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revision 1.7, Thu Jun 16 19:10:04 2005 UTC revision 1.49, Fri May 11 06:37:38 2007 UTC
# Line 7  Line 7 
7              <Fields>              <Fields>
8                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
9                      <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>  
10                  </Field>                  </Field>
11                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
12                                  <Notes>Species of the relevant organism.</Notes>                                  <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
13                                  </Field>                                  </Field>
14                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
15                          <Notes>The unique characterization identifies the particular organism instance from which the                          <Notes>The unique characterization identifies the particular organism instance from which the
16                          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
17                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
18                                          <DataGen>StringGen('PKVKVK999')</DataGen>                  </Field>
19                    <Field name="version" type="name-string">
20                        <Notes>version string for this genome, generally consisting of the genome ID followed
21                        by a period and a string of digits.</Notes>
22                  </Field>                  </Field>
23                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
24                          <Notes>The access code determines which users can look at the data relating to this genome.                          <Notes>The access code determines which users can look at the data relating to this genome.
25                          Each user is associated with a set of access codes. In order to view a genome, one of                          Each user is associated with a set of access codes. In order to view a genome, one of
26                          the user's access codes must match this value.</Notes>                          the user's access codes must match this value.</Notes>
27                                          <DataGen>RandParam('low','medium','high')</DataGen>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                    <Field name="dna-size" type="counter">
32                        <Notes>number of base pairs in the genome</Notes>
33                  </Field>                  </Field>
34                                  <Field name="taxonomy" type="text">                                  <Field name="taxonomy" type="text">
35                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
36                                          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
37                                          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
38                                          identifying string).</Notes>                                          identifying string).</Notes>
39                                          <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                  </Field>
40                                                                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                  <Field name="primary-group" type="name-string">
41                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
42                        (either based on the organism name or the default value "Supporting"), whereas there can be
43                        multiple named groups or even none.</Notes>
44                                  </Field>                                  </Field>
45                                  <Field name="group-name" type="name-string" relation="GenomeGroups">                                  <Field name="group-name" type="name-string" relation="GenomeGroups">
46                                          <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                                          <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
# Line 51  Line 60 
60                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
61                      </IndexFields>                      </IndexFields>
62                  </Index>                  </Index>
63                  <Index Unique="false">                  <Index>
64                        <Notes>This index allows the applications to find all genomes associated with
65                        a specific primary (NMPDR) group.</Notes>
66                        <IndexFields>
67                            <IndexField name="primary-group" order="ascending" />
68                            <IndexField name="genus" order="ascending" />
69                            <IndexField name="species" order="ascending" />
70                            <IndexField name="unique-characterization" order="ascending" />
71                        </IndexFields>
72                    </Index>
73                    <Index>
74                      <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
75                      species.</Notes>                      species.</Notes>
76                      <IndexFields>                      <IndexFields>
# Line 68  Line 87 
87              <Fields>              <Fields>
88                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
89                                          <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=" . $this->{id}</DataGen>  
90                                  </Field>                                  </Field>
91                  <Field name="description" type="text">                  <Field name="description" type="text">
92                                          <Notes>Description the source. The description can be a street address or a citation.</Notes>                                          <Notes>Description the source. The description can be a street address or a citation.</Notes>
                                         <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
93                                  </Field>                                  </Field>
94              </Fields>              </Fields>
95          </Entity>          </Entity>
# Line 95  Line 112 
112                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
113                                          <Notes>String consisting of the residues. Each residue is described by a single                                          <Notes>String consisting of the residues. Each residue is described by a single
114                                          character in the string.</Notes>                                          character in the string.</Notes>
                                         <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
115                                  </Field>                                  </Field>
116                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
117                                          <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
118                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
119                                          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
120                                          10^-30. A higher quality number a better chance of a correct match. It is possible                                          10^-30. A higher quality number a better chance of a correct match. It is possible
121                                          that the quality data is known for a sequence. If that is the case, the quality                      that the quality data is not known for a sequence. If that is the case, the quality
122                                          vector will contain the [b]unknown[/b].</Notes>                                          vector will contain the [b]unknown[/b].</Notes>
