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revision 1.54, Wed May 7 23:16:47 2008 UTC revision 1.55, Tue Aug 12 06:03:28 2008 UTC
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1  <?xml version="1.0" encoding="utf-8" ?>  <?xml version="1.0" encoding="utf-8" ?>
2  <Database>  <Database>
3      <Title>Sprout Genome and Subsystem Database</Title>      <Title>Sprout Genome and Subsystem Database</Title>
4      <Notes>The Sprout database contains the genetic data for all complete organisms in the [[SeedEnvironment]].      <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.
5      The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external      The data that is not in Sprout-- attributes, similarities, couplings-- is stored on external
6      servers available to the Sprout software. The Sprout database is reloaded approximately once      servers available to the Sprout software. The Sprout database is reloaded approximately once
7      per month. There is significant redundancy in the Sprout database because it has been      per month. There is significant redundancy in the Sprout database because it has been
# Line 9  Line 9 
9      feature's functional role and a list of possible search terms.</Notes>      feature's functional role and a list of possible search terms.</Notes>
10      <Entities>      <Entities>
11          <Entity name="Genome" keyType="name-string">          <Entity name="Genome" keyType="name-string">
12              <Notes>A [[Genome]] contains the sequence data for a particular individual organism.</Notes>              <DisplayInfo theme="nmpdr" col="3" row="1" />
13                <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
14              <Fields>              <Fields>
15                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
16                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
# Line 93  Line 94 
94          <Entity name="CDD" keyType="key-string">          <Entity name="CDD" keyType="key-string">
95              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
96              on a feature's protein. The ID is six-digit string assigned by the public              on a feature's protein. The ID is six-digit string assigned by the public
97              [[http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Conserved Domain Database]]. A CDD              Conserved Domain Database. A CDD
98              can occur on multiple features and a feature generally has multiple CDDs.</Notes>              can occur on multiple features and a feature generally has multiple CDDs.</Notes>
99          </Entity>          </Entity>
100          <Entity name="Source" keyType="medium-string">          <Entity name="Source" keyType="medium-string">
101              <Notes>A _source_ describes a place from which genome data was taken. This can be an organization              <Notes>A source describes a place from which genome data was taken. This can be an organization
102              or a paper citation.</Notes>              or a paper citation.</Notes>
103              <Fields>              <Fields>
104                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
# Line 109  Line 110 
110              </Fields>              </Fields>
111          </Entity>          </Entity>
112          <Entity name="Contig" keyType="name-string">          <Entity name="Contig" keyType="name-string">
113              <Notes>A _contig_ is a contiguous run of residues. The contig's ID consists of the              <DisplayInfo theme="nmpdr" col="1" row="1" />
114                <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
115              genome ID followed by a name that identifies which contig this is for the parent genome. As              genome ID followed by a name that identifies which contig this is for the parent genome. As
116              is the case with all keys in this database, the individual components are separated by a              is the case with all keys in this database, the individual components are separated by a
117              period. A contig can contain over a million residues. For performance reasons, therefore,              period. A contig can contain over a million residues. For performance reasons, therefore,
118              the contig is split into multiple pieces called _sequences_. The sequences              the contig is split into multiple pieces called sequences. The sequences
119              contain the characters that represent the residues as well as data on the quality of              contain the characters that represent the residues as well as data on the quality of
120              the residue identification.</Notes>              the residue identification.</Notes>
121          </Entity>          </Entity>
122          <Entity name="Sequence" keyType="name-string">          <Entity name="Sequence" keyType="name-string">
123              <Notes>A _sequence_ is a continuous piece of a contig. Contigs are split into              <Notes>A sequence is a continuous piece of a contig. Contigs are split into
124              sequences so that we don't have to have the entire contig in memory when we are              sequences so that we don't have to have the entire contig in memory when we are
125              manipulating it. The key of the sequence is the contig ID followed by the index of              manipulating it. The key of the sequence is the contig ID followed by the index of
126              the begin point.</Notes>              the begin point.</Notes>
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140              </Fields>              </Fields>
141          </Entity>          </Entity>
142          <Entity name="Keyword" keyType="name-string">          <Entity name="Keyword" keyType="name-string">
143              <Notes>A _keyword_ is a word stem that can be used to search the feature table. This entity              <Notes>A keyword is a word that can be used to search the feature table. This entity
144              indicates how many features correspond to each word.</Notes>              contains the keyword's stem, its phonetic form, and the number of features that
145              <Fields>              can be found by searching for the word.</Notes>
146                <Fields>
147                    <Field name="stem" type="name-string">
148                        <Notes>The stem of a keyword is a normalized form that is independent of parts
149                        of speech. The actual keywords stored in the database search index are stems.</Notes>
150                    </Field>
151                  <Field name="count" type="counter">                  <Field name="count" type="counter">
