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revision 1.11, Sun Sep 11 17:09:19 2005 UTC revision 1.50, Mon Jul 16 19:59:33 2007 UTC
# Line 7  Line 7 
7              <Fields>              <Fields>
8                  <Field name="genus" type="name-string">                  <Field name="genus" type="name-string">
9                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
                     <DataGen pass="1">RandParam('streptococcus', 'staphyloccocus', 'felis', 'homo', 'ficticio', 'strangera', 'escherischia', 'carborunda')</DataGen>  
10                  </Field>                  </Field>
11                  <Field name="species" type="name-string">                  <Field name="species" type="name-string">
12                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
                     <DataGen pass="1">StringGen('PKVKVKVKVKV')</DataGen>  
13                  </Field>                  </Field>
14                  <Field name="unique-characterization" type="medium-string">                  <Field name="unique-characterization" type="medium-string">
15                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
16                      genome is taken. It is possible to have in the database more than one genome for a                      genome is taken. It is possible to have in the database more than one genome for a
17                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
18                      <DataGen>StringGen('PKVKVK999')</DataGen>                  </Field>
19                    <Field name="version" type="name-string">
20                        <Notes>version string for this genome, generally consisting of the genome ID followed
21                        by a period and a string of digits.</Notes>
22                  </Field>                  </Field>
23                  <Field name="access-code" type="key-string">                  <Field name="access-code" type="key-string">
24                      <Notes>The access code determines which users can look at the data relating to this genome.                      <Notes>The access code determines which users can look at the data relating to this genome.
25                      Each user is associated with a set of access codes. In order to view a genome, one of                      Each user is associated with a set of access codes. In order to view a genome, one of
26                      the user's access codes must match this value.</Notes>                      the user's access codes must match this value.</Notes>
27                      <DataGen>RandParam('low','medium','high')</DataGen>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                    <Field name="dna-size" type="counter">
32                        <Notes>number of base pairs in the genome</Notes>
33                  </Field>                  </Field>
34                  <Field name="taxonomy" type="text">                  <Field name="taxonomy" type="text">
35                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                      <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
36                      separated by semi-colons (and optional white space), starting with the domain and ending with                      separated by semi-colons (and optional white space), starting with the domain and ending with
37                      the disambiguated genus and species (which is the organism's scientific name plus an                      the disambiguated genus and species (which is the organism's scientific name plus an
38                      identifying string).</Notes>                      identifying string).</Notes>
                     <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),  
                                                   ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>  
39                  </Field>                  </Field>
40                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="primary-group" type="name-string">
41                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
42                      page or of particular interest to a research group or web site. A single genome can belong to multiple                      (either based on the organism name or the default value "Supporting"), whereas there can be
43                      such groups or none at all.</Notes>                      multiple named groups or even none.</Notes>
44                  </Field>                  </Field>
45              </Fields>              </Fields>
46              <Indexes>              <Indexes>
# Line 51  Line 55 
55                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
56                      </IndexFields>                      </IndexFields>
57                  </Index>                  </Index>
58                  <Index Unique="false">                  <Index>
59                        <Notes>This index allows the applications to find all genomes associated with
60                        a specific primary (NMPDR) group.</Notes>
61                        <IndexFields>
62                            <IndexField name="primary-group" order="ascending" />
63                            <IndexField name="genus" order="ascending" />
64                            <IndexField name="species" order="ascending" />
65                            <IndexField name="unique-characterization" order="ascending" />
66                        </IndexFields>
67                    </Index>
68                    <Index>
69                      <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
70                      species.</Notes>                      species.</Notes>
71                      <IndexFields>                      <IndexFields>
# Line 62  Line 76 
76                  </Index>                  </Index>
77              </Indexes>              </Indexes>
78          </Entity>          </Entity>
79            <Entity name="CDD" keyType="key-string">
80                <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
81                on a feature's protein. The ID is six-digit string assigned by the public Conserved Domain
82                Database. A CDD can occur on multiple features and a feature generally has multiple CDDs.</Notes>
83            </Entity>
84          <Entity name="Source" keyType="medium-string">          <Entity name="Source" keyType="medium-string">
85              <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization              <Notes>A [i]source[/i] describes a place from which genome data was taken. This can be an organization
86              or a paper citation.</Notes>              or a paper citation.</Notes>
87              <Fields>              <Fields>
88                  <Field name="URL" type="string" relation="SourceURL">                  <Field name="URL" type="string" relation="SourceURL">
89                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>                      <Notes>URL the paper cited or of the organization's web site. This field optional.</Notes>
