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revision 1.18, Thu Oct 20 09:33:25 2005 UTC revision 1.45, Fri Nov 3 00:44:01 2006 UTC
# Line 7  Line 7 
7              <Fields>              <Fields>
8                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
9                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
                     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>  
10                  </Field>                  </Field>
11                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
12                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
13                  </Field>                  </Field>
14                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
15                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
16                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
17                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
                     <DataGen>StringGen('PKVKVK999')</DataGen>  
18                  </Field>                  </Field>
19                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
20                      <Notes>The access code determines which users can look at the data relating to this genome.                      <Notes>The access code determines which users can look at the data relating to this genome.
21                      Each user is associated with a set of access codes. In order to view a genome, one of                      Each user is associated with a set of access codes. In order to view a genome, one of
22                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
                     <DataGen>RandParam('low','medium','high')</DataGen>  
23                  </Field>                  </Field>
24                  <Field name="complete" type="boolean">                  <Field name="complete" type="boolean">
25                      <Notes>TRUE if the genome is complete, else FALSE</Notes>                      <Notes>TRUE if the genome is complete, else FALSE</Notes>
# Line 33  Line 29 
29                      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
30                      the disambiguated genus and species (which is the organism's scientific name plus an                      the disambiguated genus and species (which is the organism's scientific name plus an
31                      identifying string).</Notes>                      identifying string).</Notes>
32                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                  </Field>
33                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                  <Field name="primary-group" type="name-string">
34                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
35                        (either based on the organism name or the default value "Supporting"), whereas there can be
36                        multiple named groups or even none.</Notes>
37                  </Field>                  </Field>
38                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="group-name" type="name-string" relation="GenomeGroups">
39                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
# Line 54  Line 53 
53                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
54                      </IndexFields>                      </IndexFields>
55                  </Index>                  </Index>
56                  <Index Unique="false">                  <Index>
57                        <Notes>This index allows the applications to find all genomes associated with
58                        a specific primary (NMPDR) group.</Notes>
59                        <IndexFields>
60                            <IndexField name="primary-group" order="ascending" />
61                            <IndexField name="genus" order="ascending" />
62                            <IndexField name="species" order="ascending" />
63                            <IndexField name="unique-characterization" order="ascending" />
64                        </IndexFields>
65                    </Index>
66                    <Index>
67                      <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
68                      species.</Notes>                      species.</Notes>
69                      <IndexFields>                      <IndexFields>
# Line 71  Line 80 
80              <Fields>              <Fields>
81                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
82                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>  
83                  </Field>                  </Field>
84                  <Field name="description" type="text">                  <Field name="description" type="text">
85                      <Notes>Description the source. The description can be a street address or a citation.</Notes>                      <Notes>Description the source. The description can be a street address or a citation.</Notes>
                     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
86                  </Field>                  </Field>
87              </Fields>              </Fields>
88          </Entity>          </Entity>
# Line 98  Line 105 
105                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
106                      <Notes>String consisting of the residues. Each residue is described by a single                      <Notes>String consisting of the residues. Each residue is described by a single
107                      character in the string.</Notes>                      character in the string.</Notes>
                     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
108                  </Field>                  </Field>
109                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
110                      <Notes>String describing the quality data for each base pair. Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
# Line 107  Line 113 
113                      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
114                      that the quality data is not 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
115                      vector will contain the [b]unknown[/b].</Notes>                      vector will contain the [b]unknown[/b].</Notes>
                     <DataGen>unknown</DataGen>  
116                  </Field>                  </Field>
117              </Fields>              </Fields>
118          </Entity>          </Entity>
119          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
120              <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
121              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
122              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
# Line 119  Line 124 
124              <Fields>              <Fields>
125                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="string">
126                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
                     <DataGen>RandParam('peg','rna')</DataGen>  
127                  </Field>                  </Field>
128                  <Field name="alias" type="medium-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
129                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
                     <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
130                  </Field>                  </Field>
131                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
132                      <Notes>[i](optional)[/i] A translation of this feature's residues into character                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