152                      <Notes>Number of features that can be found by searching for the specified                      <Notes>Number of features that can be found by searching for the specified
153                      keyword.</Notes>                      keyword.</Notes>
154                  </Field>                  </Field>
155                    <Field name="phonex" type="name-string">
156                        <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
157                        word stem. This can be used to find alternative spellings if an matching word is not
158                        present.</Notes>
159                    </Field>
160              </Fields>              </Fields>
161                <Indexes>
162                    <Index>
163                        <Notes>This index allows the user to find words by stem.</Notes>
164                        <IndexFields>
165                            <IndexField name="stem" order="ascending" />
166                        </IndexFields>
167                    </Index>
168                    <Index>
169                        <Notes>This index allows the user to find words by phonex.</Notes>
170                        <IndexFields>
171                            <IndexField name="phonex" order="ascending" />
172                            <IndexField name="count" order="descending" />
173                        </IndexFields>
174                    </Index>
175                </Indexes>
176            </Entity>
177            <Entity name="ExternalDatabase" keyType="key-string">
178                <Notes>An external database identifies a biological database surveyed by PIR International
179                as part of an effort to determine which features are essentially identical between bioinformatics
180                organizations. Each feature in the database will have zero or more corresponding IDs that are
181                captured from the PIR data. Each corresponding ID is represented in a relationship between an external
182                database and the feature itself.</Notes>
183          </Entity>          </Entity>
184          <Entity name="Feature" keyType="id-string">          <Entity name="Feature" keyType="id-string">
185              <Notes>A _feature_ (sometimes also called a [[gene]]) is a part of a genome that is of special interest. Features              <DisplayInfo theme="nmpdr" col="3" row="3" />
186                <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
187              may be spread across multiple contigs of a genome, but never across more than              may be spread across multiple contigs of a genome, but never across more than
188              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
189              and are the targets of annotation. Each feature in the database has a unique [[FigId]].</Notes>              and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
190              <Fields>              <Fields>
191                  <Field name="feature-type" type="id-string">                  <Field name="feature-type" type="id-string">
192                      <Notes>Code indicating the type of this feature. Among the codes currently                      <Notes>Code indicating the type of this feature. Among the codes currently
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245                      the virulence information was curated. If the feature is not virulent, this field                      the virulence information was curated. If the feature is not virulent, this field
246                      will have no values; otherwise, it may have multiple values.</Notes>                      will have no values; otherwise, it may have multiple values.</Notes>
247                  </Field>                  </Field>
                 <Field name="cello" type="name-string">  
                     <Notes>The cello value specifies the expected location of the protein: cytoplasm,  
                     cell wall, inner membrane, and so forth.</Notes>  
                 </Field>  
248                  <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">                  <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
249                      <Notes>A value indicating whether or not the feature can be found in the                      <Notes>A value indicating whether or not the feature can be found in the
250                      Immune Epitope Database. If the feature has not been matched to that database,                      Immune Epitope Database. If the feature has not been matched to that database,
# Line 227  Line 258 
258                      designed to help look for features in a particular region rather than to find the location                      designed to help look for features in a particular region rather than to find the location
259                      of a feature.</Notes>                      of a feature.</Notes>
260                  </Field>                  </Field>
261                    <Field name="signal-peptide" type="name-string">
262                        <Notes>The signal peptide location for this feature. This is expressed as start and end
263                        numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
264                        peptide at the beginning of the feature's protein and extending through 22 amino acid
265                        positions. An empty string means no signal peptide is present.</Notes>
266                    </Field>
267                    <Field name="transmembrane-map" type="text">
268                        <Notes>A map indicating which sections of a protein will be embedded in a membrane.
269                        This is expressed as a comma-separated list of as start and end numbers with hyphens
270                        for the relevant amino acids. So, "10-12, 40-60" would indicate that there are two
271                        sections of the protein that become embedded in a membrane: the 10th through 12th
272                        amino acids, and the 40th through the 60th. An empty string means no
273                        transmembrane regions are known.</Notes>
274                    </Field>
275                    <Field name="similar-to-human" type="boolean">
276                        <Notes>TRUE if this feature generates a protein that is similar to one found in humans,
277                        else FALSE</Notes>
278                    </Field>
279                    <Field name="isoelectric-point" type="float">
280                        <Notes>pH in the surrounding medium at which the charge on a protein is neutral.
