keyType="name-string">
123              <Notes>A [i]sequence[/i] is a continuous piece of a [i]contig[/i]. Contigs are split into              <Notes>A sequence is a continuous piece of a contig. Contigs are split into
124              sequences so that we don't have to have the entire contig in memory when we are              sequences so that we don't have to have the entire contig in memory when we are
125              manipulating it. The key of the sequence is the contig ID followed by the index of              manipulating it. The key of the sequence is the contig ID followed by the index of
126              the begin point.</Notes>              the begin point.</Notes>
127              <Fields>              <Fields>
128                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
129                      <Notes>String consisting of the residues. Each residue is described by a single                      <Notes>String consisting of the residues (base pairs). Each residue is described by a single
130                      character in the string.</Notes>                      character in the string.</Notes>
                     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
131                  </Field>                  </Field>
132                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
133                      <Notes>String describing the quality data for each base pair. Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
134                      be separated by periods. The value represents negative exponent of the probability                      be separated by periods. The value represents negative exponent of the probability
135                      of error. Thus, for example, a quality of 30 indicates the probability of error is                      of error. Thus, for example, a quality of 30 indicates the probability of error is
136                      10^-30. A higher quality number a better chance of a correct match. It is possible                      10^-30. A higher quality number indicates a better chance of a correct match. It is
137                      that the quality data is not known for a sequence. If that is the case, the quality                      possible that the quality data is not known for a sequence. If that is the case, the
138                      vector will contain the [b]unknown[/b].</Notes>                      quality vector will contain the string =unknown=.</Notes>
                     <DataGen>unknown</DataGen>  
139                  </Field>                  </Field>
140              </Fields>              </Fields>
141          </Entity>          </Entity>
142          <Entity name="Feature" keyType="name-string">          <Entity name="Keyword" keyType="name-string">
143              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features              <Notes>A keyword is a word that can be used to search the feature table. This entity
144                contains the keyword's stem, its phonetic form, and the number of features that
145                can be found by searching for the word.</Notes>
146                <Fields>
147                    <Field name="stem" type="name-string">
148                        <Notes>The stem of a keyword is a normalized form that is independent of parts
149                        of speech. The actual keywords stored in the database search index are stems.</Notes>
150                    </Field>
151                    <Field name="count" type="counter">
152                        <Notes>Number of features that can be found by searching for the specified
153                        keyword.</Notes>
154                    </Field>
155                    <Field name="phonex" type="name-string">
156                        <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
157                        word stem. This can be used to find alternative spellings if an matching word is not
158                        present.</Notes>
159                    </Field>
160                </Fields>
161                <Indexes>
162                    <Index>
163                        <Notes>This index allows the user to find words by stem.</Notes>
164                        <IndexFields>
165                            <IndexField name="stem" order="ascending" />
166                        </IndexFields>
167                    </Index>
168                    <Index>
169                        <Notes>This index allows the user to find words by phonex.</Notes>
170                        <IndexFields>
171                            <IndexField name="phonex" order="ascending" />
172                            <IndexField name="count" order="descending" />
173                        </IndexFields>
174                    </Index>
175                </Indexes>
176            </Entity>
177            <Entity name="ExternalDatabase" keyType="key-string">
178                <Notes>An external database identifies a biological database surveyed by PIR International
179                as part of an effort to determine which features are essentially identical between bioinformatics
180                organizations. Each feature in the database will have zero or more corresponding IDs that are
181                captured from the PIR data. Each corresponding ID is represented in a relationship between an external
182                database and the feature itself.</Notes>
183            </Entity>
184            <Entity name="Feature" keyType="id-string">
185                <DisplayInfo theme="nmpdr" col="3" row="3" />
186                <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
187              may be spread across multiple contigs of a genome, but never across more than              may be spread across multiple contigs of a genome, but never across more than
188              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
189              and are the targets of annotation.</Notes>              and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
190              <Fields>              <Fields>
191                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="id-string">
192                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature. Among the codes currently
193                      <DataGen>RandParam('peg','rna')</DataGen>                      supported are =peg= for a [[protein encoding gene]], =bs= for a
194                  </Field>                      binding site, =opr= for an operon, and so forth.</Notes>
                 <Field name="alias" type="name-string" relation="FeatureAlias">  
                     <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>  
                     <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
195                  </Field>                  </Field>
196                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
197                      <Notes>[i](optional)[/i] A translation of this feature's residues into character                      <Notes>_(optional)_ A translation of this feature's residues into character
198                      codes, formed by concatenating the pieces of the feature together. For a                      codes, formed by concatenating the pieces of the feature together. For a
199                      protein encoding group, this is the protein characters. For other types                      [[protein encoding gene]], the translation contains protein characters. For other types
200                      it is the DNA characters.</Notes>                      it contains DNA characters.</Notes>
                     <DataGen testCount="0"></DataGen>  
201                  </Field>                  </Field>
202                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
203                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of                      <Notes>Upstream sequence for the feature. This includes residues preceding the feature as
204                      the feature's initial residues.</Notes>                      well as some of the feature's initial residues.</Notes>
205                      <DataGen testCount="0"></DataGen>                  </Field>
206                    <Field name="assignment" type="text">
207                        <Notes>Default functional assignment for this feature.</Notes>
208                  </Field>                  </Field>
209                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
210                      <Notes>TRUE if this feature is still considered valid, if it has been logically deleted.</Notes>                      <Notes>(This field is deprecated.) TRUE if this feature is still considered valid,
211                      <DataGen>1</DataGen>                      FALSE if it has been logically deleted.</Notes>
212                    </Field>
213                    <Field name="assignment-maker" type="name-string">
214                        <Notes>name of the user who made the functional assignment</Notes>
215                    </Field>
216                    <Field name="assignment-quality" type="char">
217                        <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
