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revision 1.7, Thu Jun 16 19:10:04 2005 UTC revision 1.42, Sat Oct 14 18:12:48 2006 UTC
# Line 25  Line 25 
25                          the user's access codes must match this value.</Notes>                          the user's access codes must match this value.</Notes>
26                                          <DataGen>RandParam('low','medium','high')</DataGen>                                          <DataGen>RandParam('low','medium','high')</DataGen>
27                  </Field>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                                  <Field name="taxonomy" type="text">                                  <Field name="taxonomy" type="text">
32                                          <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
33                                          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
# Line 33  Line 36 
36                                          <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                                          <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
37                                                                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                                                                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
38                                  </Field>                                  </Field>
39                    <Field name="primary-group" type="name-string">
40                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
41                        (either based on the organism name or the default value "Supporting"), whereas there can be
42                        multiple named groups or even none.</Notes>
43                    </Field>
44                                  <Field name="group-name" type="name-string" relation="GenomeGroups">                                  <Field name="group-name" type="name-string" relation="GenomeGroups">
45                                          <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
46                                          page or of particular interest to a research group or web site. A single genome can belong to multiple                                          page or of particular interest to a research group or web site. A single genome can belong to multiple
# Line 40  Line 48 
48                                  </Field>                                  </Field>
49              </Fields>              </Fields>
50              <Indexes>              <Indexes>
51                  <Index>                  <Index Unique="false">
52                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
53                      a specific access code, so that a complete list of the genomes users can view                      a specific access code, so that a complete list of the genomes users can view
54                      may be generated.</Notes>                      may be generated.</Notes>
# Line 52  Line 60 
60                      </IndexFields>                      </IndexFields>
61                  </Index>                  </Index>
62                  <Index Unique="false">                  <Index Unique="false">
63                        <Notes>This index allows the applications to find all genomes associated with
64                        a specific primary (NMPDR) group.</Notes>
65                        <IndexFields>
66                            <IndexField name="primary-group" order="ascending" />
67                            <IndexField name="genus" order="ascending" />
68                            <IndexField name="species" order="ascending" />
69                            <IndexField name="unique-characterization" order="ascending" />
70                        </IndexFields>
71                    </Index>
72                    <Index Unique="false">
73                      <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
74                      species.</Notes>                      species.</Notes>
75                      <IndexFields>                      <IndexFields>
# Line 98  Line 116 
116                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
117                                  </Field>                                  </Field>
118                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
119                                          <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
120                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
121                                          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
122                                          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
123                                          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
124                                          vector will contain the [b]unknown[/b].</Notes>                                          vector will contain the [b]unknown[/b].</Notes>
125                                          <DataGen>unknown</DataGen>                                          <DataGen>unknown</DataGen>
126                                  </Field>                                  </Field>
127              </Fields>              </Fields>
128          </Entity>          </Entity>
129          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
130              <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
131              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
132              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# Line 118  Line 136 
136                                          <Notes>Code indicating the type of this feature.</Notes>                                          <Notes>Code indicating the type of this feature.</Notes>
137                                          <DataGen>RandParam('peg','rna')</DataGen>                                          <DataGen>RandParam('peg','rna')</DataGen>
138                                  </Field>                                  </Field>
139                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
140                                          <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>
141                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
142                                  </Field>                                  </Field>
143                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
144                                          <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
145                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
146                        protein encoding group, this is the protein characters. For other types
147                        it is the DNA characters.</Notes>
148                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
149                                  </Field>                                  </Field>
150                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
# Line 132  Line 152 
152                                          the feature's initial residues.</Notes>                                          the feature's initial residues.</Notes>
153                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
154                                  </Field>                                  </Field>
155                    <Field name="assignment" type="text">
156                        <Notes>Default functional assignment for this feature.</Notes>
157                    </Field>
158                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
159                                          <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>
160                                          <DataGen>1</DataGen>                                          <DataGen>1</DataGen>
161                                  </Field>                                  </Field>
162                    <Field name="keywords" type="text" searchable="1">
163                        <Notes>This is a list of search keywords for the feature. It includes the
164                        functional assignment, subsystem roles, and special properties.</Notes>
165                    </Field>
166                                  <Field name="link" type="text" relation="FeatureLink">                                  <Field name="link" type="text" relation="FeatureLink">
167                                          <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
168                                          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
# Line 143  Line 170 
170                                          <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                                          <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
171                                          "&amp;Number=" . IntGen(1,99)</DataGen>                                          "&amp;Number=" . IntGen(1,99)</DataGen>
172                                  </Field>                                  </Field>
173                    <Field name="conservation" type="float" relation="FeatureConservation">
174                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
175                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
176                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
177                        between the feature and its close relatives.</Notes>
178                    </Field>
179              </Fields>              </Fields>
180                <Indexes>
181                    <Index>
182                        <Notes>This index allows the user to find the feature corresponding to
183                        the specified alias name.</Notes>
184                        <IndexFields>
185                            <IndexField name="alias" order="ascending" />
186                        </IndexFields>
187                    </Index>
188                </Indexes>
189            </Entity>
190            <Entity name="SynonymGroup" keyType="id-string">
191                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
192                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
193          </Entity>          </Entity>
194          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
195              <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.