281                        If the pH of the medium is lower than this value, the protein will have a net
282                        positive charge. If the pH of the medium is higher, then the protein will have a
283                        net negative charge.</Notes>
284                    </Field>
285                    <Field name="molecular-weight" type="float">
286                        <Notes>Molecular weight of this feature's protein, in daltons. A weight of 0
287                        indicates that no protein is created.</Notes>
288                    </Field>
289                    <Field name="sequence-length" type="counter">
290                        <Notes>Number of base pairs in this feature.</Notes>
291                    </Field>
292                    <Field name="locked" type="boolean">
293                        <Notes>TRUE if a feature's assignment is locked. A locked feature's functional
294                        role cannot be changed by automated programs.</Notes>
295                    </Field>
296                    <Field name="in-genbank" type="boolean">
297                        <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
298                    </Field>
299              </Fields>              </Fields>
             <Indexes>  
                 <Index>  
                     <Notes>This index allows us to locate a feature by its CELLO value.</Notes>  
                     <IndexFields>  
                         <IndexField name="cello" order="ascending" />  
                     </IndexFields>  
                 </Index>  
             </Indexes>  
300          </Entity>          </Entity>
301          <Entity name="FeatureAlias" keyType="medium-string">          <Entity name="FeatureAlias" keyType="medium-string">
302              <Notes>Alternative names for features. A feature can have many aliases. In general,              <Notes>Alternative names for features. A feature can have many aliases. In general,
303              each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>              each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
304          </Entity>          </Entity>
305          <Entity name="SproutUser" keyType="name-string">          <Entity name="SproutUser" keyType="name-string">
306              <Notes>A _user_ is a person who can make annotations and view data in the database. The              <Notes>A user is a person who can make annotations and view data in the database. The
307              user object is keyed on the user's login name.</Notes>              user object is keyed on the user's login name.</Notes>
308              <Fields>              <Fields>
309                  <Field name="description" type="string">                  <Field name="description" type="string">
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315              </Fields>              </Fields>
316          </Entity>          </Entity>
317          <Entity name="SynonymGroup" keyType="id-string">          <Entity name="SynonymGroup" keyType="id-string">
318              <Notes>A _synonym group_ represents a group of features. Features that represent substantially              <Notes>A synonym group represents a group of features. Features that represent substantially
319              identical proteins or DNA sequences are mapped to the same synonym group, and this information is              identical proteins or DNA sequences are mapped to the same synonym group, and this information is
320              used to expand similarities.</Notes>              used to expand similarities.</Notes>
321          </Entity>          </Entity>
322          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
323              <Notes>A _role_ describes a biological function that may be fulfilled by a feature.              <DisplayInfo theme="web" col="7" row="3" />
324                <Notes>A role describes a biological function that may be fulfilled by a feature.
325              One of the main goals of the database is to record the roles of the various features.</Notes>              One of the main goals of the database is to record the roles of the various features.</Notes>
326          </Entity>          </Entity>
327          <Entity name="RoleEC" keyType="string">          <Entity name="RoleEC" keyType="string">
328              <Notes>EC code for a role.</Notes>              <Notes>EC code for a role.</Notes>
329          </Entity>          </Entity>
330          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
331              <Notes>An _annotation_ contains supplementary information about a feature. The most              <DisplayInfo theme="seed" col="1" row="3" />
332                <Notes>An annotation contains supplementary information about a feature. The most
333              important type of annotation is the assignment of a [[functional role]]; however,              important type of annotation is the assignment of a [[functional role]]; however,
334              other types of annotations are also possible.</Notes>              other types of annotations are also possible.</Notes>
335              <Fields>              <Fields>
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350              </Indexes>              </Indexes>
351          </Entity>          </Entity>
352          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
353              <Notes>A _reaction_ is a chemical process catalyzed by a protein. The reaction ID              <DisplayInfo  theme="web" col="7" row="5" />
354                <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
355              is generally a small number preceded by a letter.</Notes>              is generally a small number preceded by a letter.</Notes>
356              <Fields>              <Fields>
357                  <Field name="url" type="string" relation="ReactionURL">                  <Field name="url" type="string" relation="ReactionURL">
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364              </Fields>              </Fields>
365          </Entity>          </Entity>
366          <Entity name="Compound" keyType="name-string">          <Entity name="Compound" keyType="name-string">
367              <Notes>A _compound_ is a chemical that participates in a reaction.              <DisplayInfo  theme="web" col="7" row="7" />
368                <Notes>A compound is a chemical that participates in a reaction.