218                        (indicating experimental)</Notes>
219                    </Field>
220                    <Field name="keywords" type="text" searchable="1">
221                        <Notes>This is a list of search keywords for the feature. It includes the
222                        functional assignment, subsystem roles, and special properties.</Notes>
223                  </Field>                  </Field>
224                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
225                      <Notes>Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The                      <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
226                      links are to other websites that have useful about the gene that the feature represents, and                      links are to other websites that have useful about the gene that the feature represents, and
227                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>                      are coded as raw HTML, using &lt;a href="_link_"&gt;_text_&lt;/a&gt; notation.</Notes>
228                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
229                      "&amp;Number=" . IntGen(1,99)</DataGen>                  <Field name="conservation" type="float" relation="FeatureConservation">
230                        <Notes>_(optional)_ A number between 0 and 1 that indicates the degree to which this feature's DNA is
231                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
232                        than 1 is a reflection of the degree to which gap characters interfere in the alignment
233                        between the feature and its close relatives.</Notes>
234                    </Field>
235                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
236                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
237                        cases, this will be a word describing whether the essentiality is confirmed (essential)
238                        or potential (potential-essential), hyperlinked to the document from which the
239                        essentiality was curated. If a feature is not essential, this field will have no
240                        values; otherwise, it may have multiple values.</Notes>
241                    </Field>
242                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
243                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
244                        cases, this will be a phrase or SA number hyperlinked to the document from which
245                        the virulence information was curated. If the feature is not virulent, this field
246                        will have no values; otherwise, it may have multiple values.</Notes>
247                    </Field>
248                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
249                        <Notes>A value indicating whether or not the feature can be found in the
250                        Immune Epitope Database. If the feature has not been matched to that database,
251                        this field will have no values. Otherwise, it will have an epitope name and/or
252                        sequence, hyperlinked to the database.</Notes>
253                    </Field>
254                    <Field name="location-string" type="text">
255                        <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
256                        strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
257                        we have to painstakingly paste together the [[#IsLocatedIn]] records, which are themselves
258                        designed to help look for features in a particular region rather than to find the location
259                        of a feature.</Notes>
260                    </Field>
261                    <Field name="signal-peptide" type="name-string">
262                        <Notes>The signal peptide location for this feature. This is expressed as start and end
263                        numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
264                        peptide at the beginning of the feature's protein and extending through 22 amino acid
265                        positions. An empty string means no signal peptide is present.</Notes>
266                    </Field>
267                    <Field name="transmembrane-map" type="text">
268                        <Notes>A map indicating which sections of a protein will be embedded in a membrane.
269                        This is expressed as a comma-separated list of as start and end numbers with hyphens
270                        for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
271                        sections of the protein that become embedded in a membrane: the 10th through 12th
272                        amino acids, and the 40th through the 60th. An empty string means no
273                        transmembrane regions are known.</Notes>
274                    </Field>
275                    <Field name="similar-to-human" type="boolean">
276                        <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
277                        else FALSE</Notes>
278                    </Field>
279                    <Field name="isoelectric-point" type="float">
280                        <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
281                        If the pH of the medium is lower than this value, the protein will have a net
282                        positive charge. If the pH of the medium is higher, then the protein will have a
283                        net negative charge.</Notes>
284                    </Field>
285                    <Field name="molecular-weight" type="float">
286                        <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
287                        indicates that no protein is created.</Notes>
288                    </Field>
289                    <Field name="sequence-length" type="counter">
290                        <Notes>Number of base pairs in this feature.</Notes>
291                    </Field>
292                    <Field name="locked" type="boolean">
293                        <Notes>TRUE if a feature's assignment is locked. A locked feature's functional
294                        role cannot be changed by automated programs.</Notes>
295                    </Field>
296                    <Field name="in-genbank" type="boolean">
297                        <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
298                  </Field>                  </Field>
299              </Fields>              </Fields>
             <Indexes>  
                 <Index>  
                     <Notes>This index allows the user to find the feature corresponding to  
                     the specified alias name.</Notes>  
                     <IndexFields>  
                         <IndexField name="alias" order="ascending" />  
                     </IndexFields>  
                 </Index>  
             </Indexes>  
300          </Entity>          </Entity>
301          <Entity name="Role" keyType="string">          <Entity name="FeatureAlias" keyType="medium-string">
302              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>Alternative names for features. A feature can have many aliases. In general,
303              One of the main goals of the database is to record the roles of the various features.</Notes>              each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
304            </Entity>
305            <Entity name="SproutUser" keyType="name-string">
306                <Notes>A user is a person who can make annotations and view data in the database. The
307                user object is keyed on the user's login name.</Notes>
308              <Fields>              <Fields>
309                  <Field name="name" type="string" relation="RoleName">                  <Field name="description" type="string">
310                      <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>Full name or description of this user.</Notes>
311                      that are encoded as EC numbers.</Notes>                  </Field>
312                      <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                  <Field name="access-code" type="key-string" relation="UserAccess">
313                        <Notes>This field is deprecated.</Notes>
314                  </Field>                  </Field>
315              </Fields>              </Fields>
316          </Entity>          </Entity>
317            <Entity name="SynonymGroup" keyType="id-string">
318                <Notes>A synonym group represents a group of features. Features that represent substantially
319                identical proteins or DNA sequences are mapped to the same synonym group, and this information is
320                used to expand similarities.</Notes>
321            </Entity>
322            <Entity name="Role" keyType="string">
323                <DisplayInfo theme="web" col="7" row="3" />
324                <Notes>A role describes a biological function that may be fulfilled by a feature.