                                         <DataGen>unknown</DataGen>  
123                                  </Field>                                  </Field>
124              </Fields>              </Fields>
125          </Entity>          </Entity>
126          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
127              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
128              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
129              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# Line 116  Line 131 
131              <Fields>              <Fields>
132                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="string">
133                                          <Notes>Code indicating the type of this feature.</Notes>                                          <Notes>Code indicating the type of this feature.</Notes>
                                         <DataGen>RandParam('peg','rna')</DataGen>  
134                                  </Field>                                  </Field>
135                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
136                                          <Notes>Alternative name for this feature. feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
                                         <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
137                                  </Field>                                  </Field>
138                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
139                                          <Notes>[i](optional)[/i] A of this feature's residues into character codes, formed by concatenating                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
140                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
141                                          <DataGen testCount="0"></DataGen>                      protein encoding group, this is the protein characters. For other types
142                        it is the DNA characters.</Notes>
143                                  </Field>                                  </Field>
144                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
145                                          <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of                                          <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
146                                          the feature's initial residues.</Notes>                                          the feature's initial residues.</Notes>
147                                          <DataGen testCount="0"></DataGen>                  </Field>
148                    <Field name="assignment" type="text">
149                        <Notes>Default functional assignment for this feature.</Notes>
150                                  </Field>                                  </Field>
151                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
152                                          <Notes>TRUE if this feature is still considered valid, if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
153                                          <DataGen>1</DataGen>                  </Field>
154                    <Field name="assignment-maker" type="name-string">
155                        <Notes>name of the user who made the functional assignment</Notes>
156                    </Field>
157                    <Field name="assignment-quality" type="char">
158                        <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
159                        (indicating experimental)</Notes>
160                    </Field>
161                    <Field name="keywords" type="text" searchable="1">
162                        <Notes>This is a list of search keywords for the feature. It includes the
163                        functional assignment, subsystem roles, and special properties.</Notes>
164                                  </Field>                                  </Field>
165                                  <Field name="link" type="text" relation="FeatureLink">                                  <Field name="link" type="text" relation="FeatureLink">
166                                          <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 have no hyperlinks or it can have many. The
167                                          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
168                                          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 [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
169                                          <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
170                                          "&amp;Number=" . IntGen(1,99)</DataGen>                  <Field name="conservation" type="float" relation="FeatureConservation">
171                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
172                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
173                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
174                        between the feature and its close relatives.</Notes>
175                    </Field>
176                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
177                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
178                        cases, this will be a word describing whether the essentiality is confirmed (essential)
179                        or potential (potential-essential), hyperlinked to the document from which the
180                        essentiality was curated. If a feature is not essential, this field will have no
181                        values; otherwise, it may have multiple values.</Notes>
182                    </Field>
183                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
184                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
185                        cases, this will be a phrase or SA number hyperlinked to the document from which
186                        the virulence information was curated. If the feature is not virulent, this field
187                        will have no values; otherwise, it may have multiple values.</Notes>
188                    </Field>
189                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
190                        <Notes>A value indicating whether or not the feature can be found in the
191                        Immune Epitope Database. If the feature has not been matched to that database,
192                        this field will have no values. Otherwise, it will have an epitope name and/or
193                        sequence, hyperlinked to the database.</Notes>
194                                  </Field>                                  </Field>
195              </Fields>              </Fields>
196                <Indexes>
197                    <Index>
198                        <Notes>This index allows the user to find the feature corresponding to
199                        the specified alias name.</Notes>
200                        <IndexFields>
201                            <IndexField name="alias" order="ascending" />
202                        </IndexFields>
203                    </Index>
204                </Indexes>
205            </Entity>
206            <Entity name="SynonymGroup" keyType="id-string">
207                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
208                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
209          </Entity>          </Entity>
210          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
211              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
212              One of the main goals of the database is to record the roles of the various features.</Notes>              One of the main goals of the database is to record the roles of the various features.</Notes>