                     <DataGen>"http://www.conservativecat.com/Ferdy/TestTarget.php?Source=" . $this->{id}</DataGen>  
90                  </Field>                  </Field>
91                  <Field name="description" type="text">                  <Field name="description" type="text">
92                      <Notes>Description the source. The description can be a street address or a citation.</Notes>                      <Notes>Description the source. The description can be a street address or a citation.</Notes>
                     <DataGen>$this->{id} . ': ' . StringGen(IntGen(50,200))</DataGen>  
93                  </Field>                  </Field>
94              </Fields>              </Fields>
95          </Entity>          </Entity>
# Line 95  Line 112 
112                  <Field name="sequence" type="text">                  <Field name="sequence" type="text">
113                      <Notes>String consisting of the residues. Each residue is described by a single                      <Notes>String consisting of the residues. Each residue is described by a single
114                      character in the string.</Notes>                      character in the string.</Notes>
                     <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>  
115                  </Field>                  </Field>
116                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
117                      <Notes>String describing the quality data for each base pair. Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
# Line 104  Line 120 
120                      10^-30. A higher quality number a better chance of a correct match. It is possible                      10^-30. A higher quality number a better chance of a correct match. It is possible
121                      that the quality data is 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
122                      vector will contain the [b]unknown[/b].</Notes>                      vector will contain the [b]unknown[/b].</Notes>
                     <DataGen>unknown</DataGen>  
123                  </Field>                  </Field>
124              </Fields>              </Fields>
125          </Entity>          </Entity>
126          <Entity name="Feature" keyType="name-string">          <Entity name="Feature" keyType="id-string">
127              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features              <Notes>A [i]feature[/i] is a part of a genome that is of special interest. Features
128              may be spread across multiple contigs of a genome, but never across more than              may be spread across multiple contigs of a genome, but never across more than
129              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
130              and are the targets of annotation.</Notes>              and are the targets of annotation.</Notes>
131              <Fields>              <Fields>
132                  <Field name="feature-type" type="string">                  <Field name="feature-type" type="id-string">
133                      <Notes>Code indicating the type of this feature.</Notes>                      <Notes>Code indicating the type of this feature.</Notes>
                     <DataGen>RandParam('peg','rna')</DataGen>  
                 </Field>  
                 <Field name="alias" type="name-string" relation="FeatureAlias">  
                     <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>  
                     <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>  
134                  </Field>                  </Field>
135                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
136                      <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
137                      codes, formed by concatenating the pieces of the feature together. For a                      codes, formed by concatenating the pieces of the feature together. For a
138                      protein encoding group, this is the protein characters. For other types                      protein encoding group, this is the protein characters. For other types
139                      it is the DNA characters.</Notes>                      it is the DNA characters.</Notes>
                     <DataGen testCount="0"></DataGen>  
140                  </Field>                  </Field>
141                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
142                      <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
143                      the feature's initial residues.</Notes>                      the feature's initial residues.</Notes>
144                      <DataGen testCount="0"></DataGen>                  </Field>
145                    <Field name="assignment" type="text">
146                        <Notes>Default functional assignment for this feature.</Notes>
147                  </Field>                  </Field>
148                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
149                      <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>
150                      <DataGen>1</DataGen>                  </Field>
151                    <Field name="assignment-maker" type="name-string">
152                        <Notes>name of the user who made the functional assignment</Notes>
153                    </Field>
154                    <Field name="assignment-quality" type="char">
155                        <Notes>quality of the functional assignment, usually a space, but may be W (indicating weak) or X
156                        (indicating experimental)</Notes>
157                    </Field>
158                    <Field name="keywords" type="text" searchable="1">
159                        <Notes>This is a list of search keywords for the feature. It includes the
160                        functional assignment, subsystem roles, and special properties.</Notes>
161                  </Field>                  </Field>
162                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
163                      <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
164                      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
165                      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>
166                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                  </Field>
167                      "&amp;Number=" . IntGen(1,99)</DataGen>                  <Field name="conservation" type="float" relation="FeatureConservation">
168                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
169                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
170                        than 1 is a reflection of the degree to which gap characters interfere in the alignment
171                        between the feature and its close relatives.</Notes>
172                    </Field>
173                    <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