369              All compounds have a unique ID and may also have one or more names.</Notes>              All compounds have a unique ID and may also have one or more names.</Notes>
370              <Fields>              <Fields>
371                  <Field name="label" type="string">                  <Field name="label" type="string">
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376              </Fields>              </Fields>
377          </Entity>          </Entity>
378          <Entity name="CompoundName" keyType="string">          <Entity name="CompoundName" keyType="string">
379              <Notes>A _compound name_ is a common name for the chemical represented by a              <Notes>A compound name is a common name for the chemical represented by a
380              compound.</Notes>              compound.</Notes>
381          </Entity>          </Entity>
382          <Entity name="CompoundCAS" keyType="name-string">          <Entity name="CompoundCAS" keyType="name-string">
383              <Notes>This entity represents the [[http://www.cas.org/ Chemical Abstract Service]] ID for a              <Notes>This entity represents the Chemical Abstract Service ID for a
384              compound. Each Compound has at most one CAS ID.</Notes>              compound. Each Compound has at most one CAS ID.</Notes>
385          </Entity>          </Entity>
386          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
387              <Notes>A _subsystem_ is a collection of roles that work together in a cell. Identification of subsystems              <DisplayInfo theme="seed" col="5" row="1" />
388              is an important tool for recognizing parallel genetic features in different organisms. See also              <Notes>A subsystem is a collection of roles that work together in a cell. Identification of subsystems
389              [[Subsystems Approach]] and [[Subsystem]].</Notes>              is an important tool for recognizing parallel genetic features in different organisms.</Notes>
390              <Fields>              <Fields>
391                    <Field name="version" type="int">
392                        <Notes>Version number for the subsystem. This value is incremented each time the subsystem
393                        is backed up.</Notes>
394                    </Field>
395                  <Field name="curator" type="string">                  <Field name="curator" type="string">
396                      <Notes>Name of the person currently in charge of the subsystem.</Notes>                      <Notes>Name of the person currently in charge of the subsystem.</Notes>
397                  </Field>                  </Field>
# Line 330  Line 399 
399                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
400                  </Field>                  </Field>
401                  <Field name="description" type="text">                  <Field name="description" type="text">
402                      <Notes>Description of the subsystem's function.</Notes>                      <Notes>Description of the subsystem's function in the cell.</Notes>
403                  </Field>                  </Field>
404                  <Field name="classification" type="string" relation="SubsystemClass">                  <Field name="classification" type="string" relation="SubsystemClass">
405                      <Notes>Classification string, colon-delimited. This string organizes the                      <Notes>Classification string, colon-delimited. This string organizes the
406                      subsystems into a hierarchy.</Notes>                      subsystems into a hierarchy.</Notes>
407                  </Field>                  </Field>
408                    <Field name="hope-curation-notes" type="text" relation="SubsystemHopeNotes">
409                        <Notes>Text description of how the scenarios were curated.</Notes>
410                    </Field>
411              </Fields>              </Fields>
412          </Entity>          </Entity>
413          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
414              <Notes>A _role subset_ is a named collection of roles in a particular subsystem. The              <Notes>A role subset is a named collection of roles in a particular subsystem. The
415              subset names are generally very short, non-unique strings. The ID of the parent              subset names are generally very short, non-unique strings. The ID of the parent
416              subsystem is prefixed to the subset ID in order to make it unique.</Notes>              subsystem is prefixed to the subset ID in order to make it unique.</Notes>
417          </Entity>          </Entity>
418          <Entity name="GenomeSubset" keyType="string">          <Entity name="GenomeSubset" keyType="string">
419              <Notes>A _genome subset_ is a named collection of genomes that participate              <Notes>A genome subset is a named collection of genomes that participate
420              in a particular subsystem. The subset names are generally very short, non-unique              in a particular subsystem. The subset names are generally very short, non-unique
421              strings. The ID of the parent subsystem is prefixed to the subset ID in order              strings. The ID of the parent subsystem is prefixed to the subset ID in order
422              to make it unique.</Notes>              to make it unique.</Notes>
423          </Entity>          </Entity>
424          <Entity name="SSCell" keyType="hash-string">          <Entity name="SSCell" keyType="hash-string">
425              <Notes>Part of the process of [[SubsystemsApproach][subsystem annotation]] of [[features]]              <DisplayInfo theme="seed" col="5" row="3" />
426              is creating a spreadsheet of genomes and roles to which features are assigned. A _spreadsheet              <Notes>Part of the process of subsystem annotation of features
427              cell_ represents one of the positions on the spreadsheet.</Notes>              is creating a spreadsheet of genomes and roles to which features are assigned.