213                          <Fields>                          <Fields>
214                                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
215                                          <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>EC code for this role.</Notes>
216                                          that are encoded as EC numbers.</Notes>                  </Field>
217                                          <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                  <Field name="abbr" type="name-string">
218                        <Notes>Abbreviated name for the role, generally non-unique, but useful
219                        in column headings for HTML tables.</Notes>
220                                  </Field>                                  </Field>
221                          </Fields>                          </Fields>
222                <Indexes>
223                    <Index>
224                        <Notes>This index allows the user to find the role corresponding to
225                        an EC number.</Notes>
226                        <IndexFields>
227                            <IndexField name="EC" order="ascending" />
228                        </IndexFields>
229                    </Index>
230                </Indexes>
231          </Entity>          </Entity>
232          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
233              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
234                          are currently the only objects that may be inserted directly into the database. All other                          are currently the only objects that may be inserted directly into the database. All other
235                          information is loaded from data exported by the SEED.              information is loaded from data exported by the SEED.</Notes>
                         [p]Each annotation is associated with a target [b]Feature[/b]. The key of the annotation  
                         is the target feature ID followed by a timestamp.</Notes>  
236              <Fields>              <Fields>
237                  <Field name="time" type="date">                  <Field name="time" type="date">
238                                          <Notes>Date and time of the annotation.</Notes>                                          <Notes>Date and time of the annotation.</Notes>
# Line 170  Line 241 
241                                          <Notes>Text of the annotation.</Notes>                                          <Notes>Text of the annotation.</Notes>
242                                  </Field>                                  </Field>
243              </Fields>              </Fields>
244                <Indexes>
245                    <Index>
246                        <Notes>This index allows the user to find recent annotations.</Notes>
247                        <IndexFields>
248                            <IndexField name="time" order="descending" />
249                        </IndexFields>
250                    </Index>
251                </Indexes>
252            </Entity>
253            <Entity name="Reaction" keyType="key-string">
254                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
255                is generally a small number preceded by a letter.</Notes>
256                <Fields>
257                    <Field name="url" type="string" relation="ReactionURL">
258                        <Notes>HTML string containing a link to a web location that describes the
259                        reaction. This field is optional.</Notes>
260                    </Field>
261                    <Field name="rev" type="boolean">
262                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
263                    </Field>
264                </Fields>
265            </Entity>
266            <Entity name="Compound" keyType="name-string">
267                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
268                All compounds have a unique ID and may also have one or more names.</Notes>
269                <Fields>
270                    <Field name="name-priority" type="int" relation="CompoundName">
271                        <Notes>Priority of a compound name. The name with the loweset
272                        priority is the main name of this compound.</Notes>
273                    </Field>
274                    <Field name="name" type="name-string" relation="CompoundName">
275                        <Notes>Descriptive name for the compound. A compound may
276                        have several names.</Notes>
277                    </Field>
278                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
279                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
280                    </Field>
281                    <Field name="label" type="name-string">
282                        <Notes>Name used in reaction display strings.
283                        It is the same as the name possessing a priority of 1, but it is placed
284                        here to speed up the query used to create the display strings.</Notes>
285                    </Field>
286                </Fields>
287                <Indexes>
288                    <Index>
289                        <Notes>This index allows the user to find the compound corresponding to
290                        the specified name.</Notes>
291                        <IndexFields>
292                            <IndexField name="name" order="ascending" />
293                        </IndexFields>
294                    </Index>
295                    <Index>
296                        <Notes>This index allows the user to find the compound corresponding to
297                        the specified CAS ID.</Notes>
298                        <IndexFields>
299                            <IndexField name="cas-id" order="ascending" />
300                        </IndexFields>
301                    </Index>
302                    <Index>
303                        <Notes>This index allows the user to access the compound names in
304                        priority order.</Notes>
305                        <IndexFields>
306                            <IndexField name="id" order="ascending" />
307                            <IndexField name="name-priority" order="ascending" />
308                        </IndexFields>
309                    </Index>
310                </Indexes>
311          </Entity>          </Entity>
312          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
313              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
314              is an important tool for recognizing parallel genetic features in different organisms.</Notes>              is an important tool for recognizing parallel genetic features in different organisms.</Notes>
315                <Fields>
316                    <Field name="curator" type="string">
317                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
318                    </Field>
319                    <Field name="notes" type="text">
320                        <Notes>Descriptive notes about the subsystem.</Notes>
321                    </Field>
322                    <Field name="classification" type="string" relation="SubsystemClass">
323                        <Notes>Classification string, colon-delimited. This string organizes the
324                        subsystems into a hierarchy.</Notes>
325                    </Field>
326                </Fields>
327            </Entity>
328            <Entity name="RoleSubset" keyType="string">
329                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
330                subset names are generally very short, non-unique strings. The ID of the parent
331                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
332            </Entity>
333            <Entity name="GenomeSubset" keyType="string">
334                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