174                        <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
175                        cases, this will be a word describing whether the essentiality is confirmed (essential)
176                        or potential (potential-essential), hyperlinked to the document from which the
177                        essentiality was curated. If a feature is not essential, this field will have no
178                        values; otherwise, it may have multiple values.</Notes>
179                    </Field>
180                    <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">
181                        <Notes>A value indicating the virulence of the feature, coded as HTML. In most
182                        cases, this will be a phrase or SA number hyperlinked to the document from which
183                        the virulence information was curated. If the feature is not virulent, this field
184                        will have no values; otherwise, it may have multiple values.</Notes>
185                    </Field>
186                    <Field name="cello" type="name-string">
187                        <Notes>The cello value specifies the expected location of the protein: cytoplasm,
188                        cell wall, inner membrane, and so forth.</Notes>
189                    </Field>
190                    <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">
191                        <Notes>A value indicating whether or not the feature can be found in the
192                        Immune Epitope Database. If the feature has not been matched to that database,
193                        this field will have no values. Otherwise, it will have an epitope name and/or
194                        sequence, hyperlinked to the database.</Notes>
195                    </Field>
196                    <Field name="location-string" type="text">
197                        <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
198                        strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
199                        we have to painstakingly paste together the IsLocatedIn records, which are themselves
200                        designed to help look for genes in a particular region rather than to find the location
201                        of a gene.</Notes>
202                  </Field>                  </Field>
203              </Fields>              </Fields>
204              <Indexes>              <Indexes>
205                  <Index>                  <Index>
206                      <Notes>This index allows the user to find the feature corresponding to                      <Notes>This index allows us to locate a feature by its CELLO value.</Notes>
                     the specified alias name.</Notes>  
207                      <IndexFields>                      <IndexFields>
208                          <IndexField name="alias" order="ascending" />                          <IndexField name="cello" order="ascending" />
209                      </IndexFields>                      </IndexFields>
210                  </Index>                  </Index>
211              </Indexes>              </Indexes>
212          </Entity>          </Entity>
213            <Entity name="FeatureAlias" keyType="medium-string">
214                <Notes>Alternative names for features. A feature can have many aliases. In general,
215                each alias corresponds to only one feature, but there are exceptionsis is not strictly enforced.</Notes>
216            </Entity>
217            <Entity name="SynonymGroup" keyType="id-string">
218                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
219                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
220            </Entity>
221          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
222              <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.
223              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>
224              <Fields>          </Entity>
225                  <Field name="name" type="string" relation="RoleName">          <Entity name="RoleEC" keyType="string">
226                      <Notes>Expanded name of the role. This value is generally only available for roles              <Notes>EC code for a role.</Notes>
                     that are encoded as EC numbers.</Notes>  
                     <DataGen testCount="1">StringGen(IntGen(20,40)) . "(" . $this->{id} . ")"</DataGen>  
                 </Field>  
             </Fields>  
227          </Entity>          </Entity>
228          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="name-string">
229              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations              <Notes>An [i]annotation[/i] contains supplementary information about a feature. Annotations
230              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
231              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>  
232              <Fields>              <Fields>
233                  <Field name="time" type="date">                  <Field name="time" type="date">
234                      <Notes>Date and time of the annotation.</Notes>                      <Notes>Date and time of the annotation.</Notes>
# Line 181  Line 237 
237                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
238                  </Field>                  </Field>
239              </Fields>              </Fields>
240                <Indexes>
241                    <Index>
242                        <Notes>This index allows the user to find recent annotations.</Notes>
243                        <IndexFields>
244                            <IndexField name="time" order="descending" />
245                        </IndexFields>
246                    </Index>
247                </Indexes>
248            </Entity>
249            <Entity name="Reaction" keyType="key-string">
250                <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
251                is generally a small number preceded by a letter.</Notes>
252                <Fields>
253                    <Field name="url" type="string" relation="ReactionURL">
254                        <Notes>HTML string containing a link to a web location that describes the
255                        reaction. This field is optional.</Notes>
256                    </Field>
257                    <Field name="rev" type="boolean">
258                        <Notes>TRUE if this reaction is reversible, else FALSE</Notes>
259                    </Field>
260                </Fields>
261            </Entity>
262            <Entity name="Compound" keyType="name-string">
263                <Notes>A [i]compound[/i] is a chemical that participates in a reaction.
264                All compounds have a unique ID and may also have one or more names.</Notes>
265                <Fields>
266                    <Field name="label" type="string">
267                        <Notes>Name used in reaction display strings.