325                One of the main goals of the database is to record the roles of the various features.</Notes>
326            </Entity>
327            <Entity name="RoleEC" keyType="string">
328                <Notes>EC code for a role.</Notes>
329            </Entity>
330          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
331              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <DisplayInfo theme="seed" col="1" row="3" />
332              are currently the only objects that may be inserted directly into the database. All other              <Notes>An annotation contains supplementary information about a feature. The most
333              information is loaded from data exported by the SEED.              important type of annotation is the assignment of a [[functional role]]; however,
334              [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation              other types of annotations are also possible.</Notes>
             is the target feature ID followed by a timestamp.</Notes>  
335              <Fields>              <Fields>
336                  <Field name="time" type="date">                  <Field name="time" type="date">
337                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 181  Line 340 
340                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
341                  </Field>                  </Field>
342              </Fields>              </Fields>
343                <Indexes>
344                    <Index>
345                        <Notes>This index allows the user to find recent annotations.</Notes>
346                        <IndexFields>
347                            <IndexField name="time" order="descending" />
348                        </IndexFields>
349                    </Index>
350                </Indexes>
351          </Entity>          </Entity>
352          <Entity name="Subsystem" keyType="string">          <Entity name="Reaction" keyType="key-string">
353              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems              <DisplayInfo  theme="web" col="7" row="5" />
354              is an important tool for recognizing parallel genetic features in different organisms.</Notes>              <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
355                is generally a small number preceded by a letter.</Notes>
356                <Fields>
357                    <Field name="url" type="string" relation="ReactionURL">
358                        <Notes>HTML string containing a link to a web location that describes the
359                        reaction. This field is optional.</Notes>
360                    </Field>
361                    <Field name="rev" type="boolean">
362                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
363                    </Field>
364                </Fields>
365          </Entity>          </Entity>
366          <Entity name="SSCell" keyType="name-string">          <Entity name="Compound" keyType="name-string">
367              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of              <DisplayInfo  theme="web" col="7" row="7" />
368              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one              <Notes>A compound is a chemical that participates in a reaction.
369              of the positions on the spreadsheet.</Notes>              All compounds have a unique ID and may also have one or more names.</Notes>
370                <Fields>
371                    <Field name="label" type="string">
372                        <Notes>Name used in reaction display strings. This is the same as the name
373                        possessing a priority of 1, but it is placed here to speed up the query
374                        used to create the display strings.</Notes>
375                    </Field>
376                </Fields>
377          </Entity>          </Entity>
378          <Entity name="SproutUser" keyType="name-string">          <Entity name="CompoundName" keyType="string">
379              <Notes>A [i]user[/i] is a person who can make annotations and view data in the database. The              <Notes>A compound name is a common name for the chemical represented by a
380              user object is keyed on the user's login name.</Notes>              compound.</Notes>
381            </Entity>
382            <Entity name="CompoundCAS" keyType="name-string">
383                <Notes>This entity represents the Chemical Abstract Service ID for a
384                compound. Each Compound has at most one CAS ID.</Notes>
385            </Entity>
386            <Entity name="Subsystem" keyType="string">
387                <DisplayInfo theme="seed" col="5" row="1" />
388                <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
389                is an important tool for recognizing parallel genetic features in different organisms.</Notes>
390              <Fields>              <Fields>
391                  <Field name="description" type="string">                  <Field name="version" type="int">
392                      <Notes>Full name or description of this user.</Notes>                      <Notes>Version number for the subsystem. This value is incremented each time the subsystem
393                        is backed up.</Notes>
394                  </Field>                  </Field>
395                  <Field name="access-code" type="key-string" relation="UserAccess">                  <Field name="curator" type="string">
396                      <Notes>Access code possessed by this                      <Notes>Name of the person currently in charge of the subsystem.</Notes>
397                      user. A user can have many access codes; a genome is accessible to the user if its                  </Field>
398                      access code matches any one of the user's access codes.</Notes>                  <Field name="notes" type="text">
399                      <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>                      <Notes>Descriptive notes about the subsystem.</Notes>
400                    </Field>
401                    <Field name="description" type="text">
402                        <Notes>Description of the subsystem's function in the cell.</Notes>
403                    </Field>
404                    <Field name="classification" type="string" relation="SubsystemClass">
405                        <Notes>Classification string, colon-delimited. This string organizes the
406                        subsystems into a hierarchy.</Notes>
407                    </Field>
408                    <Field name="hope-curation-notes" type="text" relation="SubsystemHopeNotes">
409                        <Notes>Text description of how the scenarios were curated.</Notes>
410                  </Field>                  </Field>
411              </Fields>              </Fields>
412          </Entity>          </Entity>
413            <Entity name="RoleSubset" keyType="string">
414                <Notes>A role subset is a named collection of roles in a particular subsystem. The
415                subset names are generally very short, non-unique strings. The ID of the parent
416                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
417            </Entity>
418            <Entity name="GenomeSubset" keyType="string">
419                <Notes>A genome subset is a named collection of genomes that participate
420                in a particular subsystem. The subset names are generally very short, non-unique
421                strings. The ID of the parent subsystem is prefixed to the subset ID in order
422                to make it unique.</Notes>
423            </Entity>
424            <Entity name="SSCell" keyType="hash-string">
425                <DisplayInfo theme="seed" col="5" row="3" />
426                <Notes>Part of the process of subsystem annotation of features
427                is creating a spreadsheet of genomes and roles to which features are assigned.
428                A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
429            </Entity>
430          <Entity name="Property" keyType="int">          <Entity name="Property" keyType="int">
431              <Notes>A [i]property[/i] is a type of assertion that could be made about the properties of              <Notes>A property is a type of assertion that could be made about the properties of
432              a particular feature. Each property instance is a key/value pair and can be associated              a particular feature. Each property instance is a key/value pair and can be associated
433              with many different features. Conversely, a feature can be associated with many key/value              with many different features. Conversely, a feature can be associated with many key/value
434              pairs, even some that notionally contradict each other. For example, there can be evidence              pairs, even some that notionally contradict each other. For example, there can be evidence
# Line 234  Line 455 
455              </Indexes>              </Indexes>
456          </Entity>          </Entity>
457          <Entity name="Diagram" keyType="name-string">          <Entity name="Diagram" keyType="name-string">
458              <Notes>A functional diagram describes the chemical reactions, often comprising a single              <DisplayInfo theme="web" col="7" row="1" />
459                <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
460              subsystem. A diagram is identified by a short name and contains a longer descriptive name.              subsystem. A diagram is identified by a short name and contains a longer descriptive name.
