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revision 1.59, Thu Oct 9 17:21:10 2008 UTC revision 1.60, Mon Jan 19 21:46:21 2009 UTC
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 <?xml version="1.0" encoding="utf-8" ?>  
1  <Database>  <Database>
2      <Title>Sprout Genome and Subsystem Database</Title>      <Title>Sprout Genome and Subsystem Database</Title>
3      <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.      <Notes>The Sprout database contains the genetic data for all complete organisms in the SeedEnvironment.
# Line 8  Line 7 
7      optimized for searching. In particular, the Feature table contains an extra copy of the      optimized for searching. In particular, the Feature table contains an extra copy of the
8      feature's functional role and a list of possible search terms.</Notes>      feature's functional role and a list of possible search terms.</Notes>
9      <Entities>      <Entities>
10          <Entity name="Genome" keyType="name-string">          <Entity name="Genome" keyType="string">
11              <DisplayInfo theme="nmpdr" col="3" row="1" />              <DisplayInfo theme="nmpdr" col="3" row="1" />
12              <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>              <Notes>A Genome contains the sequence data for a particular individual organism.</Notes>
13              <Fields>              <Fields>
14                  <Field name="genus" type="name-string">                  <Field name="genus" type="string">
15                      <Notes>Genus of the relevant organism.</Notes>                      <Notes>Genus of the relevant organism.</Notes>
16                  </Field>                  </Field>
17                  <Field name="species" type="name-string">                  <Field name="species" type="string">
18                      <Notes>Species of the relevant organism.</Notes>                      <Notes>Species of the relevant organism.</Notes>
19                  </Field>                  </Field>
20                  <Field name="unique-characterization" type="medium-string" default="">                  <Field name="unique-characterization" type="string" default="">
21                      <Notes>The unique characterization identifies the particular organism instance from which the                      <Notes>The unique characterization identifies the particular organism instance from which the
22                      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
23                      particular species, and every individual organism has variations in its DNA.</Notes>                      particular species, and every individual organism has variations in its DNA.</Notes>
24                  </Field>                  </Field>
25                  <Field name="version" type="name-string">                  <Field name="scientific-name" type="string">
26                      <Notes>version string for this genome, generally consisting of the genome ID followed                      <Notes>Scientific name of this genome, usually consisting of the genus,
27                        species, and unique characterization.</Notes>
28                    </Field>
29                    <Field name="version" type="string">
30                        <Notes>Version string for this genome, generally consisting of the genome ID followed
31                      by a period and a string of digits.</Notes>                      by a period and a string of digits.</Notes>
32                  </Field>                  </Field>
33                  <Field name="complete" type="boolean">                  <Field name="complete" type="boolean">
# Line 34  Line 37 
37                      <Notes>number of base pairs in the genome</Notes>                      <Notes>number of base pairs in the genome</Notes>
38                  </Field>                  </Field>
39                  <Field name="taxonomy" type="text">                  <Field name="taxonomy" type="text">
40                      <Notes>The taxonomy string contains the full [[Wikipedia:taxonomy]] of the organism, while individual elements                      <Notes>The taxonomy string contains the full taxonomy of the organism, with individual elements
41                      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
42                      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
43                      identifying string).</Notes>                      identifying string).</Notes>
44                  </Field>                  </Field>
45                  <Field name="primary-group" type="name-string">                  <Field name="primary-group" type="string">
46                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group                      <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
47                      per organism (either based on the organism name or the default value =Supporting=). In general,                      per organism (either based on the organism name or a default value for supporting
48                      more data is kept on organisms in NMPDR groups than on supporting organisms.</Notes>                      genomes). In general, more data is kept on organisms in NMPDR groups than on supporting
49                        organisms.</Notes>
50                  </Field>                  </Field>
51                  <Field name="contigs" type="int">                  <Field name="contigs" type="int">
52                      <Notes>Number of contigs for this organism.</Notes>                      <Notes>Number of contigs for this organism.</Notes>
53                  </Field>                  </Field>
54                  <Field name="pegs" type="int">                  <Field name="pegs" type="int">
55                      <Notes>Number of [[protein encoding genes]] for this organism</Notes>                      <Notes>Number of protein encoding genes for this organism</Notes>
56                  </Field>                  </Field>
57                  <Field name="rnas" type="int">                  <Field name="rnas" type="int">
58                      <Notes>Number of RNA features found for this organism.</Notes>                      <Notes>Number of RNA features found for this organism.</Notes>
59                  </Field>                  </Field>
60                    <Field name="endospore" type="semi-boolean">
61                        <Notes>Y/N/? flag indicating whether or not this organism produces endospores.</Notes>
62                    </Field>
63                    <Field name="gc-content" type="float">
64                        <Notes>Percentage of the genome that consists of G and C base pairs.</Notes>