268                        It is the same as the name possessing a priority of 1, but it is placed
269                        here to speed up the query used to create the display strings.</Notes>
270                    </Field>
271                </Fields>
272            </Entity>
273            <Entity name="CompoundName" keyType="string">
274                <Notes>A [i]compound name[/i] is a common name for the chemical represented by a
275                compound.</Notes>
276            </Entity>
277            <Entity name="CompoundCAS" keyType="name-string">
278                <Notes>This entity represents the Chemical Abstract Service ID for a compound. Each
279                Compound has at most one CAS ID.</Notes>
280          </Entity>          </Entity>
281          <Entity name="Subsystem" keyType="string">          <Entity name="Subsystem" keyType="string">
282              <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
283              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>
284                <Fields>
285                    <Field name="curator" type="string">
286                        <Notes>Name of the person currently in charge of the subsystem.</Notes>
287                    </Field>
288                    <Field name="notes" type="text">
289                        <Notes>Descriptive notes about the subsystem.</Notes>
290                    </Field>
291                    <Field name="classification" type="string" relation="SubsystemClass">
292                        <Notes>Classification string, colon-delimited. This string organizes the
293                        subsystems into a hierarchy.</Notes>
294                    </Field>
295                </Fields>
296            </Entity>
297            <Entity name="RoleSubset" keyType="string">
298                <Notes>A [i]role subset[/i] is a named collection of roles in a particular subsystem. The
299                subset names are generally very short, non-unique strings. The ID of the parent
300                subsystem is prefixed to the subset ID in order to make it unique.</Notes>
301            </Entity>
302            <Entity name="GenomeSubset" keyType="string">
303                <Notes>A [i]genome subset[/i] is a named collection of genomes that participate
304                in a particular subsystem. The subset names are generally very short, non-unique
305                strings. The ID of the parent subsystem is prefixed to the subset ID in order
306                to make it unique.</Notes>
307          </Entity>          </Entity>
308          <Entity name="SSCell" keyType="name-string">          <Entity name="SSCell" keyType="hash-string">
309              <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
310              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
311              of the positions on the spreadsheet.</Notes>              of the positions on the spreadsheet.</Notes>
# Line 202  Line 321 
321                      <Notes>Access code possessed by this                      <Notes>Access code possessed by this
322                      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
323                      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>  
324                  </Field>                  </Field>
325              </Fields>              </Fields>
326          </Entity>          </Entity>
# Line 267  Line 385 
385                      </Field>                      </Field>
386                  </Fields>                  </Fields>
387          </Entity>          </Entity>
388          <Entity name="Coupling" keyType="medium-string">          <Entity name="Family" keyType="id-string">
389              <Notes>A coupling is a relationship between two features. The features are              <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
390              physically close on the contig, and there is evidence that they generally              families provide a mechanism for verifying the accuracy of functional assignments
391              belong together. The key of this entity is formed by combining the coupled              and are also used in determining phylogenetic trees.</Notes>
392              feature IDs with a space.</Notes>              <Fields>
393              <Fields>                  <Field name="function" type="text">
394                  <Field name="score" type="int">                      <Notes>The functional assignment expected for all PEGs in this family.</Notes>
395                      <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH                  </Field>
396                      indicates that two genes near each other on one genome are very similar to                  <Field name="size" type="int">
397                      genes near each other on another genome. The score only counts PCHs for which                      <Notes>The number of proteins in this family. This may be larger than the
398                      the genomes are very different. (In other words, we have a pairing that persists                      number of PEGs included in the family, since the family may also contain external
399                      between different organisms.) A higher score implies a stronger meaning to the                      IDs.</Notes>
                     clustering.</Notes>  
400                  </Field>                  </Field>
401              </Fields>              </Fields>
402          </Entity>          </Entity>
403          <Entity name="PCH" keyType="string">          <Entity name="PDB" keyType="id-string">
404              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PDB is a protein database containing information that can be used to determine
405              pair of physically close features on a contig) to a second pair of physically              the shape of the protein and the energies required to dock with it. The ID is the
406              close features that are similar to the first. Essentially, the PCH is a              four-character name used on the PDB web site.</Notes>
407              relationship between two clusterings in which the first clustering's features              <Fields>
408              are similar to the second clustering's features. The simplest model for                  <Field name="docking-count" type="int">
409              this would be to simply relate clusterings to each other; however, not all                      <Notes>The number of ligands that have been docked against this PDB.</Notes>
410              physically close pairs qualify as clusterings, so we relate a clustering to                  </Field>
411              a pair of features. The key is the clustering key followed by the IDs              </Fields>
412              of the features in the second pair.</Notes>              <Indexes>
413              <Fields>                  <Index>
414                  <Field name="used" type="boolean">                      <IndexFields>