335                in a particular subsystem. The subset names are generally very short, non-unique
336                strings. The ID of the parent subsystem is prefixed to the subset ID in order
337                to make it unique.</Notes>
338          </Entity>          </Entity>
339          <Entity name="SSCell" keyType="name-string">          <Entity name="SSCell" keyType="hash-string">
340              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of              <Notes>Part of the process of locating and assigning features is creating a spreadsheet of
341              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one              genomes and roles to which features are assigned. A [i]spreadsheet cell[/i] represents one
342              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 191  Line 352 
352                                          <Notes>Access code possessed by this                                          <Notes>Access code possessed by this
353                      user. A user can have many access codes; a genome is accessible to the user if its                      user. A user can have many access codes; a genome is accessible to the user if its
354                      access code matches any one of the user's access codes.</Notes>                      access code matches any one of the user's access codes.</Notes>
                                         <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>  
355                                  </Field>                                  </Field>
356              </Fields>              </Fields>
357          </Entity>          </Entity>
# Line 256  Line 416 
416                                          </Field>                                          </Field>
417                                  </Fields>                                  </Fields>
418                  </Entity>                  </Entity>
419          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
420              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
421              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
422              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 272  Line 432 
432                  </Field>                  </Field>
433              </Fields>              </Fields>
434          </Entity>          </Entity>
435          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
436              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
437              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
438              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 280  Line 440 
440              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
441              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
442              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
443              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
444              <Fields>              <Fields>
445                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
446                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 292  Line 451 
451                  </Field>                  </Field>
452              </Fields>              </Fields>
453          </Entity>          </Entity>
454            <Entity name="Family" keyType="id-string">
455                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
456                families provide a mechanism for verifying the accuracy of functional assignments
457                and are also used in determining phylogenetic trees.</Notes>
458                <Fields>
459                    <Field name="function" type="text">
460                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
461                    </Field>
462                    <Field name="size" type="int">
463                        <Notes>The number of proteins in this family. This may be larger than the
464                        number of PEGs included in the family, since the family may also contain external
465                        IDs.</Notes>
466                    </Field>
467                </Fields>
468            </Entity>
469            <Entity name="PDB" keyType="id-string">
470                <Notes>A PDB is a protein database containing information that can be used to determine
471                the shape of the protein and the energies required to dock with it. The ID is the
472                four-character name used on the PDB web site.</Notes>
473                <Fields>
474                    <Field name="docking-count" type="int">
475                        <Notes>The number of ligands that have been docked against this PDB.</Notes>
476                    </Field>
477                </Fields>
478                <Indexes>
479                    <Index>
480                        <IndexFields>
481                            <IndexField name="docking-count" order="descending" />
482                            <IndexField name="id" order="ascending" />
483                        </IndexFields>
484                    </Index>
485                </Indexes>
486            </Entity>
487            <Entity name="Ligand" keyType="id-string">
488                <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
489                The ID of the ligand is an 8-digit ZINC ID number.</Notes>
490                <Fields>
491                    <Field name="name" type="long-string">
492                        <Notes>Chemical name of this ligand.</Notes>
493                    </Field>
494                </Fields>
495            </Entity>
496      </Entities>      </Entities>
497      <Relationships>      <Relationships>
498            <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
499                <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
500                <Fields>
501                    <Field name="score" type="float">
502                        <Notes>Similarity score for the comparison between the feature and
503                        the PDB protein. A lower score indicates a better match.</Notes>
504                    </Field>
505                    <Field name="start-location" type="int">
506                        <Notes>Starting location within the feature of the matching region.</Notes>
507                    </Field>
508                    <Field name="end-location" type="int">
509                        <Notes>Ending location within the feature of the matching region.</Notes>
510                    </Field>
511                </Fields>
512                <ToIndex>
513                    <Notes>This index enables the application to view the PDBs of a
514                    feature in order from the closest match to the furthest.</Notes>
515                    <IndexFields>
516                        <IndexField name="score" order="ascending" />
517                    </IndexFields>
518                </ToIndex>
519                <FromIndex>
520                    <Notes>This index enables the application to view the features of
521                    a PDB in order from the closest match to the furthest.</Notes>
522                    <IndexFields>
523                        <IndexField name="score" order="ascending" />
524                    </IndexFields>
525                </FromIndex>
526            </Relationship>
527            <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
528                <Notes>Indicates that a docking result exists between a PDB and a ligand. The
529                docking result describes the energy required for the ligand to dock with
530                the protein described by the PDB. A lower energy indicates the ligand has a
531                good chance of disabling the protein. At the current time, only the best
532                docking results are kept.</Notes>
533                <Fields>
534                    <Field name="reason" type="id-string">
535                        <Notes>Indication of the reason for determining the docking result.