461              The actual diagram shows which functional roles guide the reactions along with the inputs              The actual diagram shows which functional roles guide the reactions along with the inputs
462              and outputs; the database, however, only indicate which roles belong to a particular              and outputs; the database, however, only indicates which roles belong to a particular
463              map.</Notes>              diagram's map.</Notes>
464              <Fields>              <Fields>
465                  <Field name="name" type="text">                  <Field name="name" type="text">
466                      <Notes>Descriptive name of this diagram.</Notes>                      <Notes>Descriptive name of this diagram.</Notes>
467                  </Field>                  </Field>
468              </Fields>              </Fields>
469          </Entity>          </Entity>
470          <Entity name="ExternalAliasOrg" keyType="name-string">          <Entity name="Family" keyType="id-string">
471              <Notes>An external alias is a feature name for a functional assignment that is not a              <DisplayInfo theme="seed" col="5" row="5" />
472              FIG ID. Functional assignments for external aliases are kept in a separate section of              <Notes>A family (also called a FigFam) is a group of homologous features believed to have
473              the database. This table contains a description of the relevant organism for an              the same function. Families provide a mechanism for verifying the accuracy of functional
474              external alias functional assignment.</Notes>              assignments and are also used in Rapid Annotation and in determining phylogenetic trees.</Notes>
475                  <Fields>              <Fields>
476                      <Field name="org" type="text">                  <Field name="function" type="text">
477                          <Notes>Descriptive name of the target organism for this external alias.</Notes>                      <Notes>The functional assignment expected for all PEGs in this family.</Notes>
478                      </Field>                      </Field>
479                  </Fields>                  <Field name="size" type="int">
480          </Entity>                      <Notes>The number of proteins in this family. This may be larger than the
481          <Entity name="ExternalAliasFunc" keyType="name-string">                      number of PEGs included in the family, since the family may also contain external
482              <Notes>An external alias is a feature name for a functional assignment that is not a                      IDs.</Notes>
             FIG ID. Functional assignments for external aliases are kept in a separate section of  
             the database. This table contains the functional role for the external alias functional  
             assignment.</Notes>  
                 <Fields>  
                     <Field name="func" type="text">  
                         <Notes>Functional role for this external alias.</Notes>  
483                      </Field>                      </Field>
484                  </Fields>                  </Fields>
485          </Entity>          </Entity>
486          <Entity name="Coupling" keyType="medium-string">          <Entity name="PDB" keyType="id-string">
487              <Notes>A coupling is a relationship between two features. The features are              <DisplayInfo theme="web" col="3" row="5" />
488              physically close on the contig, and there is evidence that they generally              <Notes>A PDB is a protein data bank entry containing information that can be used
489              belong together. The key of this entity is formed by combining the coupled              to determine the shape of the protein and the energies required to dock with it.
490              feature IDs with a space.</Notes>              The ID is the four-character name used on the PDB web site.</Notes>
491              <Fields>              <Fields>
492                  <Field name="score" type="int">                  <Field name="docking-count" type="int">
493                      <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH                      <Notes>The number of ligands that have been docked against this PDB.</Notes>
                     indicates that two genes near each other on one genome are very similar to  
                     genes near each other on another genome. The score only counts PCHs for which  
                     the genomes are very different. (In other words, we have a pairing that persists  
                     between different organisms.) A higher score implies a stronger meaning to the  
                     clustering.</Notes>  
494                  </Field>                  </Field>
495              </Fields>              </Fields>
496                <Indexes>
497                    <Index>
498                        <IndexFields>
499                            <IndexField name="docking-count" order="descending" />
500                            <IndexField name="id" order="ascending" />
501                        </IndexFields>
502                    </Index>
503                </Indexes>
504          </Entity>          </Entity>
505          <Entity name="PCH" keyType="string">          <Entity name="Ligand" keyType="id-string">
506              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <DisplayInfo theme="web" col="3" row="7" />
507              pair of physically close features on a contig) to a second pair of physically              <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
508              close features that are similar to the first. Essentially, the PCH is a              The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>
509              relationship between two clusterings in which the first clustering's features              <Fields>
510              are similar to the second clustering's features. The simplest model for                  <Field name="name" type="long-string">
511              this would be to simply relate clusterings to each other; however, not all                      <Notes>Chemical name of this ligand.</Notes>
             physically close pairs qualify as clusterings, so we relate a clustering to  
             a pair of features. The key is the clustering key followed by the IDs  
             of the features in the second pair.</Notes>  
             <Fields>  
                 <Field name="used" type="boolean">  
                     <Notes>TRUE if this PCH is used in scoring the attached clustering,  
                     else FALSE. If a clustering has a PCH for a particular genome and many  
                     similar genomes are present, then a PCH will probably exist for the  
                     similar genomes as well. When this happens, only one of the PCHs will  
                     be scored: the others are considered duplicates of the same evidence.</Notes>  
512                  </Field>                  </Field>
513              </Fields>              </Fields>
514          </Entity>          </Entity>
515            <Entity name="CellLocation" keyType="key-string">
516                <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
517                membrane, outside the cell, inside the cell, and so forth.</Notes>
518            </Entity>
519            <Entity name="Scenario" keyType="string">
520                <Notes>A scenario used to verify the validity of subsystem assignments. Each
521                scenario converrts input compounds to output compounds using reactions.
522                The scenario may use all of the reactions controlled by a subsystem or only
523                some, and may also incorporate additional reactions.</Notes>
524            </Entity>
525      </Entities>      </Entities>
526      <Relationships>      <Relationships>
527          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
528              <Notes>This relationship connects a feature to all the functional couplings              <DisplayInfo theme="web" />
529              in which it participates. A functional coupling is a recognition of the fact              <Notes>This relationship connects a role to the reactions it catalyzes.