415                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                          <IndexField name="docking-count" order="descending" />
416                      else FALSE. If a clustering has a PCH for a particular genome and many                          <IndexField name="id" order="ascending" />
417                      similar genomes are present, then a PCH will probably exist for the                      </IndexFields>
418                      similar genomes as well. When this happens, only one of the PCHs will                  </Index>
419                      be scored: the others are considered duplicates of the same evidence.</Notes>              </Indexes>
420            </Entity>
421            <Entity name="Ligand" keyType="id-string">
422                <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
423                The ID of the ligand is an 8-digit ZINC ID number.</Notes>
424                <Fields>
425                    <Field name="name" type="long-string">
426                        <Notes>Chemical name of this ligand.</Notes>
427                  </Field>                  </Field>
428              </Fields>              </Fields>
429          </Entity>          </Entity>
430      </Entities>      </Entities>
431      <Relationships>      <Relationships>
432          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
433              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to its CDD protein domains. The
434              in which it participates. A functional coupling is a recognition of the fact              match score is included as intersection data.</Notes>
435              that the features are close to each other on a chromosome, and similar              <Fields>
436              features in other genomes also tend to be close.</Notes>                  <Field name="score" type="float">
437              <Fields>                      <Notes>This is the match score between the feature and the CDD. A
438                  <Field name="pos" type="int">                      lower score is a better match.</Notes>
439                      <Notes>Ordinal position of the feature in the coupling. Currently,                  </Field>
440                      this is either "1" or "2".</Notes>              </Fields>
441                <FromIndex>
442                    <IndexFields>
443                        <IndexField name="score" order="ascending" />
444                    </IndexFields>
445                </FromIndex>
446            </Relationship>
447            <Relationship name="IsIdentifiedByCAS" from="Compound" to="CompoundCAS" arity="MM">
448                <Notes>Relates a compound's CAS ID to the compound itself. Every CAS ID is
449                associated with a compound, and some are associated with two compounds, but not
450                all compounds have CAS IDs.</Notes>
451            </Relationship>
452            <Relationship name="IsIdentifiedByEC" from="Role" to="RoleEC" arity="MM">
453                <Notes>Relates a role to its EC number. Every EC number is associated with a
454                role, but not all roles have EC numbers.</Notes>
455            </Relationship>
456            <Relationship name="IsAliasOf" from="FeatureAlias" to="Feature" arity="MM">
457                <Notes>Connects an alias to the feature it represents. Every alias connects
458                to at least 1 feature, and a feature connects to many aliases.</Notes>
459            </Relationship>
460            <Relationship name="HasCompoundName" from="Compound" to="CompoundName" arity="MM">
461                <Notes>Connects a compound to its names. A compound generally has several
462                names</Notes>
463                <Fields>
464                    <Field name="priority" type="int">
465                        <Notes>Priority of this name, with 1 being the highest priority, 2
466                        the next highest, and so forth.</Notes>
467                    </Field>
468                </Fields>
469                <FromIndex>
470                    <Notes>This index enables the application to view the names of a compound
471                    in priority order.</Notes>
472                    <IndexFields>
473                        <IndexField name="priority" order="ascending" />
474                    </IndexFields>
475                </FromIndex>
476            </Relationship>
477            <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
478                <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
479                <Fields>
480                    <Field name="score" type="float">
481                        <Notes>Similarity score for the comparison between the feature and
482                        the PDB protein. A lower score indicates a better match.</Notes>
483                    </Field>
484                    <Field name="start-location" type="int">
485                        <Notes>Starting location within the feature of the matching region.</Notes>
486                    </Field>
487                    <Field name="end-location" type="int">
488                        <Notes>Ending location within the feature of the matching region.</Notes>
489                  </Field>                  </Field>
490              </Fields>              </Fields>
491              <ToIndex>              <ToIndex>
492                    <Notes>This index enables the application to view the PDBs of a
493                    feature in order from the closest match to the furthest.</Notes>
494                    <IndexFields>
495                        <IndexField name="score" order="ascending" />
496                    </IndexFields>
497                </ToIndex>
498                <FromIndex>
499                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of
500                  a coupling in the proper order. The order influences the way the                  a PDB in order from the closest match to the furthest.</Notes>
501                  PCHs are examined.</Notes>                  <IndexFields>
502                        <IndexField name="score" order="ascending" />
503                    </IndexFields>
504                </FromIndex>
505            </Relationship>
506            <Relationship name="DocksWith" from="PDB" to="Ligand" arity="MM">
507                <Notes>Indicates that a docking result exists between a PDB and a ligand. The
508                docking result describes the energy required for the ligand to dock with
509                the protein described by the PDB. A lower energy indicates the ligand has a
510                good chance of disabling the protein. At the current time, only the best
511                docking results are kept.</Notes>
512                <Fields>
513                    <Field name="reason" type="id-string">
514                        <Notes>Indication of the reason for determining the docking result.