428                A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
429          </Entity>          </Entity>
430          <Entity name="Property" keyType="int">          <Entity name="Property" keyType="int">
431              <Notes>A _property_ is a type of assertion that could be made about the properties of              <Notes>A property is a type of assertion that could be made about the properties of
432              a particular feature. Each property instance is a key/value pair and can be associated              a particular feature. Each property instance is a key/value pair and can be associated
433              with many different features. Conversely, a feature can be associated with many key/value              with many different features. Conversely, a feature can be associated with many key/value
434              pairs, even some that notionally contradict each other. For example, there can be evidence              pairs, even some that notionally contradict each other. For example, there can be evidence
# Line 382  Line 455 
455              </Indexes>              </Indexes>
456          </Entity>          </Entity>
457          <Entity name="Diagram" keyType="name-string">          <Entity name="Diagram" keyType="name-string">
458              <Notes>A functional diagram describes a network chemical reactions, often comprising a single              <DisplayInfo theme="web" col="7" row="1" />
459                <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
460              subsystem. A diagram is identified by a short name and contains a longer descriptive name.              subsystem. A diagram is identified by a short name and contains a longer descriptive name.
461              The actual diagram shows which functional roles guide the reactions along with the inputs              The actual diagram shows which functional roles guide the reactions along with the inputs
462              and outputs; the database, however, only indicates which roles belong to a particular              and outputs; the database, however, only indicates which roles belong to a particular
# Line 393  Line 467 
467                  </Field>                  </Field>
468              </Fields>              </Fields>
469          </Entity>          </Entity>
         <Entity name="ExternalAliasOrg" keyType="name-string">  
             <Notes>An external alias is a feature name for a functional assignment that is not a  
             FIG ID. Functional assignments for external aliases are kept in a separate section of  
             the database. This table contains a description of the relevant organism for an  
             external alias functional assignment.</Notes>  
                 <Fields>  
                     <Field name="org" type="text">  
                         <Notes>Descriptive name of the target organism for this external alias.</Notes>  
                     </Field>  
                 </Fields>  
         </Entity>  
         <Entity name="ExternalAliasFunc" keyType="name-string">  
             <Notes>An external alias is a feature name for a functional assignment that is not a  
             FIG ID. Functional assignments for external aliases are kept in a separate section of  
             the database. This table contains the functional role for the external alias functional  
             assignment.</Notes>  
                 <Fields>  
                     <Field name="func" type="text">  
                         <Notes>Functional role for this external alias.</Notes>  
                     </Field>  
                 </Fields>  
         </Entity>  
470          <Entity name="Family" keyType="id-string">          <Entity name="Family" keyType="id-string">
471              <Notes>A _family_ (also called a [[FigFam]]) is a group of homologous features believed to have              <DisplayInfo theme="seed" col="5" row="5" />
472              the same function. Families provide a mechanism for verifying the accuracy of functional assignments              <Notes>A family (also called a FigFam) is a group of homologous features believed to have
473              and are also used in [[Rapid Annotation]] and in determining phylogenetic trees.</Notes>              the same function. Families provide a mechanism for verifying the accuracy of functional
474                assignments and are also used in Rapid Annotation and in determining phylogenetic trees.</Notes>
475              <Fields>              <Fields>
476                  <Field name="function" type="text">                  <Field name="function" type="text">
477                      <Notes>The functional assignment expected for all PEGs in this family.</Notes>                      <Notes>The functional assignment expected for all PEGs in this family.</Notes>
# Line 431  Line 484 
484              </Fields>              </Fields>
485          </Entity>          </Entity>
486          <Entity name="PDB" keyType="id-string">          <Entity name="PDB" keyType="id-string">
487                <DisplayInfo theme="web" col="3" row="5" />
488              <Notes>A PDB is a protein data bank entry containing information that can be used              <Notes>A PDB is a protein data bank entry containing information that can be used
489              to determine the shape of the protein and the energies required to dock with it.              to determine the shape of the protein and the energies required to dock with it.
490              The ID is the four-character name used on the [[http://www.rcsb.org PDB web site]].</Notes>              The ID is the four-character name used on the PDB web site.</Notes>
491              <Fields>              <Fields>
492                  <Field name="docking-count" type="int">                  <Field name="docking-count" type="int">
493                      <Notes>The number of ligands that have been docked against this PDB.</Notes>                      <Notes>The number of ligands that have been docked against this PDB.</Notes>
# Line 449  Line 503 
503              </Indexes>              </Indexes>
504          </Entity>          </Entity>
505          <Entity name="Ligand" keyType="id-string">          <Entity name="Ligand" keyType="id-string">
506                <DisplayInfo theme="web" col="3" row="7" />
507              <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.              <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
508              The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>              The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>
509              <Fields>              <Fields>
# Line 457  Line 512 
512                  </Field>                  </Field>
513              </Fields>              </Fields>
514          </Entity>          </Entity>
515            <Entity name="CellLocation" keyType="key-string">
516                <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
517                membrane, outside the cell, inside the cell, and so forth.</Notes>
518            </Entity>
519            <Entity name="Scenario" keyType="string">
520                <Notes>A scenario used to verify the validity of subsystem assignments. Each
521                scenario converrts input compounds to output compounds using reactions.