536                        A value of [b]Random[/b] indicates the docking was attempted as a part
537                        of a random survey used to determine the docking characteristics of the
538                        PDB. A value of [b]Rich[/b] indicates the docking was attempted because
539                        a low-energy docking result was predicted for the ligand with respect
540                        to the PDB.</Notes>
541                    </Field>
542                    <Field name="tool" type="id-string">
543                        <Notes>Name of the tool used to produce the docking result.</Notes>
544                    </Field>
545                    <Field name="total-energy" type="float">
546                        <Notes>Total energy required for the ligand to dock with the PDB
547                        protein, in kcal/mol. A negative value means energy is released.</Notes>
548                    </Field>
549                    <Field name="vanderwalls-energy" type="float">
550                        <Notes>Docking energy in kcal/mol that results from the geometric fit
551                        (Van der Waals force) between the PDB and the ligand.</Notes>
552                    </Field>
553                    <Field name="electrostatic-energy" type="float">
554                        <Notes>Docking energy in kcal/mol that results from the movement of
555                        electrons (electrostatic force) between the PDB and the ligan.</Notes>
556                    </Field>
557                </Fields>
558                <FromIndex>
559                    <Notes>This index enables the application to view a PDB's docking results from
560                    the lowest energy (best docking) to highest energy (worst docking).</Notes>
561                    <IndexFields>
562                        <IndexField name="total-energy" order="ascending" />
563                    </IndexFields>
564                </FromIndex>
565                <ToIndex>
566                    <Notes>This index enables the application to view a ligand's docking results from
567                    the lowest energy (best docking) to highest energy (worst docking). Note that
568                    since we only keep the best docking results for a PDB, this index is not likely
569                    to provide useful results.</Notes>
570                </ToIndex>
571            </Relationship>
572            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
573                <Notes>This relationship connects a protein family to all of its PEGs and connects
574                each PEG to all of its protein families.</Notes>
575            </Relationship>
576          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
577              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
578              in which it participates. A functional coupling is a recognition of the fact              in which it participates. A functional coupling is a recognition of the fact
# Line 314  Line 593 
593                  </IndexFields>                  </IndexFields>
594              </ToIndex>              </ToIndex>
595          </Relationship>          </Relationship>
596            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
597                <Notes>This relation connects a synonym group to the features that make it
598                up.</Notes>
599            </Relationship>
600            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
601                <Notes>This relationship connects a genome to all of its features. This
602                relationship is redundant in a sense, because the genome ID is part
603                of the feature ID; however, it makes the creation of certain queries more
604                convenient because you can drag in filtering information for a feature's
605                genome.</Notes>
606                <Fields>
607                    <Field name="type" type="key-string">
608                        <Notes>Feature type (eg. peg, rna)</Notes>
609                    </Field>
610                </Fields>
611                <FromIndex>
612                    <Notes>This index enables the application to view the features of a
613                    Genome sorted by type.</Notes>
614                    <IndexFields>
615                        <IndexField name="type" order="ascending" />
616                    </IndexFields>
617                </FromIndex>
618            </Relationship>
619          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
620              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
621              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 384  Line 686 
686              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
687              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
688              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
689                <Fields>
690                    <Field name="variant-code" type="key-string">
691                        <Notes>Code indicating the subsystem variant to which this
692                        genome belongs. Each subsystem can have multiple variants. A variant
693                        code of [b]-1[/b] indicates that the genome does not have a functional
694                        variant of the subsystem. A variant code of [b]0[/b] indicates that
695                        the genome's participation is considered iffy.</Notes>
696                    </Field>
697                </Fields>
698                <ToIndex>
699                    <Notes>This index enables the application to find all of the genomes using