515                        A value of [b]Random[/b] indicates the docking was attempted as a part
516                        of a random survey used to determine the docking characteristics of the
517                        PDB. A value of [b]Rich[/b] indicates the docking was attempted because
518                        a low-energy docking result was predicted for the ligand with respect
519                        to the PDB.</Notes>
520                    </Field>
521                    <Field name="tool" type="id-string">
522                        <Notes>Name of the tool used to produce the docking result.</Notes>
523                    </Field>
524                    <Field name="total-energy" type="float">
525                        <Notes>Total energy required for the ligand to dock with the PDB
526                        protein, in kcal/mol. A negative value means energy is released.</Notes>
527                    </Field>
528                    <Field name="vanderwalls-energy" type="float">
529                        <Notes>Docking energy in kcal/mol that results from the geometric fit
530                        (Van der Waals force) between the PDB and the ligand.</Notes>
531                    </Field>
532                    <Field name="electrostatic-energy" type="float">
533                        <Notes>Docking energy in kcal/mol that results from the movement of
534                        electrons (electrostatic force) between the PDB and the ligan.</Notes>
535                    </Field>
536                </Fields>
537                <FromIndex>
538                    <Notes>This index enables the application to view a PDB's docking results from
539                    the lowest energy (best docking) to highest energy (worst docking).</Notes>
540                  <IndexFields>                  <IndexFields>
541                      <IndexField name="pos" order="ascending" />                      <IndexField name="total-energy" order="ascending" />
542                  </IndexFields>                  </IndexFields>
543                </FromIndex>
544                <ToIndex>
545                    <Notes>This index enables the application to view a ligand's docking results from
546                    the lowest energy (best docking) to highest energy (worst docking). Note that
547                    since we only keep the best docking results for a PDB, this index is not likely
548                    to provide useful results.</Notes>
549              </ToIndex>              </ToIndex>
550          </Relationship>          </Relationship>
551          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
552              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a protein family to all of its PEGs and connects
553              close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>              each PEG to all of its protein families.</Notes>
554          </Relationship>          </Relationship>
555          <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">          <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
556              <Notes>This relationship connects a PCH to the features that represent its              <Notes>This relation connects a synonym group to the features that make it
557              evidence. Each PCH is connected to a parent coupling that relates two features              up.</Notes>
558              on a specific genome. The PCH's evidence that the parent coupling is functional          </Relationship>
559              is the existence of two physically close features on a different genome that          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
560              correspond to the features in the coupling. Those features are found on the              <Notes>This relationship connects a genome to all of its features. This
561              far side of this relationship.</Notes>              relationship is redundant in a sense, because the genome ID is part
562              <Fields>              of the feature ID; however, it makes the creation of certain queries more
563                  <Field name="pos" type="int">              convenient because you can drag in filtering information for a feature's
564                      <Notes>Ordinal position of the feature in the coupling that corresponds              genome.</Notes>
565                      to our target feature. There is a one-to-one correspondence between the              <Fields>
566                      features connected to the PCH by this relationship and the features                  <Field name="type" type="key-string">
567                      connected to the PCH's parent coupling. The ordinal position is used                      <Notes>Feature type (eg. peg, rna)</Notes>
                     to decode that relationship. Currently, this field is either "1" or  
                     "2".</Notes>  
568                  </Field>                  </Field>
569              </Fields>              </Fields>
570              <FromIndex>              <FromIndex>
571                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of a
572                  a PCH in the proper order.</Notes>                  Genome sorted by type.</Notes>
573                  <IndexFields>                  <IndexFields>
574                      <IndexField name="pos" order="ascending" />                      <IndexField name="type" order="ascending" />
575                  </IndexFields>                  </IndexFields>
576              </FromIndex>              </FromIndex>
577          </Relationship>          </Relationship>
# Line 395  Line 616 
616              <Notes>This relationship connects subsystems to the genomes that use              <Notes>This relationship connects subsystems to the genomes that use
617              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
618              connected to the genome features through the [b]SSCell[/b] object.</Notes>              connected to the genome features through the [b]SSCell[/b] object.</Notes>
619                <Fields>