530              that the features are close to each other on a chromosome, and similar              The purpose of a role is to create proteins that trigger certain
531              features in other genomes also tend to be close.</Notes>              chemical reactions. A single reaction can be triggered by many roles,
532              <Fields>              and a role can trigger many reactions.</Notes>
533                  <Field name="pos" type="int">          </Relationship>
534                      <Notes>Ordinal position of the feature in the coupling. Currently,          <Relationship name="ExcludesReaction" from="Scenario" to="Reaction" arity="MM">
535                      this is either "1" or "2".</Notes>              <Notes>This relationship connects a scenario to reactions of the parent
536                subsystem that do not participate in it.</Notes>
537            </Relationship>
538            <Relationship name="IncludesReaction" from="Scenario" to="Reaction" arity="MM">
539                <Notes>This relationship connects a scenario to reactions that participate
540                in it but are not part of the parent subsystem.</Notes>
541            </Relationship>
542            <Relationship name="HasScenario" from="Subsystem" to="Scenario" arity="MM">
543                <Notes>This relationship connects a role to the scenarios used to
544                validate it.</Notes>
545            </Relationship>
546            <Relationship name="IsInputFor" from="Compound" to="Scenario" arity="MM">
547                <Notes>This relationship connects a scenario to its input compounds.</Notes>
548            </Relationship>
549            <Relationship name="IsOutputOf" from="Compound" to="Scenario" arity="MM">
550                <Notes>This relationship connects a scenario to its output compounds</Notes>
551                <Fields>
552                    <Field name="auxiliary" type="boolean">
553                        <Notes>TRUE if this is an auxiliary output compound, FALSE if it is a
554                        main output compound.</Notes>
555                    </Field>
556                </Fields>
557            </Relationship>
558            <Relationship name="IsOnDiagram" from="Scenario" to="Diagram" arity="MM">
559                <Notes>This relationship connects a scenario to related diagrams.</Notes>
560            </Relationship>
561            <Relationship name="IsPossiblePlaceFor" from="CellLocation" to="Feature" arity="MM">
562                <Notes>This relationship connects a feature with the various places in a cell that the feature
563                might be found. The confidence factor is included as intersection data.</Notes>
564                <Fields>
565                    <Field name="confidence" type="float">
566                        <Notes>Confidence that the protein will be found in this location, expressed as a
567                        value from 0 to 10.</Notes>
568                    </Field>
569                </Fields>
570            </Relationship>
571            <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
572                <Notes>This relationship connects a feature to its CDD protein domains. The
573                match score is included as intersection data.</Notes>
574                <Fields>
575                    <Field name="score" type="float">
576                        <Notes>This is the match score between the feature and the CDD. A
577                        lower score is a better match.</Notes>
578                    </Field>
579                </Fields>
580                <FromIndex>
581                    <IndexFields>
582                        <IndexField name="score" order="ascending" />
583                    </IndexFields>
584                </FromIndex>
585            </Relationship>
586            <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
587                <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
588                associated with a compound, and some are associated with two compounds, but not
589                all compounds have CAS IDs.</Notes>
590            </Relationship>
591            <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
592                <Notes>Relates a role to its EC number. Every EC number is associated with a
593                role, but not all roles have EC numbers.</Notes>
594            </Relationship>
595            <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
596                <Notes>Connects an alias to the feature it represents. Every alias connects
597                to at least 1 feature, and a feature connects to many aliases.</Notes>
598            </Relationship>
599            <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
600                <Notes>Connects a compound to its names. A compound generally has several
601                names</Notes>
602                <Fields>
603                    <Field name="priority" type="int">
604                        <Notes>Priority of this name, with 1 being the highest priority, 2
605                        the next highest, and so forth.</Notes>
606                    </Field>
607                </Fields>
608                <FromIndex>
609                    <Notes>This index enables the application to view the names of a compound
610                    in priority order.</Notes>
611                    <IndexFields>
612                        <IndexField name="priority" order="ascending" />
613                    </IndexFields>
614                </FromIndex>
615            </Relationship>
616            <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
617                <DisplayInfo caption="Is Protein\nFor Feature" theme="web" />
618                <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
619                <Fields>
620                    <Field name="score" type="float">
621                        <Notes>Similarity score for the comparison between the feature and
622                        the PDB protein. A lower score indicates a better match.</Notes>
623                    </Field>
624                    <Field name="start-location" type="int">
625                        <Notes>Starting location within the feature of the matching region.</Notes>
626                    </Field>
627                    <Field name="end-location" type="int">
628                        <Notes>Ending location within the feature of the matching region.</Notes>
629                  </Field>                  </Field>
630              </Fields>              </Fields>
631              <ToIndex>              <ToIndex>
632                    <Notes>This index enables the application to view the PDBs of a
633                    feature in order from the closest match to the furthest.</Notes>
634                    <IndexFields>
635                        <IndexField name="score" order="ascending" />
636                    </IndexFields>
637                </ToIndex>
638                <FromIndex>
639                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of
640                  a coupling in the proper order. The order influences the way the                  a PDB in order from the closest match to the furthest.</Notes>
641                  PCHs are examined.</Notes>                  <IndexFields>
642                        <IndexField name="score" order="ascending" />
643                    </IndexFields>
644                </FromIndex>
645            </Relationship>
646            <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
647                <DisplayInfo caption="Docks With" theme="web" />
648                <Notes>Indicates that a docking result exists between a PDB and a ligand. The
649                docking result describes the energy required for the ligand to dock with
650                the protein described by the PDB. A lower energy indicates the ligand has a
651                good chance of disabling the protein. At the current time, only the best
652                docking results are kept.</Notes>
653                <Fields>
654                    <Field name="reason" type="id-string">
655                        <Notes>Indication of the reason for determining the docking result.