133                      codes, formed by concatenating the pieces of the feature together. For a                      codes, formed by concatenating the pieces of the feature together. For a
134                      protein encoding group, this is the protein characters. For other types                      protein encoding group, this is the protein characters. For other types
135                      it is the DNA characters.</Notes>                      it is the DNA characters.</Notes>
                     <DataGen testCount="0"></DataGen>  
136                  </Field>                  </Field>
137                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
138                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of                      <Notes>Upstream sequence the feature. This includes residues preceding the feature as well as some of
139                      the feature's initial residues.</Notes>                      the feature's initial residues.</Notes>
140                      <DataGen testCount="0"></DataGen>                  </Field>
141                    <Field name="assignment" type="text">
142                        <Notes>Default functional assignment for this feature.</Notes>
143                  </Field>                  </Field>
144                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
145                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
146                      <DataGen>1</DataGen>                  </Field>
147                    <Field name="keywords" type="text" searchable="1">
148                        <Notes>This is a list of search keywords for the feature. It includes the
149                        functional assignment, subsystem roles, and special properties.</Notes>
150                  </Field>                  </Field>
151                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
152                      <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
153                      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
154                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>                      are coded as raw HTML, using [b]&lt;a href="[i]link[/i]"&gt;[i]text[/i]&lt;/a&gt;[/b] notation.</Notes>
155                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
156                      "&amp;Number=" . IntGen(1,99)</DataGen>                  <Field name="conservation" type="float" relation="FeatureConservation">
157                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
158                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
159                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
160                        between the feature and its close relatives.</Notes>
161                    </Field>
162                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
163                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
164                        cases, this will be a word describing whether the essentiality is confirmed (essential)
165                        or potential (potential-essential), hyperlinked to the document from which the
166                        essentiality was curated. If a feature is not essential, this field will have no
167                        values; otherwise, it may have multiple values.</Notes>
168                    </Field>
169                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
170                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
171                        cases, this will be a phrase or SA number hyperlinked to the document from which
172                        the virulence information was curated. If the feature is not virulent, this field
173                        will have no values; otherwise, it may have multiple values.</Notes>
174                    </Field>
175                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
176                        <Notes>A value indicating whether or not the feature can be found in the
177                        Immune Epitope Database. If the feature has not been matched to that database,
178                        this field will have no values. Otherwise, it will have an epitope name and/or
179                        sequence, hyperlinked to the database.</Notes>
180                  </Field>                  </Field>
181              </Fields>              </Fields>
182              <Indexes>              <Indexes>
# Line 159  Line 189 
189                  </Index>                  </Index>
190              </Indexes>              </Indexes>
191          </Entity>          </Entity>
192            <Entity name="SynonymGroup" keyType="id-string">
193                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
194                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
195            </Entity>
196          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
197              <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.
198              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>
199              <Fields>              <Fields>
200                  <Field name="EC" type="string" relation="RoleEC">                  <Field name="EC" type="string" relation="RoleEC">
201                      <Notes>EC code for this role.</Notes>                      <Notes>EC code for this role.</Notes>
                     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>  
202                  </Field>                  </Field>
203                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="name-string">
204                      <Notes>Abbreviated name for the role, generally non-unique, but useful                      <Notes>Abbreviated name for the role, generally non-unique, but useful
# Line 185  Line 218 
218          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
219              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
220              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
221              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>  
222              <Fields>              <Fields>
223                  <Field name="time" type="date">                  <Field name="time" type="date">
224                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 196  Line 227 
227                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
228                  </Field>                  </Field>
229              </Fields>              </Fields>
230                <Indexes>
231                    <Index>
232                        <Notes>This index allows the user to find recent annotations.</Notes>
233                        <IndexFields>
234                            <IndexField name="time" order="descending" />
235                        </IndexFields>
236                    </Index>
237                </Indexes>
238          </Entity>          </Entity>
239          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
240              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
# Line 225  Line 264 
264                  <Field name="cas-id" type="name-string" relation="CompoundCAS">                  <Field name="cas-id" type="name-string" relation="CompoundCAS">
265                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>                      <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
266                  </Field>                  </Field>
267                    <Field name="label" type="name-string">
268                        <Notes>Name used in reaction display strings.