196              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>
197                          <Fields>                          <Fields>
198                                  <Field name="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
199                                          <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>EC code for this role.</Notes>
                                         that are encoded as EC numbers.</Notes>  
200                                          <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                                          <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>
201                                  </Field>                                  </Field>
202                    <Field name="abbr" type="name-string">
203                        <Notes>Abbreviated name for the role, generally non-unique, but useful
204                        in column headings for HTML tables.</Notes>
205                    </Field>
206                          </Fields>                          </Fields>
207                <Indexes>
208                    <Index>
209                        <Notes>This index allows the user to find the role corresponding to
210                        an EC number.</Notes>
211                        <IndexFields>
212                            <IndexField name="EC" order="ascending" />
213                        </IndexFields>
214                    </Index>
215                </Indexes>
216          </Entity>          </Entity>
217          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
218              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
219                          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
220                          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>  
221              <Fields>              <Fields>
222                  <Field name="time" type="date">                  <Field name="time" type="date">
223                                          <Notes>Date and time of the annotation.</Notes>                                          <Notes>Date and time of the annotation.</Notes>
# Line 170  Line 226 
226                                          <Notes>Text of the annotation.</Notes>                                          <Notes>Text of the annotation.</Notes>
227                                  </Field>                                  </Field>
228              </Fields>              </Fields>
229                <Indexes>
230                    <Index>
231                        <Notes>This index allows the user to find recent annotations.</Notes>
232                        <IndexFields>
233                            <IndexField name="time" order="descending" />
234                        </IndexFields>
235                    </Index>
236                </Indexes>
237            </Entity>
238            <Entity name="Reaction" keyType="key-string">
239                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
240                is generally a small number preceded by a letter.</Notes>
241                <Fields>
242                    <Field name="url" type="string" relation="ReactionURL">
243                        <Notes>HTML string containing a link to a web location that describes the
244                        reaction. This field is optional.</Notes>
245                    </Field>
246                    <Field name="rev" type="boolean">
247                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
248                    </Field>
249                </Fields>
250            </Entity>
251            <Entity name="Compound" keyType="name-string">
252                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
253                All compounds have a unique ID and may also have one or more names.</Notes>
254                <Fields>
255                    <Field name="name-priority" type="int" relation="CompoundName">
256                        <Notes>Priority of a compound name. The name with the loweset
257                        priority is the main name of this compound.</Notes>
258                    </Field>
259                    <Field name="name" type="name-string" relation="CompoundName">
260                        <Notes>Descriptive name for the compound. A compound may
261                        have several names.</Notes>
262                    </Field>
263                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
264                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
265                    </Field>
266                    <Field name="label" type="name-string">
267                        <Notes>Name used in reaction display strings.