700                    a subsystem in order by variant code, which is how we wish to display them
701                    in the spreadsheets.</Notes>
702                    <IndexFields>
703                        <IndexField name="variant-code" order="ascending" />
704                    </IndexFields>
705                </ToIndex>
706          </Relationship>          </Relationship>
707          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
708              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
709                <Fields>
710                    <Field name="column-number" type="int">
711                        <Notes>Column number for this role in the specified subsystem's
712                        spreadsheet.</Notes>
713                    </Field>
714                </Fields>
715                <ToIndex>
716                    <Notes>This index enables the application to see the subsystem roles
717                    in column order. The ordering of the roles is usually significant,
718                    so it is important to preserve it.</Notes>
719                    <IndexFields>
720                        <IndexField name="column-number" order="ascending" />
721                    </IndexFields>
722                </ToIndex>
723          </Relationship>          </Relationship>
724          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
725              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 399  Line 732 
732          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
733              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
734              features assigned to it.</Notes>              features assigned to it.</Notes>
735                <Fields>
736                    <Field name="cluster-number" type="int">
737                        <Notes>ID of this feature's cluster. Clusters represent families of
738                        related proteins participating in a subsystem.</Notes>
739                    </Field>
740                </Fields>
741            </Relationship>
742            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
743                <Notes>This relationship connects a reaction to the compounds that participate
744                in it.</Notes>
745                <Fields>
746                    <Field name="product" type="boolean">
747                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
748                        it is a substrate. When a reaction is written on paper in
749                        chemical notation, the substrates are left of the arrow and the
750                        products are to the right. Sorting on this field will cause
751                        the substrates to appear first, followed by the products. If the
752                        reaction is reversible, then the notion of substrates and products
753                        is not at intuitive; however, a value here of FALSE still puts the
754                        compound left of the arrow and a value of TRUE still puts it to the
755                        right.</Notes>
756                    </Field>
757                    <Field name="stoichiometry" type="key-string">
758                        <Notes>Number of molecules of the compound that participate in a
759                        single instance of the reaction. For example, if a reaction
760                        produces two water molecules, the stoichiometry of water for the
761                        reaction would be two. When a reaction is written on paper in
762                        chemical notation, the stoichiometry is the number next to the
763                        chemical formula of the compound.</Notes>
764                    </Field>
765                    <Field name="main" type="boolean">
766                        <Notes>TRUE if this compound is one of the main participants in
767                        the reaction, else FALSE. It is permissible for none of the
768                        compounds in the reaction to be considered main, in which
769                        case this value would be FALSE for all of the relevant
770                        compounds.</Notes>
771                    </Field>
772                    <Field name="loc" type="key-string">
773                        <Notes>An optional character string that indicates the relative
774                        position of this compound in the reaction's chemical formula. The
775                        location affects the way the compounds present as we cross the
776                        relationship from the reaction side. The product/substrate flag
777                        comes first, then the value of this field, then the main flag.
778                        The default value is an empty string; however, the empty string
779                        sorts first, so if this field is used, it should probably be
780                        used for every compound in the reaction.</Notes>
781                    </Field>
782                    <Field name="discriminator" type="int">
783                        <Notes>A unique ID for this record. The discriminator does not
784                        provide any useful data, but it prevents identical records from
785                        being collapsed by the SELECT DISTINCT command used by ERDB to
786                        retrieve data.</Notes>
787                    </Field>
788                </Fields>
789                <ToIndex>
790                    <Notes>This index presents the compounds in the reaction in the
791                    order they should be displayed when writing it in chemical notation.