656                        A value of =Random= indicates the docking was attempted as a part
657                        of a random survey used to determine the docking characteristics of the
658                        PDB. A value of =Rich= indicates the docking was attempted because
659                        a low-energy docking result was predicted for the ligand with respect
660                        to the PDB.</Notes>
661                    </Field>
662                    <Field name="tool" type="id-string">
663                        <Notes>Name of the tool used to produce the docking result.</Notes>
664                    </Field>
665                    <Field name="total-energy" type="float">
666                        <Notes>Total energy required for the ligand to dock with the PDB
667                        protein, in kcal/mol. A negative value means energy is released.</Notes>
668                    </Field>
669                    <Field name="vanderwalls-energy" type="float">
670                        <Notes>Docking energy in kcal/mol that results from the geometric fit
671                        (Van der Waals force) between the PDB and the ligand.</Notes>
672                    </Field>
673                    <Field name="electrostatic-energy" type="float">
674                        <Notes>Docking energy in kcal/mol that results from the movement of
675                        electrons (electrostatic force) between the PDB and the ligand.</Notes>
676                    </Field>
677                </Fields>
678                <FromIndex>
679                    <Notes>This index enables the application to view a PDB's docking results from
680                    the lowest energy (best docking) to highest energy (worst docking).</Notes>
681                  <IndexFields>                  <IndexFields>
682                      <IndexField name="pos" order="ascending" />                      <IndexField name="total-energy" order="ascending" />
683                  </IndexFields>                  </IndexFields>
684                </FromIndex>
685                <ToIndex>
686                    <Notes>This index enables the application to view a ligand's docking results from
687                    the lowest energy (best docking) to highest energy (worst docking).</Notes>
688              </ToIndex>              </ToIndex>
689          </Relationship>          </Relationship>
690          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsAlsoFoundIn" from="Feature" to="ExternalDatabase" arity="MM">
691              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a feature to external databases that contain
692              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              essentially identical features. The name used in the external database is stored
693          </Relationship>              in the relationship as intersection data.</Notes>
694          <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">              <Fields>
695              <Notes>This relationship connects a PCH to the features that represent its                  <Field name="alias" type="name-string">
696              evidence. Each PCH is connected to a parent coupling that relates two features                      <Notes>ID of the feature in the specified external database.</Notes>
697              on a specific genome. The PCH's evidence that the parent coupling is functional                  </Field>
698              is the existence of two physically close features on a different genome that              </Fields>
699              correspond to the features in the coupling. Those features are found on the              <Indexes>
700              far side of this relationship.</Notes>                  <Index>
701              <Fields>                      <Notes>This index allows direct access to features by external ID.</Notes>
702                  <Field name="pos" type="int">                      <IndexFields>
703                      <Notes>Ordinal position of the feature in the coupling that corresponds                          <IndexField name="alias" order="ascending" />
704                      to our target feature. There is a one-to-one correspondence between the                      </IndexFields>
705                      features connected to the PCH by this relationship and the features                  </Index>
706                      connected to the PCH's parent coupling. The ordinal position is used              </Indexes>
707                      to decode that relationship. Currently, this field is either "1" or          </Relationship>
708                      "2".</Notes>          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
709                <DisplayInfo caption="Belongs To" theme="seed" />
710                <Notes>This relationship connects a protein family to all of its PEGs and connects
711                each PEG to all of its protein families.</Notes>
712            </Relationship>
713            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
714                <Notes>This relation connects a synonym group to the features that make it
715                up.</Notes>
716            </Relationship>
717            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
718                <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
719                <Notes>This relationship connects a genome to all of its features. This
720                relationship is redundant in a sense, because the genome ID is part
721                of the feature ID; however, it makes the creation of certain queries more
722                convenient because you can drag in filtering information for a feature's
723                genome.</Notes>
724                <Fields>
725                    <Field name="type" type="key-string">
726                        <Notes>Feature type (eg. peg, rna)</Notes>
727                  </Field>                  </Field>
728              </Fields>              </Fields>
729              <FromIndex>              <FromIndex>
730                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of a
731                  a PCH in the proper order.</Notes>                  Genome sorted by type.</Notes>
732                  <IndexFields>                  <IndexFields>
733                      <IndexField name="pos" order="ascending" />                      <IndexField name="type" order="ascending" />
734                  </IndexFields>                  </IndexFields>
735              </FromIndex>              </FromIndex>
736          </Relationship>          </Relationship>
737          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
738                <DisplayInfo caption="Is Part Of" theme="nmpdr" />
739              <Notes>This relationship connects a genome to the contigs that contain the actual genetic              <Notes>This relationship connects a genome to the contigs that contain the actual genetic
740              information.</Notes>              information.</Notes>
741          </Relationship>          </Relationship>
# Line 386  Line 767 
767              </FromIndex>              </FromIndex>
768          </Relationship>          </Relationship>
769          <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">          <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
770                <DisplayInfo caption="Targets" theme="seed" />
771              <Notes>This relationship connects a feature to its annotations.</Notes>              <Notes>This relationship connects a feature to its annotations.</Notes>
772          </Relationship>          </Relationship>
773          <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">          <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
774              <Notes>This relationship connects an annotation to the user who made it.</Notes>              <Notes>This relationship connects an annotation to the user who made it.</Notes>
775          </Relationship>          </Relationship>
776          <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">          <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
777                <DisplayInfo caption="\nParticipates\nIn" theme="seed" />
778              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
779              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
780              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the *SSCell* object.</Notes>
781                <Fields>
782                    <Field name="variant-code" type="key-string">
783                        <Notes>Code indicating the subsystem variant to which this
784                        genome belongs. Each subsystem can have multiple variants. A variant
785                        code of =-1= indicates that the genome does not have a functional
786                        variant of the subsystem. A variant code of =0= indicates that
787                        the genome's participation is considered iffy.</Notes>
788                    </Field>
789                </Fields>
790                <ToIndex>
791                    <Notes>This index enables the application to find all of the genomes using
792                    a subsystem in order by variant code, which is how we wish to display them
793                    in the spreadsheets.</Notes>
794                    <IndexFields>
795                        <IndexField name="variant-code" order="ascending" />
796                    </IndexFields>
797                </ToIndex>
798          </Relationship>          </Relationship>
799          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
800                <DisplayInfo caption="Uses" theme="seed" />
801              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
802                <Fields>
803                    <Field name="abbr" type="name-string">
804                        <Notes>Abbreviated name for the role, generally non-unique, but useful
805                        in column headings for HTML tables.</Notes>
806                    </Field>
807                    <Field name="column-number" type="int">
808                        <Notes>Column number for this role in the specified subsystem's
809                        spreadsheet.</Notes>
810                    </Field>
811                    <Field name="auxiliary" type="boolean">
812                        <Notes>If TRUE, then this role is ancillary to the purpose of the subsystem.