268                        It is the same as the name possessing a priority of 1, but it is placed
269                        here to speed up the query used to create the display strings.</Notes>
270                    </Field>
271                </Fields>
272                <Indexes>
273                    <Index>
274                        <Notes>This index allows the user to find the compound corresponding to
275                        the specified name.</Notes>
276                        <IndexFields>
277                            <IndexField name="name" order="ascending" />
278                        </IndexFields>
279                    </Index>
280                    <Index>
281                        <Notes>This index allows the user to find the compound corresponding to
282                        the specified CAS ID.</Notes>
283                        <IndexFields>
284                            <IndexField name="cas-id" order="ascending" />
285                        </IndexFields>
286                    </Index>
287                    <Index>
288                        <Notes>This index allows the user to access the compound names in
289                        priority order.</Notes>
290                        <IndexFields>
291                            <IndexField name="id" order="ascending" />
292                            <IndexField name="name-priority" order="ascending" />
293                        </IndexFields>
294                    </Index>
295                </Indexes>
296          </Entity>          </Entity>
297          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
298              <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
299              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>
300                <Fields>
301                    <Field name="curator" type="string">
302                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
303                    </Field>
304                    <Field name="notes" type="text">
305                        <Notes>Descriptive notes about the subsystem.</Notes>
306                    </Field>
307                    <Field name="classification" type="string" relation="SubsystemClass">
308                        <Notes>Classification string, space-delimited. This string organizes the
309                        subsystems into a hierarchy.</Notes>
310                    </Field>
311                </Fields>
312            </Entity>
313            <Entity name="RoleSubset" keyType="string">
314                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
315                subset names are generally very short, non-unique strings. The ID of the parent
316                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
317          </Entity>          </Entity>
318          <Entity name="SSCell" keyType="name-string">          <Entity name="GenomeSubset" keyType="string">
319                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
320                in a particular subsystem. The subset names are generally very short, non-unique
321                strings. The ID of the parent subsystem is prefixed to the subset ID in order
322                to make it unique.</Notes>
323            </Entity>
324            <Entity name="SSCell" keyType="hash-string">
325              <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
326              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
327              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 256  Line 402 
402                                          </Field>                                          </Field>
403                                  </Fields>                                  </Fields>
404                  </Entity>                  </Entity>
405          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
406              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
407              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
408              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 418 
418                  </Field>                  </Field>
419              </Fields>              </Fields>
420          </Entity>          </Entity>
421          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
422              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
423              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
424              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 426 
426              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
427              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
428              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
429              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>  
430              <Fields>              <Fields>
431                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
432                      <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 437 
437                  </Field>                  </Field>
438              </Fields>              </Fields>
439          </Entity>          </Entity>
440            <Entity name="Family" keyType="id-string">
441                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
442                families provide a mechanism for verifying the accuracy of functional assignments
443                and are also used in determining phylogenetic trees.</Notes>
444                <Fields>
445                    <Field name="function" type="text">
446                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
447                    </Field>
448                    <Field name="size" type="int">
449                        <Notes>The number of proteins in this family. This may be larger than the
450                        number of PEGs included in the family, since the family may also contain external
451                        IDs.</Notes>
452                    </Field>
453                </Fields>
454            </Entity>
455            <Entity name="DrugProject" keyType="name-string">
456                <Notes>A drug project is a coherent sent of drug target data that came through the
457                pipeline. In other words, data is put into the database one drug project at a time.
458                This makes it easier to manage the incoming data and to track where a particular
459                piece of data originated.</Notes>
460            </Entity>
461            <Entity name="DrugTopic" keyType="int">
462                <Notes>A drug topic organizes the data in a project relating to a single organism
463                group's features as they apply to a specific category of activity. Categories include
464                features essential to the organism's survival, those that are targets or inhibitors
465                of anti-biotics, and those associated with virulence. Thus, a drug topic consists
466                of data from a single project for features that make good drug targets for the same
467                reason. Drug topics have an artificial, internally-generated key.</Notes>
468                <Fields>
469                    <Field name="identifier" type="name-string">
470                        <Notes>The topic identifier, consisting usually of a generalized organism name
471                        (e.g. Staphylococcus) and the last name of the project's author. More than
472                        one topic may have the same identifier, which is why this isn't the key.</Notes>
473                    </Field>
474                    <Field name="function" type="name-string">
475                        <Notes>A short phrase describing the topic.</Notes>
476                    </Field>
477                    <Field name="URL" type="string">