792                    All the substrates appear before all the products, and within that
793                    ordering, the main compounds appear first.</Notes>
794                    <IndexFields>
795                        <IndexField name="product" order="ascending" />
796                        <IndexField name="loc" order="ascending" />
797                        <IndexField name="main" order="descending" />
798                    </IndexFields>
799                </ToIndex>
800          </Relationship>          </Relationship>
801          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
802              <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
# Line 428  Line 826 
826                          [b]-[/b] if it is backward.</Notes>                          [b]-[/b] if it is backward.</Notes>
827                  </Field>                  </Field>
828              </Fields>              </Fields>
829              <FromIndex Unique="false">              <FromIndex>
830                  <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
831                  the proper order.</Notes>                  the proper order.</Notes>
832                  <IndexFields>                  <IndexFields>
# Line 443  Line 841 
841                  </IndexFields>                  </IndexFields>
842              </ToIndex>              </ToIndex>
843          </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>  
844                  <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">                  <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
845                          <Notes>This relationship connects a feature to its known property values.                          <Notes>This relationship connects a feature to its known property values.
846                          The relationship contains text data that indicates the paper or organization                          The relationship contains text data that indicates the paper or organization
# Line 498  Line 874 
874                          If no trusted users are specified in the database, the user                          If no trusted users are specified in the database, the user
875                          also implicitly trusts the user [b]FIG[/b].</Notes>                          also implicitly trusts the user [b]FIG[/b].</Notes>
876                  </Relationship>                  </Relationship>
877            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
878                <Notes>This relationship connects a role subset to the roles that it covers.
879                A subset is, essentially, a named group of roles belonging to a specific
880                subsystem, and this relationship effects that. Note that will a role
881                may belong to many subsystems, a subset belongs to only one subsystem,
882                and all roles in the subset must have that subsystem in common.</Notes>
883            </Relationship>
884            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
885                <Notes>This relationship connects a subset to the genomes that it covers.
886                A subset is, essentially, a named group of genomes participating in a specific
887                subsystem, and this relationship effects that. Note that while a genome
888                may belong to many subsystems, a subset belongs to only one subsystem,
889                and all genomes in the subset must have that subsystem in common.</Notes>
890            </Relationship>
891            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
892                <Notes>This relationship connects a subsystem to its constituent
893                role subsets. Note that some roles in a subsystem may not belong to a
894                subset, so the relationship between roles and subsystems cannot be
895                derived from the relationships going through the subset.</Notes>
896            </Relationship>
897            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
898                <Notes>This relationship connects a subsystem to its constituent
899                genome subsets. Note that some genomes in a subsystem may not belong to a
900                subset, so the relationship between genomes and subsystems cannot be
901                derived from the relationships going through the subset.</Notes>
902            </Relationship>
903            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
904                <Notes>This relationship connects a role to the reactions it catalyzes.
905                The purpose of a role is to create proteins that trigger certain
906                chemical reactions. A single reaction can be triggered by many roles,
907                and a role can trigger many reactions.</Notes>
908            </Relationship>
909            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
910                <Notes>This relationship connects a feature to the subsystems in which it
911                participates. This is technically redundant information, but it is used
912                so often that it deserves its own table.</Notes>
913                <Fields>
914                    <Field name="genome" type="name-string">
915                        <Notes>ID of the genome containing the feature</Notes>
916                    </Field>
917                    <Field name="type" type="key-string">
918                        <Notes>Feature type (eg. peg, rna)</Notes>
919                    </Field>
920                </Fields>
921                <ToIndex>
922                    <Notes>This index enables the application to view the features of a
923                    subsystem sorted by genome and feature type.</Notes>
924                    <IndexFields>
925                        <IndexField name="genome" order="ascending" />
926                        <IndexField name="type" order="ascending" />
927                    </IndexFields>
928                </ToIndex>
929            </Relationship>
930      </Relationships>      </Relationships>
931  </Database>  </Database>

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