620                    <Field name="variant-code" type="key-string">
621                        <Notes>Code indicating the subsystem variant to which this
622                        genome belongs. Each subsystem can have multiple variants. A variant
623                        code of [b]-1[/b] indicates that the genome does not have a functional
624                        variant of the subsystem. A variant code of [b]0[/b] indicates that
625                        the genome's participation is considered iffy.</Notes>
626                    </Field>
627                </Fields>
628                <ToIndex>
629                    <Notes>This index enables the application to find all of the genomes using
630                    a subsystem in order by variant code, which is how we wish to display them
631                    in the spreadsheets.</Notes>
632                    <IndexFields>
633                        <IndexField name="variant-code" order="ascending" />
634                    </IndexFields>
635                </ToIndex>
636          </Relationship>          </Relationship>
637          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">
638              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>              <Notes>This relationship connects roles to the subsystems that implement them. </Notes>
639                <Fields>
640                    <Field name="abbr" type="name-string">
641                        <Notes>Abbreviated name for the role, generally non-unique, but useful
642                        in column headings for HTML tables.</Notes>
643                    </Field>
644                    <Field name="column-number" type="int">
645                        <Notes>Column number for this role in the specified subsystem's
646                        spreadsheet.</Notes>
647                    </Field>
648                </Fields>
649                <ToIndex>
650                    <Notes>This index enables the application to see the subsystem roles
651                    in column order. The ordering of the roles is usually significant,
652                    so it is important to preserve it.</Notes>
653                    <IndexFields>
654                        <IndexField name="column-number" order="ascending" />
655                    </IndexFields>
656                </ToIndex>
657          </Relationship>          </Relationship>
658          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">          <Relationship name="IsGenomeOf" from="Genome" to="SSCell" arity="1M">
659              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
# Line 410  Line 666 
666          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">          <Relationship name="ContainsFeature" from="SSCell" to="Feature" arity="MM">
667              <Notes>This relationship connects a subsystem's spreadsheet cell to the              <Notes>This relationship connects a subsystem's spreadsheet cell to the
668              features assigned to it.</Notes>              features assigned to it.</Notes>
669                <Fields>
670                    <Field name="cluster-number" type="int">
671                        <Notes>ID of this feature's cluster. Clusters represent families of
672                        related proteins participating in a subsystem.</Notes>
673                    </Field>
674                </Fields>
675            </Relationship>
676            <Relationship name="IsAComponentOf" from="Compound" to="Reaction" arity="MM">
677                <Notes>This relationship connects a reaction to the compounds that participate
678                in it.</Notes>
679                <Fields>
680                    <Field name="product" type="boolean">
681                        <Notes>TRUE if the compound is a product of the reaction, FALSE if
682                        it is a substrate. When a reaction is written on paper in
683                        chemical notation, the substrates are left of the arrow and the
684                        products are to the right. Sorting on this field will cause
685                        the substrates to appear first, followed by the products. If the
686                        reaction is reversible, then the notion of substrates and products
687                        is not at intuitive; however, a value here of FALSE still puts the
688                        compound left of the arrow and a value of TRUE still puts it to the
689                        right.</Notes>
690                    </Field>
691                    <Field name="stoichiometry" type="key-string">
692                        <Notes>Number of molecules of the compound that participate in a
693                        single instance of the reaction. For example, if a reaction
694                        produces two water molecules, the stoichiometry of water for the
695                        reaction would be two. When a reaction is written on paper in
696                        chemical notation, the stoichiometry is the number next to the
697                        chemical formula of the compound.</Notes>
698                    </Field>
699                    <Field name="main" type="boolean">
700                        <Notes>TRUE if this compound is one of the main participants in
701                        the reaction, else FALSE. It is permissible for none of the
702                        compounds in the reaction to be considered main, in which
703                        case this value would be FALSE for all of the relevant
704                        compounds.</Notes>
705                    </Field>
706                    <Field name="loc" type="key-string">
707                        <Notes>An optional character string that indicates the relative
708                        position of this compound in the reaction's chemical formula. The
709                        location affects the way the compounds present as we cross the
710                        relationship from the reaction side. The product/substrate flag
711                        comes first, then the value of this field, then the main flag.