522                The scenario may use all of the reactions controlled by a subsystem or only
523                some, and may also incorporate additional reactions.</Notes>
524            </Entity>
525      </Entities>      </Entities>
526      <Relationships>      <Relationships>
527            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
528                <DisplayInfo theme="web" />
529                <Notes>This relationship connects a role to the reactions it catalyzes.
530                The purpose of a role is to create proteins that trigger certain
531                chemical reactions. A single reaction can be triggered by many roles,
532                and a role can trigger many reactions.</Notes>
533            </Relationship>
534            <Relationship name="ExcludesReaction" from="Scenario" to="Reaction" arity="MM">
535                <Notes>This relationship connects a scenario to reactions of the parent
536                subsystem that do not participate in it.</Notes>
537            </Relationship>
538            <Relationship name="IncludesReaction" from="Scenario" to="Reaction" arity="MM">
539                <Notes>This relationship connects a scenario to reactions that participate
540                in it but are not part of the parent subsystem.</Notes>
541            </Relationship>
542            <Relationship name="HasScenario" from="Subsystem" to="Scenario" arity="MM">
543                <Notes>This relationship connects a role to the scenarios used to
544                validate it.</Notes>
545            </Relationship>
546            <Relationship name="IsInputFor" from="Compound" to="Scenario" arity="MM">
547                <Notes>This relationship connects a scenario to its input compounds.</Notes>
548            </Relationship>
549            <Relationship name="IsOutputOf" from="Compound" to="Scenario" arity="MM">
550                <Notes>This relationship connects a scenario to its output compounds</Notes>
551                <Fields>
552                    <Field name="auxiliary" type="boolean">
553                        <Notes>TRUE if this is an auxiliary output compound, FALSE if it is a
554                        main output compound.</Notes>
555                    </Field>
556                </Fields>
557            </Relationship>
558            <Relationship name="IsOnDiagram" from="Scenario" to="Diagram" arity="MM">
559                <Notes>This relationship connects a scenario to related diagrams.</Notes>
560            </Relationship>
561            <Relationship name="IsPossiblePlaceFor" from="CellLocation" to="Feature" arity="MM">
562                <Notes>This relationship connects a feature with the various places in a cell that the feature
563                might be found. The confidence factor is included as intersection data.</Notes>
564                <Fields>
565                    <Field name="confidence" type="float">
566                        <Notes>Confidence that the protein will be found in this location, expressed as a
567                        value from 0 to 10.</Notes>
568                    </Field>
569                </Fields>
570            </Relationship>
571          <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">          <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
572              <Notes>This relationship connects a feature to its CDD protein domains. The              <Notes>This relationship connects a feature to its CDD protein domains. The
573              match score is included as intersection data.</Notes>              match score is included as intersection data.</Notes>
# Line 505  Line 614 
614              </FromIndex>              </FromIndex>
615          </Relationship>          </Relationship>
616          <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">          <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
617                <DisplayInfo caption="Is Protein\nFor Feature" theme="web" />
618              <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>              <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
619              <Fields>              <Fields>
620                  <Field name="score" type="float">                  <Field name="score" type="float">
# Line 534  Line 644 
644              </FromIndex>              </FromIndex>
645          </Relationship>          </Relationship>
646          <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">          <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
647              <Notes>Indicates that a [[docking result]] exists between a PDB and a ligand. The              <DisplayInfo caption="Docks With" theme="web" />
648                <Notes>Indicates that a docking result exists between a PDB and a ligand. The
649              docking result describes the energy required for the ligand to dock with              docking result describes the energy required for the ligand to dock with
650              the protein described by the PDB. A lower energy indicates the ligand has a              the protein described by the PDB. A lower energy indicates the ligand has a
651              good chance of disabling the protein. At the current time, only the best              good chance of disabling the protein. At the current time, only the best
# Line 576  Line 687 
687                  the lowest energy (best docking) to highest energy (worst docking).</Notes>                  the lowest energy (best docking) to highest energy (worst docking).</Notes>
688              </ToIndex>              </ToIndex>