478                        <Notes>A URL for the paper from which the topic was gathered.</Notes>
479                    </Field>
480                    <Field name="category" type="key-string">
481                        <Notes>The code for this topic's activity category.</Notes>
482                    </Field>
483                </Fields>
484                <Indexes>
485                    <Index>
486                        <Notes>This index enables the application to find all topics with a specified
487                        category, ordered by function.</Notes>
488                        <IndexFields>
489                            <IndexField name="category" order="ascending" />
490                            <IndexField name="function" order="ascending" />
491                        </IndexFields>
492                    </Index>
493                    <Index>
494                        <Notes>This index enables the application to find all topics with a specified
495                        identifier, ordered by category.</Notes>
496                        <IndexFields>
497                            <IndexField name="identifier" order="ascending" />
498                            <IndexField name="category" order="ascending" />
499                        </IndexFields>
500                    </Index>
501                </Indexes>
502            </Entity>
503            <Entity name="PDB" keyType="key-string">
504                <Notes>A PDB is a database of protein structure and related information of use
505                in drug targeting. The purpose of drug targeting is to analyze the ability
506                of drug molecules, or ligands, to bond to proteins. A PDB for a protein already
507                attached to a ligand is called a bound PDB. A PDB for the protein by itself is
508                called a free PDB. The key of the PDB is its code name on the Protein Data
509                Bank web site.</Notes>
510                <Fields>
511                    <Field name="type" type="id-string">
512                        <Notes>The type of PDB: "bound" or "free".</Notes>
513                    </Field>
514                    <Field name="title" type="string">
515                        <Notes>The descriptive title of this PDB.</Notes>
516                    </Field>
517                </Fields>
518            </Entity>
519            <Entity name="Ligand" keyType="string">
520                <Notes>A ligand is a molecule that can bind to a PDB. The CLIBE analysis
521                for a PDB is an attribute of the relationship between a PDB and a ligand.</Notes>
522            </Entity>
523      </Entities>      </Entities>
524      <Relationships>      <Relationships>
525            <Relationship name="BindsWith" from="PDB" to="Ligand" arity="MM">
526                <Notes>This relationship describes the energy required for a ligand to bind
527                to the protein described by a PDB. The total energy required to bind
528                the ligand to the protein is described in this relationship by four
529                quantities. A negative value is energy released; a positive value is
530                energy required.</Notes>
531                <Fields>
532                    <Field name="URL" type="string">
533                        <Notes>URL for viewing the CLIBE data for this binding relationship.</Notes>
534                    </Field>
535                    <Field name="vanderwaals-energy" type="float">
536                        <Notes>kCal/mol of energy due to Van der Waals force.</Notes>
537                    </Field>
538                    <Field name="hbond-energy" type="float">
539                        <Notes>kCal/mol of energy due to hydrogen bonding.</Notes>
540                    </Field>
541                    <Field name="ionic-energy" type="float">
542                        <Notes>kCal/mol of energy due to ionic bonding.</Notes>
543                    </Field>
544                    <Field name="solvation-energy" type="float">
545                        <Notes>kCal/mol of energy due to attraction to the solvent in which
546                        the ligand is immersed.</Notes>
547                    </Field>
548                </Fields>
549            </Relationship>
550            <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="1M">
551                <Notes>This relationship describes the analysis of a free PDB as produced from a
552                particular topic.</Notes>
553                <Fields>
554                    <Field name="pass-asp-info" type="int">
555                        <Notes>The number of Active Site Points at which ligands can bind to
556                        the protein.</Notes>
557                    </Field>
558                    <Field name="ramsol-file" type="string">
559                        <Notes>The URL of a file that can be downloaded by the user and
560                        passed to the Ramsol program for viewing the protein.</Notes>
561                    </Field>
562                    <Field name="pass-weight" type="float">
563                        <Notes>A score for the largest pocket into which a ligand can bind. A
564                        higher score makes for a better target.</Notes>
565                    </Field>
566                    <Field name="pass-file" type="string">
567                        <Notes>The URL for a GIF file that shows the active sites on the protein.</Notes>
568                    </Field>
569                </Fields>
570            </Relationship>
571            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="1M">
572                <Note>This relationship connects a free PDB to its bound counterparts.</Note>
573            </Relationship>
574            <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
575                <Notes>This relationship connects a feature to a protein database (PDB) that
576                is relevant for determining drugs that target the feature.</Notes>
577                <Fields>
578                    <Field name="score" type="float">
579                        <Notes>The BLAST score for the feature as it relates to the PDB's
580                        protein, expressed as a small positive number. Generally only a
581                        very low BLAST score (1e-15 or less) indicates a good match.</Notes>
582                    </Field>
583                    <Field name="distance" type="float">
584                        <Notes>A distance value indicating how far the PDB's protein is
585                        from the feature's protein. A distance of 0 indicates a perfect
586                        match.</Notes>
587                    </Field>
588                </Fields>
589                <FromIndex>
590                    <Notes>This index yields the Features for a PDB in order from best
591                    score to worst.</Notes>
592                    <IndexFields>
593                        <IndexField name="score" order="ascending" />
594                    </IndexFields>
595                </FromIndex>
596                <ToIndex>
597                    <Notes>This index yields the Features for a PDB in order from best
598                    score to worst.</Notes>
599                    <IndexFields>
600                        <IndexField name="score" order="ascending" />
601                    </IndexFields>
602                </ToIndex>
603            </Relationship>
604            <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">
605                <Notes>This relationship connects a drug target project to all of its
606                topics.</Notes>
607            </Relationship>
608            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
