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revision 1.7, Thu Jun 16 19:10:04 2005 UTC revision 1.46, Wed Nov 29 20:32:06 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>
23                                          <DataGen>RandParam('low','medium','high')</DataGen>                  </Field>
24                    <Field name="complete" type="boolean">
25                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
26                  </Field>                  </Field>
27                                  <Field name="taxonomy" type="text">                                  <Field name="taxonomy" type="text">
28                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
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 51  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 68  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 95  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 . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
111                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
112                                          of error. Thus, for example, a quality of 30 indicates the probability of error is                                          of error. Thus, for example, a quality of 30 indicates the probability of error is
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 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 116  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="name-string" relation="FeatureAlias">                  <Field name="alias" type="medium-string" relation="FeatureAlias">
129                                          <Notes>Alternative name for this feature. feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
                                         <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
130                                  </Field>                                  </Field>
131                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
132                                          <Notes>[i](optional)[/i] A of this feature's residues into character codes, formed by concatenating                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
133                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
134                                          <DataGen testCount="0"></DataGen>                      protein encoding group, this is the protein characters. For other types
135                        it is the DNA characters.</Notes>
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, 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>
183                    <Index>
184                        <Notes>This index allows the user to find the feature corresponding to
185                        the specified alias name.</Notes>
186                        <IndexFields>
187                            <IndexField name="alias" order="ascending" />
188                        </IndexFields>
189                    </Index>
190                </Indexes>
191            </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>          </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="name" type="string" relation="RoleName">                  <Field name="EC" type="string" relation="RoleEC">
201                                          <Notes>Expanded name of the role. This value is generally only available for roles                      <Notes>EC code for this role.</Notes>
202                                          that are encoded as EC numbers.</Notes>                  </Field>
203                                          <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>                  <Field name="abbr" type="name-string">
204                        <Notes>Abbreviated name for the role, generally non-unique, but useful
205                        in column headings for HTML tables.</Notes>
206                                  </Field>                                  </Field>
207                          </Fields>                          </Fields>
208                <Indexes>
209                    <Index>
210                        <Notes>This index allows the user to find the role corresponding to
211                        an EC number.</Notes>
212                        <IndexFields>
213                            <IndexField name="EC" order="ascending" />
214                        </IndexFields>
215                    </Index>
216                </Indexes>
217          </Entity>          </Entity>
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 170  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>
239            <Entity name="Reaction" keyType="key-string">
240                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
241                is generally a small number preceded by a letter.</Notes>
242                <Fields>
243                    <Field name="url" type="string" relation="ReactionURL">
244                        <Notes>HTML string containing a link to a web location that describes the
245                        reaction. This field is optional.</Notes>
246                    </Field>
247                    <Field name="rev" type="boolean">
248                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
249                    </Field>
250                </Fields>
251            </Entity>
252            <Entity name="Compound" keyType="name-string">
253                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
254                All compounds have a unique ID and may also have one or more names.</Notes>
255                <Fields>
256                    <Field name="name-priority" type="int" relation="CompoundName">
257                        <Notes>Priority of a compound name. The name with the loweset
258                        priority is the main name of this compound.</Notes>
259                    </Field>
260                    <Field name="name" type="name-string" relation="CompoundName">
261                        <Notes>Descriptive name for the compound. A compound may
262                        have several names.</Notes>
263                    </Field>
264                    <Field name="cas-id" type="name-string" relation="CompoundCAS">
265                        <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>
266                    </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>
273                <Indexes>
274                    <Index>
275                        <Notes>This index allows the user to find the compound corresponding to
276                        the specified name.</Notes>
277                        <IndexFields>
278                            <IndexField name="name" order="ascending" />
279                        </IndexFields>
280                    </Index>
281                    <Index>
282                        <Notes>This index allows the user to find the compound corresponding to
283                        the specified CAS ID.</Notes>
284                        <IndexFields>
285                            <IndexField name="cas-id" order="ascending" />
286                        </IndexFields>
287                    </Index>
288                    <Index>
289                        <Notes>This index allows the user to access the compound names in
290                        priority order.</Notes>
291                        <IndexFields>
292                            <IndexField name="id" order="ascending" />
293                            <IndexField name="name-priority" order="ascending" />
294                        </IndexFields>
295                    </Index>
296                </Indexes>
297          </Entity>          </Entity>
298          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
299              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems              <Notes>A [i]subsystem[/i] is a collection of roles that work together in a cell. Identification of subsystems
300              is an important tool for recognizing parallel genetic features in different organisms.</Notes>              is an important tool for recognizing parallel genetic features in different organisms.</Notes>