269                        It is the same as the name possessing a priority of 1, but it is placed
270                        here to speed up the query used to create the display strings.</Notes>
271                    </Field>
272              </Fields>              </Fields>
273              <Indexes>              <Indexes>
274                  <Index>                  <Index>
# Line 261  Line 305 
305                  <Field name="notes" type="text">                  <Field name="notes" type="text">
306                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
307                  </Field>                  </Field>
308                    <Field name="classification" type="string" relation="SubsystemClass">
309                        <Notes>Classification string, colon-delimited. This string organizes the
310                        subsystems into a hierarchy.</Notes>
311                    </Field>
312              </Fields>              </Fields>
313          </Entity>          </Entity>
314          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 274  Line 322 
322              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
323              to make it unique.</Notes>              to make it unique.</Notes>
324          </Entity>          </Entity>
325          <Entity name="SSCell" keyType="medium-string">          <Entity name="SSCell" keyType="hash-string">
326              <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
327              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
328              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 290  Line 338 
338                      <Notes>Access code possessed by this                      <Notes>Access code possessed by this
339                      user. A user can have many access codes; a genome is accessible to the user if its                      user. A user can have many access codes; a genome is accessible to the user if its
340                      access code matches any one of the user's access codes.</Notes>                      access code matches any one of the user's access codes.</Notes>
                     <DataGen testCount="2">RandParam('low', 'medium', 'high')</DataGen>  
341                  </Field>                  </Field>
342              </Fields>              </Fields>
343          </Entity>          </Entity>
# Line 355  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 371  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 379  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 391  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="tag" 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 tag.</Notes>
488                        <IndexFields>
489                            <IndexField name="category" order="ascending" />
490                            <IndexField name="tag" 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="MM">
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="IncludesBound" from="DrugTopic" to="PDB" arity="MM">
572                <Note>This relationship connects a drug topic to its bound PDBs. (A separate
573                relationship is used to connect the free PDBs.)</Note>
574            </Relationship>
575            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="MM">
576                <Note>This relationship connects free PDBs to their bound counterparts.</Note>
577            </Relationship>
578            <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
579                <Notes>This relationship connects a feature to a protein database (PDB) that
580                is relevant for determining drugs that target the feature.</Notes>
581                <Fields>
582                    <Field name="score" type="float">
583                        <Notes>The BLAST score for the feature as it relates to the PDB's
584                        protein, expressed as a small positive number. Generally only a
585                        very low BLAST score (1e-15 or less) indicates a good match.</Notes>
586                    </Field>
587                    <Field name="distance" type="float">
588                        <Notes>A distance value indicating how far the PDB's protein is
589                        from the feature's protein. A distance of 0 indicates a perfect
590                        match.</Notes>
591                    </Field>
592                </Fields>
593                <FromIndex>
594                    <Notes>This index yields the Features for a PDB in order from best
595                    score to worst.</Notes>
596                    <IndexFields>
597                        <IndexField name="score" order="ascending" />
598                    </IndexFields>
599                </FromIndex>
600                <ToIndex>
601                    <Notes>This index yields the Features for a PDB in order from best
602                    score to worst.</Notes>
603                    <IndexFields>
604                        <IndexField name="score" order="ascending" />
605                    </IndexFields>
606                </ToIndex>
607            </Relationship>
608            <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">
609                <Notes>This relationship connects a drug target project to all of its
610                topics.</Notes>
611            </Relationship>
612            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
613                <Notes>This relationship connects a protein family to all of its PEGs and connects
614                each PEG to all of its protein families.</Notes>
615            </Relationship>
616          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
617              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
618              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 413  Line 633 
633                  </IndexFields>                  </IndexFields>
634              </ToIndex>              </ToIndex>
635          </Relationship>          </Relationship>
636            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
637                <Notes>This relation connects a synonym group to the features that make it
638                up.</Notes>
639            </Relationship>
640            <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
641                <Notes>This relationship connects a genome to all of its features. This
642                relationship is redundant in a sense, because the genome ID is part
643                of the feature ID; however, it makes the creation of certain queries more
644                convenient because you can drag in filtering information for a feature's
645                genome.</Notes>
646                <Fields>
647                    <Field name="type" type="key-string">
648                        <Notes>Feature type (eg. peg, rna)</Notes>
649                    </Field>
650                </Fields>
651                <FromIndex>
652                    <Notes>This index enables the application to view the features of a
653                    Genome sorted by type.</Notes>
654                    <IndexFields>
655                        <IndexField name="type" order="ascending" />
656                    </IndexFields>
657                </FromIndex>
658            </Relationship>
659          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
660              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
661              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>
# Line 485  Line 728 
728              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
729              <Fields>              <Fields>