609                <Notes>This relationship connects a protein family to all of its PEGs and connects
610                each PEG to all of its protein families.</Notes>
611            </Relationship>
612          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
613              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
614              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 629 
629                  </IndexFields>                  </IndexFields>
630              </ToIndex>              </ToIndex>
631          </Relationship>          </Relationship>
632            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
633                <Notes>This relation connects a synonym group to the features that make it
634                up.</Notes>
635            </Relationship>
636            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
637                <Notes>This relationship connects a genome to all of its features. This
638                relationship is redundant in a sense, because the genome ID is part
639                of the feature ID; however, it makes the creation of certain queries more
640                convenient because you can drag in filtering information for a feature's
641                genome.</Notes>
642                <Fields>
643                    <Field name="type" type="key-string">
644                        <Notes>Feature type (eg. peg, rna)</Notes>
645                    </Field>
646                </Fields>
647                <FromIndex>
648                    <Notes>This index enables the application to view the features of a
649                    Genome sorted by type.</Notes>
650                    <IndexFields>
651                        <IndexField name="type" order="ascending" />
652                    </IndexFields>
653                </FromIndex>
654            </Relationship>
655          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
656              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
657              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 722 
722              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
723              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
724              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
725                <Fields>
726                    <Field name="variant-code" type="key-string">
727                        <Notes>Code indicating the subsystem variant to which this
728                        genome belongs. Each subsystem can have multiple variants. A variant
729                        code of [b]-1[/b] indicates that the genome does not have a functional
730                        variant of the subsystem. A variant code of [b]0[/b] indicates that
731                        the genome's participation is considered iffy.</Notes>
732                    </Field>
733                </Fields>
734                <ToIndex>
735                    <Notes>This index enables the application to find all of the genomes using
736                    a subsystem in order by variant code, which is how we wish to display them
737                    in the spreadsheets.</Notes>
738                    <IndexFields>
739                        <IndexField name="variant-code" order="ascending" />
740                    </IndexFields>
741                </ToIndex>
742          </Relationship>          </Relationship>
743          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
744              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
745                <Fields>
746                    <Field name="column-number" type="int">
747                        <Notes>Column number for this role in the specified subsystem's
748                        spreadsheet.</Notes>
749                    </Field>
750                </Fields>
751                <ToIndex>
752                    <Notes>This index enables the application to see the subsystem roles
753                    in column order. The ordering of the roles is usually significant,
754                    so it is important to preserve it.</Notes>
755                    <IndexFields>
756                        <IndexField name="column-number" order="ascending" />
757                    </IndexFields>
758                </ToIndex>
759          </Relationship>          </Relationship>
760          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
761              <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 768 
768          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
769              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
770              features assigned to it.</Notes>              features assigned to it.</Notes>
771                <Fields>
772                    <Field name="cluster-number" type="int">
773                        <Notes>ID of this feature's cluster. Clusters represent families of
774                        related proteins participating in a subsystem.</Notes>
775                    </Field>
776                </Fields>
777            </Relationship>
778            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
779                <Notes>This relationship connects a reaction to the compounds that participate
780                in it.</Notes>
781                <Fields>
782                    <Field name="product" type="boolean">
783                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
784                        it is a substrate. When a reaction is written on paper in
785                        chemical notation, the substrates are left of the arrow and the
786                        products are to the right. Sorting on this field will cause
787                        the substrates to appear first, followed by the products. If the
788                        reaction is reversible, then the notion of substrates and products
789                        is not at intuitive; however, a value here of FALSE still puts the
790                        compound left of the arrow and a value of TRUE still puts it to the
791                        right.</Notes>
792                    </Field>
793                    <Field name="stoichiometry" type="key-string">
794                        <Notes>Number of molecules of the compound that participate in a
795                        single instance of the reaction. For example, if a reaction
796                        produces two water molecules, the stoichiometry of water for the
797                        reaction would be two. When a reaction is written on paper in
798                        chemical notation, the stoichiometry is the number next to the
799                        chemical formula of the compound.</Notes>
800                    </Field>
801                    <Field name="main" type="boolean">
802                        <Notes>TRUE if this compound is one of the main participants in
803                        the reaction, else FALSE. It is permissible for none of the
804                        compounds in the reaction to be considered main, in which
805                        case this value would be FALSE for all of the relevant
806                        compounds.</Notes>
807                    </Field>
808                    <Field name="loc" type="key-string">
809                        <Notes>An optional character string that indicates the relative
810                        position of this compound in the reaction's chemical formula. The
811                        location affects the way the compounds present as we cross the
812                        relationship from the reaction side. The product/substrate flag
813                        comes first, then the value of this field, then the main flag.