301                <Fields>
302                    <Field name="curator" type="string">
303                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
304                    </Field>
305                    <Field name="notes" type="text">
306                        <Notes>Descriptive notes about the subsystem.</Notes>
307                    </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>
313            </Entity>
314            <Entity name="RoleSubset" keyType="string">
315                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
316                subset names are generally very short, non-unique strings. The ID of the parent
317                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
318            </Entity>
319            <Entity name="GenomeSubset" keyType="string">
320                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
321                in a particular subsystem. The subset names are generally very short, non-unique
322                strings. The ID of the parent subsystem is prefixed to the subset ID in order
323                to make it unique.</Notes>
324          </Entity>          </Entity>
325          <Entity name="SSCell" keyType="name-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 191  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 256  Line 402 
402                                          </Field>                                          </Field>
403                                  </Fields>                                  </Fields>
404                  </Entity>                  </Entity>
405          <Entity name="Coupling" keyType="medium-string">          <Entity name="Coupling" keyType="id-string">
406              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
407              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
408              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 272  Line 418 
418                  </Field>                  </Field>
419              </Fields>              </Fields>
420          </Entity>          </Entity>
421          <Entity name="PCH" keyType="string">          <Entity name="PCH" keyType="counter">
422              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
423              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
424              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 280  Line 426 
426              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
427              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
428              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
429              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
430              <Fields>              <Fields>
431                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
432                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 292  Line 437 
437                  </Field>                  </Field>
438              </Fields>              </Fields>
439          </Entity>          </Entity>
440            <Entity name="Family" keyType="id-string">
441                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
442                families provide a mechanism for verifying the accuracy of functional assignments
443                and are also used in determining phylogenetic trees.</Notes>
444                <Fields>
445                    <Field name="function" type="text">
446                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
447                    </Field>
448                    <Field name="size" type="int">
449                        <Notes>The number of proteins in this family. This may be larger than the
450                        number of PEGs included in the family, since the family may also contain external
451                        IDs.</Notes>
452                    </Field>
453                </Fields>
454            </Entity>
455            <Entity name="DrugProject" keyType="name-string">
456                <Notes>A drug project is a coherent sent of drug target data that came through the
457                pipeline. In other words, data is put into the database one drug project at a time.
458                This makes it easier to manage the incoming data and to track where a particular
459                piece of data originated.</Notes>
460            </Entity>
461            <Entity name="DrugTopic" keyType="int">
462                <Notes>A drug topic organizes the data in a project relating to a single organism
463                group's features as they apply to a specific category of activity. Categories include
464                features essential to the organism's survival, those that are targets or inhibitors
465                of anti-biotics, and those associated with virulence. Thus, a drug topic consists
466                of data from a single project for features that make good drug targets for the same
467                reason. Drug topics have an artificial, internally-generated key.</Notes>
468                <Fields>
469                    <Field name="identifier" type="name-string">
470                        <Notes>The topic identifier, consisting usually of a generalized organism name
471                        (e.g. Staphylococcus) and the last name of the project's author. More than
472                        one topic may have the same identifier, which is why this isn't the key.</Notes>
473                    </Field>
474                    <Field name="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                <Notes>This relationship connects a drug topic to its bound PDBs. (A separate
573                relationship is used to connect the free PDBs.)</Notes>
574            </Relationship>
575            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="MM">
576                <Notes>This relationship connects free PDBs to their bound counterparts.</Notes>
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 314  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 384  Line 726 
726              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
727              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
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>
730                    <Field name="variant-code" type="key-string">
731                        <Notes>Code indicating the subsystem variant to which this
732                        genome belongs. Each subsystem can have multiple variants. A variant
733                        code of [b]-1[/b] indicates that the genome does not have a functional
734                        variant of the subsystem. A variant code of [b]0[/b] indicates that
735                        the genome's participation is considered iffy.</Notes>
736                    </Field>
737                </Fields>
738                <ToIndex>
739                    <Notes>This index enables the application to find all of the genomes using
740                    a subsystem in order by variant code, which is how we wish to display them
741                    in the spreadsheets.</Notes>
742                    <IndexFields>
743                        <IndexField name="variant-code" order="ascending" />
744                    </IndexFields>
745                </ToIndex>
746          </Relationship>          </Relationship>
747          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
748              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
749                <Fields>
750                    <Field name="column-number" type="int">
751                        <Notes>Column number for this role in the specified subsystem's
752                        spreadsheet.</Notes>
753                    </Field>
754                </Fields>
755                <ToIndex>
756                    <Notes>This index enables the application to see the subsystem roles
757                    in column order. The ordering of the roles is usually significant,