730                  <Field name="variant-code" type="key-string">                  <Field name="variant-code" type="key-string">
731                      <Notes>Numeric code indicating the subsystem variant to which this                      <Notes>Code indicating the subsystem variant to which this
732                      genome belongs. Each subsystem can have multiple variants. A variant                      genome belongs. Each subsystem can have multiple variants. A variant
733                      code of [b]-1[/b] indicates that the genome's roles apply to all                      code of [b]-1[/b] indicates that the genome does not have a functional
734                      variants. A variant code of [b]0[/b] indicates that the genome's                      variant of the subsystem. A variant code of [b]0[/b] indicates that
735                      participation is considered iffy.</Notes>                      the genome's participation is considered iffy.</Notes>
736                  </Field>                  </Field>
737              </Fields>              </Fields>
738              <ToIndex>              <ToIndex>
# Line 551  Line 794 
794                      compound left of the arrow and a value of TRUE still puts it to the                      compound left of the arrow and a value of TRUE still puts it to the
795                      right.</Notes>                      right.</Notes>
796                  </Field>                  </Field>
797                  <Field name="stoichometry" type="key-string">                  <Field name="stoichiometry" type="key-string">
798                      <Notes>Number of molecules of the compound that participate in a                      <Notes>Number of molecules of the compound that participate in a
799                      single instance of the reaction. For example, if a reaction                      single instance of the reaction. For example, if a reaction
800                      produces two water molecules, the stoichometry of water for the                      produces two water molecules, the stoichiometry of water for the
801                      reaction would be two. When a reaction is written on paper in                      reaction would be two. When a reaction is written on paper in
802                      chemical notation, the stoichometry is the number next to the                      chemical notation, the stoichiometry is the number next to the
803                      chemical formula of the compound.</Notes>                      chemical formula of the compound.</Notes>
804                  </Field>                  </Field>
805                  <Field name="main" type="boolean">                  <Field name="main" type="boolean">
# Line 576  Line 819 
819                      sorts first, so if this field is used, it should probably be                      sorts first, so if this field is used, it should probably be
820                      used for every compound in the reaction.</Notes>                      used for every compound in the reaction.</Notes>
821                  </Field>                  </Field>
822                    <Field name="discriminator" type="int">
823                        <Notes>A unique ID for this record. The discriminator does not
824                        provide any useful data, but it prevents identical records from
825                        being collapsed by the SELECT DISTINCT command used by ERDB to
826                        retrieve data.</Notes>
827                    </Field>
828              </Fields>              </Fields>
829              <ToIndex>              <ToIndex>
830                  <Notes>This index presents the compounds in the reaction in the                  <Notes>This index presents the compounds in the reaction in the
831                  order they should be displayed when writing it in chemical notation.                  order they should be displayed when writing it in chemical notation.
832                  All the substrates appear before all the products, and within that                  All the substrates appear before all the products, and within that
833                  ordering, the main compounds appear first.</Notes>                  ordering, the main compounds appear first.</Notes>
834                    <IndexFields>
835                  <IndexField name="product" order="ascending" />                  <IndexField name="product" order="ascending" />
836                  <IndexField name="loc" order="ascending" />                  <IndexField name="loc" order="ascending" />
837                  <IndexField name="main" order="descending" />                  <IndexField name="main" order="descending" />
838                    </IndexFields>
839              </ToIndex>              </ToIndex>
840          </Relationship>          </Relationship>
841          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
# Line 615  Line 866 
866                      [b]-[/b] if it is backward.</Notes>                      [b]-[/b] if it is backward.</Notes>
867                  </Field>                  </Field>
868              </Fields>              </Fields>
869              <FromIndex Unique="false">              <FromIndex>
870                  <Notes>This index allows the application to find all the segments of a feature in                  <Notes>This index allows the application to find all the segments of a feature in
871                  the proper order.</Notes>                  the proper order.</Notes>
872                  <IndexFields>                  <IndexFields>
# Line 630  Line 881 
881                  </IndexFields>                  </IndexFields>
882              </ToIndex>              </ToIndex>
883          </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>  
884          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
885              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
886              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 717  Line 946 
946              chemical reactions. A single reaction can be triggered by many roles,              chemical reactions. A single reaction can be triggered by many roles,
947              and a role can trigger many reactions.</Notes>              and a role can trigger many reactions.</Notes>
948          </Relationship>          </Relationship>
949            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
950                <Notes>This relationship connects a feature to the subsystems in which it
951                participates. This is technically redundant information, but it is used
952                so often that it deserves its own table.</Notes>
953                <Fields>
954                    <Field name="genome" type="name-string">
955                        <Notes>ID of the genome containing the feature</Notes>
956                    </Field>
957                    <Field name="type" type="key-string">
958                        <Notes>Feature type (eg. peg, rna)</Notes>
959                    </Field>
960                </Fields>
961                <ToIndex>
962                    <Notes>This index enables the application to view the features of a
963                    subsystem sorted by genome and feature type.</Notes>
964                    <IndexFields>
965                        <IndexField name="genome" order="ascending" />
966                        <IndexField name="type" order="ascending" />
967                    </IndexFields>
968                </ToIndex>
969            </Relationship>
970      </Relationships>      </Relationships>
971  </Database>  </Database>

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