712                        The default value is an empty string; however, the empty string
713                        sorts first, so if this field is used, it should probably be
714                        used for every compound in the reaction.</Notes>
715                    </Field>
716                    <Field name="discriminator" type="int">
717                        <Notes>A unique ID for this record. The discriminator does not
718                        provide any useful data, but it prevents identical records from
719                        being collapsed by the SELECT DISTINCT command used by ERDB to
720                        retrieve data.</Notes>
721                    </Field>
722                </Fields>
723                <ToIndex>
724                    <Notes>This index presents the compounds in the reaction in the
725                    order they should be displayed when writing it in chemical notation.
726                    All the substrates appear before all the products, and within that
727                    ordering, the main compounds appear first.</Notes>
728                    <IndexFields>
729                        <IndexField name="product" order="ascending" />
730                        <IndexField name="loc" order="ascending" />
731                        <IndexField name="main" order="descending" />
732                    </IndexFields>
733                </ToIndex>
734          </Relationship>          </Relationship>
735          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">          <Relationship name="IsLocatedIn" from="Feature" to="Contig" arity="MM">
736              <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 439  Line 760 
760                      [b]-[/b] if it is backward.</Notes>                      [b]-[/b] if it is backward.</Notes>
761                  </Field>                  </Field>
762              </Fields>              </Fields>
763              <FromIndex Unique="false">              <FromIndex>
764                  <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
765                  the proper order.</Notes>                  the proper order.</Notes>
766                  <IndexFields>                  <IndexFields>
# Line 454  Line 775 
775                  </IndexFields>                  </IndexFields>
776              </ToIndex>              </ToIndex>
777          </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>  
778          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
779              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
780              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 509  Line 808 
808              If no trusted users are specified in the database, the user              If no trusted users are specified in the database, the user
809              also implicitly trusts the user [b]FIG[/b].</Notes>              also implicitly trusts the user [b]FIG[/b].</Notes>
810          </Relationship>          </Relationship>
811            <Relationship name="ConsistsOfRoles" from="RoleSubset" to="Role" arity="MM">
812                <Notes>This relationship connects a role subset to the roles that it covers.
813                A subset is, essentially, a named group of roles belonging to a specific
814                subsystem, and this relationship effects that. Note that will a role
815                may belong to many subsystems, a subset belongs to only one subsystem,
816                and all roles in the subset must have that subsystem in common.</Notes>
817            </Relationship>
818            <Relationship name="ConsistsOfGenomes" from="GenomeSubset" to="Genome" arity="MM">
819                <Notes>This relationship connects a subset to the genomes that it covers.
820                A subset is, essentially, a named group of genomes participating in a specific
821                subsystem, and this relationship effects that. Note that while a genome
822                may belong to many subsystems, a subset belongs to only one subsystem,
823                and all genomes in the subset must have that subsystem in common.</Notes>
824            </Relationship>
825            <Relationship name="HasRoleSubset" from="Subsystem" to="RoleSubset" arity="1M">
826                <Notes>This relationship connects a subsystem to its constituent
827                role subsets. Note that some roles in a subsystem may not belong to a
828                subset, so the relationship between roles and subsystems cannot be
829                derived from the relationships going through the subset.</Notes>
830            </Relationship>
831            <Relationship name="HasGenomeSubset" from="Subsystem" to="GenomeSubset" arity="1M">
832                <Notes>This relationship connects a subsystem to its constituent
833                genome subsets. Note that some genomes in a subsystem may not belong to a
834                subset, so the relationship between genomes and subsystems cannot be
835                derived from the relationships going through the subset.</Notes>
836            </Relationship>
837            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">
838                <Notes>This relationship connects a role to the reactions it catalyzes.
839                The purpose of a role is to create proteins that trigger certain
840                chemical reactions. A single reaction can be triggered by many roles,
841                and a role can trigger many reactions.</Notes>
842            </Relationship>
843            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
844                <Notes>This relationship connects a feature to the subsystems in which it
845                participates. This is technically redundant information, but it is used
846                so often that it deserves its own table.</Notes>
847                <Fields>
848                    <Field name="genome" type="name-string">
849                        <Notes>ID of the genome containing the feature</Notes>
850                    </Field>
851                    <Field name="type" type="key-string">
852                        <Notes>Feature type (eg. peg, rna)</Notes>
853                    </Field>
854                </Fields>
855                <ToIndex>
856                    <Notes>This index enables the application to view the features of a
857                    subsystem sorted by genome and feature type.</Notes>
858                    <IndexFields>
859                        <IndexField name="genome" order="ascending" />
860                        <IndexField name="type" order="ascending" />
861                    </IndexFields>
862                </ToIndex>
863            </Relationship>
864      </Relationships>      </Relationships>
865  </Database>  </Database>

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