689          </Relationship>          </Relationship>
690            <Relationship name="IsAlsoFoundIn" from="Feature" to="ExternalDatabase" arity="MM">
691                <Notes>This relationship connects a feature to external databases that contain
692                essentially identical features. The name used in the external database is stored
693                in the relationship as intersection data.</Notes>
694                <Fields>
695                    <Field name="alias" type="name-string">
696                        <Notes>ID of the feature in the specified external database.</Notes>
697                    </Field>
698                </Fields>
699                <Indexes>
700                    <Index>
701                        <Notes>This index allows direct access to features by external ID.</Notes>
702                        <IndexFields>
703                            <IndexField name="alias" order="ascending" />
704                        </IndexFields>
705                    </Index>
706                </Indexes>
707            </Relationship>
708          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
709                <DisplayInfo caption="Belongs To" theme="seed" />
710              <Notes>This relationship connects a protein family to all of its PEGs and connects              <Notes>This relationship connects a protein family to all of its PEGs and connects
711              each PEG to all of its protein families.</Notes>              each PEG to all of its protein families.</Notes>
712          </Relationship>          </Relationship>
# Line 585  Line 715 
715              up.</Notes>              up.</Notes>
716          </Relationship>          </Relationship>
717          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
718                <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
719              <Notes>This relationship connects a genome to all of its features. This              <Notes>This relationship connects a genome to all of its features. This
720              relationship is redundant in a sense, because the genome ID is part              relationship is redundant in a sense, because the genome ID is part
721              of the feature ID; however, it makes the creation of certain queries more              of the feature ID; however, it makes the creation of certain queries more
# Line 604  Line 735 
735              </FromIndex>              </FromIndex>
736          </Relationship>          </Relationship>
737          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
738                <DisplayInfo caption="Is Part Of" theme="nmpdr" />
739              <Notes>This relationship connects a genome to the contigs that contain the actual genetic              <Notes>This relationship connects a genome to the contigs that contain the actual genetic
740              information.</Notes>              information.</Notes>
741          </Relationship>          </Relationship>
# Line 635  Line 767 
767              </FromIndex>              </FromIndex>
768          </Relationship>          </Relationship>
769          <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">          <Relationship name="IsTargetOfAnnotation" from="Feature" to="Annotation" arity="1M">
770                <DisplayInfo caption="Targets" theme="seed" />
771              <Notes>This relationship connects a feature to its annotations.</Notes>              <Notes>This relationship connects a feature to its annotations.</Notes>
772          </Relationship>          </Relationship>
773          <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">          <Relationship name="MadeAnnotation" from="SproutUser" to="Annotation" arity="1M">
774              <Notes>This relationship connects an annotation to the user who made it.</Notes>              <Notes>This relationship connects an annotation to the user who made it.</Notes>
775          </Relationship>          </Relationship>
776          <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">          <Relationship name="ParticipatesIn" from="Genome" to="Subsystem" arity="MM">
777                <DisplayInfo caption="\nParticipates\nIn" theme="seed" />
778              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
779              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be              it. If the subsystem has been curated for the genome, then the subsystem's roles will also be
780              connected to the genome features through the *SSCell* object.</Notes>              connected to the genome features through the *SSCell* object.</Notes>
# Line 663  Line 797 
797              </ToIndex>              </ToIndex>
798          </Relationship>          </Relationship>
799          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
800                <DisplayInfo caption="Uses" theme="seed" />
801              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
802              <Fields>              <Fields>
803                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="name-string">
# Line 673  Line 808 
808                      <Notes>Column number for this role in the specified subsystem's                      <Notes>Column number for this role in the specified subsystem's
809                      spreadsheet.</Notes>                      spreadsheet.</Notes>
810                  </Field>                  </Field>
811                    <Field name="auxiliary" type="boolean">
812                        <Notes>If TRUE, then this role is ancillary to the purpose of the subsystem.