813                        If FALSE, it is essential to its metabolic pathway.</Notes>
814                    </Field>
815                    <Field name="hope_reaction_note" type="text">
816                        <Notes>A description of the status of a role in relation to the
817                        reactions it produces as determined by the scenarios. If present,
818                        will indicate if the role has been determined to be auxiliary,
819                        if it has been examined to verify an automatic assignment, and so
820                        forth.</Notes>
821                    </Field>
822                    <Field name="hope_reaction_link" type="text">
823                        <Notes>A description of the mapping between the reactions of
824                        this role and the scenarios used to validate it.</Notes>
825                    </Field>
826                </Fields>
827                <ToIndex>
828                    <Notes>This index enables the application to see the subsystem roles
829                    in column order. The ordering of the roles is usually significant,
830                    so it is important to preserve it.</Notes>
831                    <IndexFields>
832                        <IndexField name="column-number" order="ascending" />
833                    </IndexFields>
834                </ToIndex>
835          </Relationship>          </Relationship>
836          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
837                <DisplayInfo caption="Is Row Of" theme="seed" />
838              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
839              genome for the spreadsheet column.</Notes>              genome for the spreadsheet column.</Notes>
840          </Relationship>          </Relationship>
841          <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">          <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
842                <DisplayInfo caption="Is In\nColumn\nFor" theme="seed" />
843              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
844              role for the spreadsheet row.</Notes>              role for the spreadsheet row.</Notes>
845          </Relationship>          </Relationship>
846          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
847                <DisplayInfo caption="Is\nContained\nIn" theme="seed" />
848              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
849              features assigned to it.</Notes>              features assigned to it.</Notes>
850                <Fields>
851                    <Field name="cluster-number" type="int">
852                        <Notes>ID of this feature's cluster. Clusters represent families of
853                        related proteins participating in a subsystem.</Notes>
854                    </Field>
855                </Fields>
856            </Relationship>
857            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
858                <DisplayInfo caption="Involves" theme="web" />
859                <Notes>This relationship connects a reaction to the compounds that participate
860                in it.</Notes>
861                <Fields>
862                    <Field name="product" type="boolean">
863                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
864                        it is a substrate. When a reaction is written on paper in
865                        chemical notation, the substrates are left of the arrow and the
866                        products are to the right. Sorting on this field will cause
867                        the substrates to appear first, followed by the products. If the
868                        reaction is reversible, then the notion of substrates and products
869                        is not at intuitive; however, a value here of FALSE still puts the
870                        compound left of the arrow and a value of TRUE still puts it to the
871                        right.</Notes>
872                    </Field>
873                    <Field name="stoichiometry" type="key-string">
874                        <Notes>Number of molecules of the compound that participate in a
875                        single instance of the reaction. For example, if a reaction
876                        produces two water molecules, the stoichiometry of water for the
877                        reaction would be two. When a reaction is written on paper in
878                        chemical notation, the stoichiometry is the number next to the
879                        chemical formula of the compound.</Notes>
880                    </Field>
881                    <Field name="main" type="boolean">
882                        <Notes>TRUE if this compound is one of the main participants in
883                        the reaction, else FALSE. It is permissible for none of the
884                        compounds in the reaction to be considered main, in which
885                        case this value would be FALSE for all of the relevant
886                        compounds.</Notes>
887                    </Field>
888                    <Field name="loc" type="key-string">
889                        <Notes>An optional character string that indicates the relative
890                        position of this compound in the reaction's chemical formula. The
891                        location affects the way the compounds present as we cross the
892                        relationship from the reaction side. The product/substrate flag
893                        comes first, then the value of this field, then the main flag.
894                        The default value is an empty string; however, the empty string
895                        sorts first, so if this field is used, it should probably be
896                        used for every compound in the reaction.</Notes>
897                    </Field>
898                    <Field name="discriminator" type="int">
899                        <Notes>A unique ID for this record. The discriminator does not
900                        provide any useful data, but it prevents identical records from
901                        being collapsed by the SELECT DISTINCT command used by ERDB to
902                        retrieve data.</Notes>
903                    </Field>
904                </Fields>
905                <ToIndex>
906                    <Notes>This index presents the compounds in the reaction in the
907                    order they should be displayed when writing it in chemical notation.
908                    All the substrates appear before all the products, and within that
909                    ordering, the main compounds appear first.</Notes>
910                    <IndexFields>
911                        <IndexField name="product" order="ascending" />
912                        <IndexField name="loc" order="ascending" />
913                        <IndexField name="main" order="descending" />
914                    </IndexFields>
915                </ToIndex>
916          </Relationship>          </Relationship>
917          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
918                <DisplayInfo caption="Is\nLocation\nOf" theme="nmpdr" />
919              <Notes>This relationship connects a feature to the contig segments that work together              <Notes>This relationship connects a feature to the contig segments that work together
920              to effect it. The segments are numbered sequentially starting from 1. The database is              to effect it. The segments are numbered sequentially starting from 1. The database is
921              required to place an upper limit on the length of each segment. If a segment is longer              required to place an upper limit on the length of each segment. If a segment is longer
922              than the maximum, it can be broken into smaller bits.              than the maximum, it can be broken into smaller bits.  The upper limit enables applications
923              [p]The upper limit enables applications to locate all features that contain a specific              to locate all features that contain a specific residue. For example, if the upper limit
924              residue. For example, if the upper limit is 100 and we are looking for a feature that              is 100 and we are looking for a feature that contains residue 234 of contig *ABC*, we
925              contains residue 234 of contig [b]ABC[/b], we can look for features with a begin point              can look for features with a begin point between 135 and 333. The results can then be
926              between 135 and 333. The results can then be filtered by direction and length of the              filtered by direction and length of the segment.</Notes>
             segment.</Notes>  
927              <Fields>              <Fields>
928                  <Field name="locN" type="int">                  <Field name="locN" type="int">
929                      <Notes>Sequence number of this segment.</Notes>                      <Notes>Sequence number of this segment.</Notes>
# Line 435  Line 938 
938                      is forward and the point after the residue if the direction is backward.</Notes>                      is forward and the point after the residue if the direction is backward.</Notes>