814                        The default value is an empty string; however, the empty string
815                        sorts first, so if this field is used, it should probably be
816                        used for every compound in the reaction.</Notes>
817                    </Field>
818                    <Field name="discriminator" type="int">
819                        <Notes>A unique ID for this record. The discriminator does not
820                        provide any useful data, but it prevents identical records from
821                        being collapsed by the SELECT DISTINCT command used by ERDB to
822                        retrieve data.</Notes>
823                    </Field>
824                </Fields>
825                <ToIndex>
826                    <Notes>This index presents the compounds in the reaction in the
827                    order they should be displayed when writing it in chemical notation.
828                    All the substrates appear before all the products, and within that
829                    ordering, the main compounds appear first.</Notes>
830                    <IndexFields>
831                        <IndexField name="product" order="ascending" />
832                        <IndexField name="loc" order="ascending" />
833                        <IndexField name="main" order="descending" />
834                    </IndexFields>
835                </ToIndex>
836          </Relationship>          </Relationship>
837          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
838              <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 443  Line 877 
877                  </IndexFields>                  </IndexFields>
878              </ToIndex>              </ToIndex>
879          </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>  
880                  <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">                  <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
881                          <Notes>This relationship connects a feature to its known property values.                          <Notes>This relationship connects a feature to its known property values.
882                          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 910 
910                          If no trusted users are specified in the database, the user                          If no trusted users are specified in the database, the user
911                          also implicitly trusts the user [b]FIG[/b].</Notes>                          also implicitly trusts the user [b]FIG[/b].</Notes>
912                  </Relationship>                  </Relationship>
913            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
914                <Notes>This relationship connects a role subset to the roles that it covers.
915                A subset is, essentially, a named group of roles belonging to a specific
916                subsystem, and this relationship effects that. Note that will a role
917                may belong to many subsystems, a subset belongs to only one subsystem,
918                and all roles in the subset must have that subsystem in common.</Notes>
919            </Relationship>
920            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
921                <Notes>This relationship connects a subset to the genomes that it covers.
922                A subset is, essentially, a named group of genomes participating in a specific
923                subsystem, and this relationship effects that. Note that while a genome
924                may belong to many subsystems, a subset belongs to only one subsystem,
925                and all genomes in the subset must have that subsystem in common.</Notes>
926            </Relationship>
927            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
928                <Notes>This relationship connects a subsystem to its constituent
929                role subsets. Note that some roles in a subsystem may not belong to a
930                subset, so the relationship between roles and subsystems cannot be
931                derived from the relationships going through the subset.</Notes>
932            </Relationship>
933            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
934                <Notes>This relationship connects a subsystem to its constituent
935                genome subsets. Note that some genomes in a subsystem may not belong to a
936                subset, so the relationship between genomes and subsystems cannot be
937                derived from the relationships going through the subset.</Notes>
938            </Relationship>
939            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
940                <Notes>This relationship connects a role to the reactions it catalyzes.
941                The purpose of a role is to create proteins that trigger certain
942                chemical reactions. A single reaction can be triggered by many roles,
943                and a role can trigger many reactions.</Notes>
944            </Relationship>
945            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
946                <Notes>This relationship connects a feature to the subsystems in which it
947                participates. This is technically redundant information, but it is used
948                so often that it deserves its own table.</Notes>
949                <Fields>
950                    <Field name="genome" type="name-string">
951                        <Notes>ID of the genome containing the feature</Notes>
952                    </Field>
953                    <Field name="type" type="key-string">
954                        <Notes>Feature type (eg. peg, rna)</Notes>
955                    </Field>
956                </Fields>
957                <ToIndex>
958                    <Notes>This index enables the application to view the features of a
959                    subsystem sorted by genome and feature type.</Notes>
960                    <IndexFields>
961                        <IndexField name="genome" order="ascending" />
962                        <IndexField name="type" order="ascending" />
963                    </IndexFields>
964                </ToIndex>
965            </Relationship>
966      </Relationships>      </Relationships>
967  </Database>  </Database>

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