813                        If FALSE, it is essential to its metabolic pathway.</Notes>
814                    </Field>
815                    <Field name="hope_reaction_note" type="text">
816                        <Notes>A description of the status of a role in relation to the
817                        reactions it produces as determined by the scenarios. If present,
818                        will indicate if the role has been determined to be auxiliary,
819                        if it has been examined to verify an automatic assignment, and so
820                        forth.</Notes>
821                    </Field>
822                    <Field name="hope_reaction_link" type="text">
823                        <Notes>A description of the mapping between the reactions of
824                        this role and the scenarios used to validate it.</Notes>
825                    </Field>
826              </Fields>              </Fields>
827              <ToIndex>              <ToIndex>
828                  <Notes>This index enables the application to see the subsystem roles                  <Notes>This index enables the application to see the subsystem roles
# Line 684  Line 834 
834              </ToIndex>              </ToIndex>
835          </Relationship>          </Relationship>
836          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
837                <DisplayInfo caption="Is Row Of" theme="seed" />
838              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
839              genome for the spreadsheet column.</Notes>              genome for the spreadsheet column.</Notes>
840          </Relationship>          </Relationship>
841          <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">          <Relationship name="IsRoleOf" from="Role" to="SSCell" arity="1M">
842                <DisplayInfo caption="Is In\nColumn\nFor" theme="seed" />
843              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
844              role for the spreadsheet row.</Notes>              role for the spreadsheet row.</Notes>
845          </Relationship>          </Relationship>
846          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
847                <DisplayInfo caption="Is\nContained\nIn" theme="seed" />
848              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
849              features assigned to it.</Notes>              features assigned to it.</Notes>
850              <Fields>              <Fields>
# Line 702  Line 855 
855              </Fields>              </Fields>
856          </Relationship>          </Relationship>
857          <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">          <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
858                <DisplayInfo caption="Involves" theme="web" />
859              <Notes>This relationship connects a reaction to the compounds that participate              <Notes>This relationship connects a reaction to the compounds that participate
860              in it.</Notes>              in it.</Notes>
861              <Fields>              <Fields>
# Line 761  Line 915 
915              </ToIndex>              </ToIndex>
916          </Relationship>          </Relationship>
917          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
918                <DisplayInfo caption="Is\nLocation\nOf" theme="nmpdr" />
919              <Notes>This relationship connects a feature to the contig segments that work together              <Notes>This relationship connects a feature to the contig segments that work together
920              to effect it. The segments are numbered sequentially starting from 1. The database is              to effect it. The segments are numbered sequentially starting from 1. The database is
921              required to place an upper limit on the length of each segment. If a segment is longer              required to place an upper limit on the length of each segment. If a segment is longer
# Line 817  Line 972 
972              </Fields>              </Fields>
973          </Relationship>          </Relationship>
974          <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">          <Relationship name="RoleOccursIn" from="Role" to="Diagram" arity="MM">
975                <DisplayInfo caption="Shows" theme="web" />
976              <Notes>This relationship connects a role to the diagrams on which it              <Notes>This relationship connects a role to the diagrams on which it
977              appears. A role frequently identifies an enzyme, and can appear in many              appears. A role frequently identifies an enzyme, and can appear in many
978              diagrams. A diagram generally contains many different roles.</Notes>              diagrams. A diagram generally contains many different roles.</Notes>
979          </Relationship>          </Relationship>
980          <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">          <Relationship name="HasSSCell" from="Subsystem" to="SSCell" arity="1M">
981                <DisplayInfo caption="Is Container Of" theme="seed" />
982              <Notes>This relationship connects a subsystem to the spreadsheet cells              <Notes>This relationship connects a subsystem to the spreadsheet cells
983              used to analyze and display it. The cells themselves can be thought of              used to analyze and display it. The cells themselves can be thought of
984              as a grid with Roles on one axis and Genomes on the other. The              as a grid with Roles on one axis and Genomes on the other. The
# Line 861  Line 1018 
1018              subset, so the relationship between genomes and subsystems cannot be              subset, so the relationship between genomes and subsystems cannot be
1019              derived from the relationships going through the subset.</Notes>              derived from the relationships going through the subset.</Notes>
1020          </Relationship>          </Relationship>
         <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">  
             <Notes>This relationship connects a role to the reactions it catalyzes.  
             The purpose of a role is to create proteins that trigger certain  
             chemical reactions. A single reaction can be triggered by many roles,  
             and a role can trigger many reactions.</Notes>  
         </Relationship>  
1021          <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">          <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
1022              <Notes>This relationship connects a feature to the subsystems in which it              <Notes>This relationship connects a feature to the subsystems in which it
1023              participates. This is technically redundant information, but it is used              participates. This is technically redundant information, but it is used
# Line 889  Line 1040 
1040              </ToIndex>              </ToIndex>
1041          </Relationship>          </Relationship>
1042      </Relationships>      </Relationships>
1043    <Shapes>
1044        <Shape type="oval" name="Pins">
1045            <DisplayInfo theme="nmpdr" col="1" row="4.5" fixed="1" />
1046            <Notes>The Pin Server provides information about functional couplings between features.</Notes>
1047        </Shape>
1048        <Shape type="oval" name="Sims">
1049            <DisplayInfo theme="nmpdr" col="1.5" row="5" fixed="1" />
1050            <Notes>The Similarity Server contains a high-performance custom database of similarities between features.</Notes>
1051        </Shape>
1052        <Shape type="oval" name="BBHs">
1053            <DisplayInfo theme="nmpdr" col="2" row="5.5" fixed="1" />
1054            <Notes>For each feature, the BBH Server has that feature's bidirectional best hits in other genomes.</Notes>
1055        </Shape>
1056        <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1057            <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1058        </Shape>
1059    </Shapes>
1060  </Database>  </Database>

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