939                  </Field>                  </Field>
940                  <Field name="dir" type="char">                  <Field name="dir" type="char">
941                      <Notes>Direction of the segment: [b]+[/b] if it is forward and                      <Notes>Direction of the segment: =+= if it is forward and
942                      [b]-[/b] if it is backward.</Notes>                      =-= if it is backward.</Notes>
943                  </Field>                  </Field>
944              </Fields>              </Fields>
945              <FromIndex Unique="false">              <FromIndex>
946                  <Notes>This index allows the application to find all the segments of a feature in                  <Notes>This index allows the application to find all the segments of a feature in
947                  the proper order.</Notes>                  the proper order.</Notes>
948                  <IndexFields>                  <IndexFields>
# Line 454  Line 957 
957                  </IndexFields>                  </IndexFields>
958              </ToIndex>              </ToIndex>
959          </Relationship>          </Relationship>
         <Relationship name="IsBidirectionalBestHitOf" from="Feature" to="Feature" arity="MM">  
             <Notes>This relationship is one of two that relate features to each other. It  
             connects features that are very similar but on separate genomes. A  
             bidirectional best hit relationship exists between two features [b]A[/b]  
             and [b]B[/b] if [b]A[/b] is the best match for [b]B[/b] on [b]A[/b]'s genome  
             and [b]B[/b] is the best match for [b]A[/b] on [b]B[/b]'s genome. </Notes>  
             <Fields>  
                 <Field name="genome" type="name-string">  
                     <Notes>ID of the genome containing the target (to) feature.</Notes>  
                 </Field>  
                 <Field name="sc" type="float">  
                     <Notes>score for this relationship</Notes>  
                 </Field>  
             </Fields>  
             <FromIndex>  
                 <Notes>This index allows the application to find a feature's best hit for  
                 a specific target genome.</Notes>  
                 <IndexFields>  
                     <IndexField name="genome" order="ascending" />  
                 </IndexFields>  
             </FromIndex>  
         </Relationship>  
960          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
961              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
962              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 491  Line 972 
972              </Fields>              </Fields>
973          </Relationship>          </Relationship>
974          <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">          <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
975                <DisplayInfo caption="Shows" theme="web" />
976              <Notes>This relationship connects a role to the diagrams on which it              <Notes>This relationship connects a role to the diagrams on which it
977              appears. A role frequently identifies an enzyme, and can appear in many              appears. A role frequently identifies an enzyme, and can appear in many
978              diagrams. A diagram generally contains many different roles.</Notes>              diagrams. A diagram generally contains many different roles.</Notes>
979          </Relationship>          </Relationship>
980          <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">          <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
981                <DisplayInfo caption="Is Container Of" theme="seed" />
982              <Notes>This relationship connects a subsystem to the spreadsheet cells              <Notes>This relationship connects a subsystem to the spreadsheet cells
983              used to analyze and display it. The cells themselves can be thought of              used to analyze and display it. The cells themselves can be thought of
984              as a grid with Roles on one axis and Genomes on the other. The              as a grid with Roles on one axis and Genomes on the other. The
# Line 507  Line 990 
990              assignment displayed is the most recent one by a user trusted              assignment displayed is the most recent one by a user trusted
991              by the current user. The current user implicitly trusts himself.              by the current user. The current user implicitly trusts himself.
992              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
993              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user =FIG=.</Notes>
994            </Relationship>
995            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
996                <Notes>This relationship connects a role subset to the roles that it covers.
997                A subset is, essentially, a named group of roles belonging to a specific
998                subsystem, and this relationship effects that. Note that will a role
999                may belong to many subsystems, a subset belongs to only one subsystem,
1000                and all roles in the subset must have that subsystem in common.</Notes>
1001            </Relationship>
1002            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
1003                <Notes>This relationship connects a subset to the genomes that it covers.
1004                A subset is, essentially, a named group of genomes participating in a specific
1005                subsystem, and this relationship effects that. Note that while a genome
1006                may belong to many subsystems, a subset belongs to only one subsystem,
1007                and all genomes in the subset must have that subsystem in common.</Notes>
1008            </Relationship>
1009            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
1010                <Notes>This relationship connects a subsystem to its constituent
1011                role subsets. Note that some roles in a subsystem may not belong to a
1012                subset, so the relationship between roles and subsystems cannot be
1013                derived from the relationships going through the subset.</Notes>
1014            </Relationship>
1015            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
1016                <Notes>This relationship connects a subsystem to its constituent
1017                genome subsets. Note that some genomes in a subsystem may not belong to a
1018                subset, so the relationship between genomes and subsystems cannot be
1019                derived from the relationships going through the subset.</Notes>
1020            </Relationship>
1021            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
1022                <Notes>This relationship connects a feature to the subsystems in which it
1023                participates. This is technically redundant information, but it is used
1024                so often that it gets its own table for performance reasons.</Notes>
1025                <Fields>
1026                    <Field name="genome" type="name-string">
1027                        <Notes>ID of the genome containing the feature</Notes>
1028                    </Field>
1029                    <Field name="type" type="key-string">
1030                        <Notes>Feature type (eg. peg, rna)</Notes>
1031                    </Field>
1032                </Fields>
1033                <ToIndex>
1034                    <Notes>This index enables the application to view the features of a
1035                    subsystem sorted by genome and feature type.</Notes>
1036                    <IndexFields>
1037                        <IndexField name="genome" order="ascending" />
1038                        <IndexField name="type" order="ascending" />
1039                    </IndexFields>
1040                </ToIndex>
1041          </Relationship>          </Relationship>
1042      </Relationships>      </Relationships>
1043        <Shapes>
1044            <Shape type="oval" name="Pins">
1045                <DisplayInfo theme="nmpdr" col="1" row="4.5" fixed="1" />
1046                <Notes>The Pin Server provides information about functional couplings between features.</Notes>
1047            </Shape>
1048            <Shape type="oval" name="Sims">
1049                <DisplayInfo theme="nmpdr" col="1.5" row="5" fixed="1" />
1050                <Notes>The Similarity Server contains a high-performance custom database of similarities between features.</Notes>
1051            </Shape>
1052            <Shape type="oval" name="BBHs">
1053                <DisplayInfo theme="nmpdr" col="2" row="5.5" fixed="1" />
1054                <Notes>For each feature, the BBH Server has that feature's bidirectional best hits in other genomes.</Notes>
1055            </Shape>
1056            <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1057                <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1058            </Shape>
1059        </Shapes>
1060  </Database>  </Database>

Legend:
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changed lines
  Added in v.1.56

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