758                    so it is important to preserve it.</Notes>
759                    <IndexFields>
760                        <IndexField name="column-number" order="ascending" />
761                    </IndexFields>
762                </ToIndex>
763          </Relationship>          </Relationship>
764          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
765              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 399  Line 772 
772          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
773              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
774              features assigned to it.</Notes>              features assigned to it.</Notes>
775                <Fields>
776                    <Field name="cluster-number" type="int">
777                        <Notes>ID of this feature's cluster. Clusters represent families of
778                        related proteins participating in a subsystem.</Notes>
779                    </Field>
780                </Fields>
781            </Relationship>
782            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
783                <Notes>This relationship connects a reaction to the compounds that participate
784                in it.</Notes>
785                <Fields>
786                    <Field name="product" type="boolean">
787                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
788                        it is a substrate. When a reaction is written on paper in
789                        chemical notation, the substrates are left of the arrow and the
790                        products are to the right. Sorting on this field will cause
791                        the substrates to appear first, followed by the products. If the
792                        reaction is reversible, then the notion of substrates and products
793                        is not at intuitive; however, a value here of FALSE still puts the
794                        compound left of the arrow and a value of TRUE still puts it to the
795                        right.</Notes>
796                    </Field>
797                    <Field name="stoichiometry" type="key-string">
798                        <Notes>Number of molecules of the compound that participate in a
799                        single instance of the reaction. For example, if a reaction
800                        produces two water molecules, the stoichiometry of water for the
801                        reaction would be two. When a reaction is written on paper in
802                        chemical notation, the stoichiometry is the number next to the
803                        chemical formula of the compound.</Notes>
804                    </Field>
805                    <Field name="main" type="boolean">
806                        <Notes>TRUE if this compound is one of the main participants in
807                        the reaction, else FALSE. It is permissible for none of the
808                        compounds in the reaction to be considered main, in which
809                        case this value would be FALSE for all of the relevant
810                        compounds.</Notes>
811                    </Field>
812                    <Field name="loc" type="key-string">
813                        <Notes>An optional character string that indicates the relative
814                        position of this compound in the reaction's chemical formula. The
815                        location affects the way the compounds present as we cross the
816                        relationship from the reaction side. The product/substrate flag
817                        comes first, then the value of this field, then the main flag.
818                        The default value is an empty string; however, the empty string
819                        sorts first, so if this field is used, it should probably be
820                        used for every compound in the reaction.</Notes>
821                    </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>
829                <ToIndex>
830                    <Notes>This index presents the compounds in the reaction in the
831                    order they should be displayed when writing it in chemical notation.
832                    All the substrates appear before all the products, and within that
833                    ordering, the main compounds appear first.</Notes>
834                    <IndexFields>
835                        <IndexField name="product" order="ascending" />
836                        <IndexField name="loc" order="ascending" />
837                        <IndexField name="main" order="descending" />
838                    </IndexFields>
839                </ToIndex>
840          </Relationship>          </Relationship>
841          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
842              <Notes>This relationship connects a feature to the contig segments that work together              <Notes>This relationship connects a feature to the contig segments that work together
# Line 428  Line 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 443  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 498  Line 914 
914                          If no trusted users are specified in the database, the user                          If no trusted users are specified in the database, the user
915                          also implicitly trusts the user [b]FIG[/b].</Notes>                          also implicitly trusts the user [b]FIG[/b].</Notes>
916                  </Relationship>                  </Relationship>
917            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
918                <Notes>This relationship connects a role subset to the roles that it covers.
919                A subset is, essentially, a named group of roles belonging to a specific
920                subsystem, and this relationship effects that. Note that will a role
921                may belong to many subsystems, a subset belongs to only one subsystem,
922                and all roles in the subset must have that subsystem in common.</Notes>
923            </Relationship>
924            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
925                <Notes>This relationship connects a subset to the genomes that it covers.
926                A subset is, essentially, a named group of genomes participating in a specific
927                subsystem, and this relationship effects that. Note that while a genome
928                may belong to many subsystems, a subset belongs to only one subsystem,
929                and all genomes in the subset must have that subsystem in common.</Notes>
930            </Relationship>
931            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
932                <Notes>This relationship connects a subsystem to its constituent
933                role subsets. Note that some roles in a subsystem may not belong to a
934                subset, so the relationship between roles and subsystems cannot be
935                derived from the relationships going through the subset.</Notes>
936            </Relationship>
937            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
938                <Notes>This relationship connects a subsystem to its constituent
939                genome subsets. Note that some genomes in a subsystem may not belong to a
940                subset, so the relationship between genomes and subsystems cannot be
941                derived from the relationships going through the subset.</Notes>
942            </Relationship>
943            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
944                <Notes>This relationship connects a role to the reactions it catalyzes.
945                The purpose of a role is to create proteins that trigger certain
946                chemical reactions. A single reaction can be triggered by many roles,
947                and a role can trigger many reactions.</Notes>
948            </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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