65                    </Field>
66                    <Field name="habitat" type="string">
67                        <Notes>Preferred habitat of organism.</Notes>
68                    </Field>
69                    <Field name="gram-stain" type="semi-boolean">
70                        <Notes>Gram stain behaviour of organism-- positive, negative, or unknown.</Notes>
71                    </Field>
72                    <Field name="motility" type="semi-boolean">
73                        <Notes>Y/N/? flag indicating whether or not this organism can move under
74                        its own power.</Notes>
75                    </Field>
76                    <Field name="oxygen" type="string">
77                        <Notes>Indication of this organism's behavior relating to environmental oxygen.</Notes>
78                    </Field>
79                    <Field name="temperature-min" type="float">
80                        <Notes>Minimum optimal temperature for this organism, in degrees Celsius.</Notes>
81                    </Field>
82                    <Field name="temperature-max" type="float">
83                        <Notes>Maximum optimal temperature for this organism, in degrees Celsius.</Notes>
84                    </Field>
85                    <Field name="pathogenic" type="semi-boolean">
86                        <Notes>Y/N/? flag indicating whether or not this organism is pathogenic.</Notes>
87                    </Field>
88                    <Field name="salinity" type="string">
89                        <Notes>Indication of this organism's behavior relating to environmental
90                        salinity.</Notes>
91                    </Field>
92                    <Field name="optimal-temperature-range" type="string">
93                        <Notes>Indication of this organism's behavior relating to environmental
94                        temperature.</Notes>
95                    </Field>
96              </Fields>              </Fields>
97              <Indexes>              <Indexes>
98                  <Index>                  <Index>
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106                      </IndexFields>                      </IndexFields>
107                  </Index>                  </Index>
108                  <Index>                  <Index>
109                      <Notes>This index allows the applications to find all genomes for a particular                      <Notes>This index allows the applications to retrieve all genomes by genus and species
110                      species.</Notes>                      groupings.</Notes>
111                      <IndexFields>                      <IndexFields>
112                          <IndexField name="genus" order="ascending" />                          <IndexField name="genus" order="ascending" />
113                          <IndexField name="species" order="ascending" />                          <IndexField name="species" order="ascending" />
114                          <IndexField name="unique-characterization" order="ascending" />                          <IndexField name="unique-characterization" order="ascending" />
115                      </IndexFields>                      </IndexFields>
116                  </Index>                  </Index>
117                    <Index>
118                        <Notes>This index allows the applications to search for genome by scientific
119                        name.</Notes>
120                        <IndexFields>
121                            <IndexField name="scientific-name" order="ascending" />
122                        </IndexFields>
123                    </Index>
124              </Indexes>              </Indexes>
125          </Entity>          </Entity>
126          <Entity name="CDD" keyType="key-string">          <Entity name="ProteinFamily" keyType="string">
127                <Notes>A protein family represents a group of proteins with related
128                functions. Some protein families are downloaded from the PFAM database
129                and some are FIGfams. The protein family keys all begin with the letters
130                PF and the FIGfams with the letters FIG.</Notes>
131                <Fields>
132                    <Field name="common-name" type="string" relation="ProteinFamilyName">
133                        <Notes>Ontological name for the protein family. Not all families
134                        have ontological names.</Notes>
135                    </Field>
136                </Fields>
137                <Indexes>
138                    <Index>
139                        <Notes>This index allows the user to locate protein families
140                        by name.</Notes>
141                        <IndexFields>
142                            <IndexField name="common-name" order="ascending" />
143                        </IndexFields>
144                    </Index>
145                </Indexes>
146            </Entity>
147            <Entity name="Host" keyType="string">
148                <Notes>A host is a particular type of creature in which an organism has
149                pathogenic behavior. Hosts can be specific (Human) or general
150                (Animal).</Notes>
151            </Entity>
152            <Entity name="CDD" keyType="string">
153              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit              <Notes>A CDD is a protein domain designator. It represents the shape of a molecular unit
154              on a feature's protein. The ID is six-digit string assigned by the public              on a feature's protein. The ID is six-digit string assigned by the public
155              Conserved Domain Database. A CDD can occur on multiple features and a feature              Conserved Domain Database. A CDD can occur on multiple features and a feature
156              generally has multiple CDDs.</Notes>              generally has multiple CDDs.</Notes>
157          </Entity>          </Entity>
158          <Entity name="Source" keyType="medium-string">          <Entity name="Source" keyType="string">
159              <Notes>A source describes a place from which genome data was taken. This can be an organization              <Notes>A source describes a place from which genome data was taken. This can be an organization
160              or a paper citation.</Notes>              or a paper citation.</Notes>
161              <Fields>              <Fields>
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167                  </Field>                  </Field>
168              </Fields>              </Fields>
169          </Entity>          </Entity>
170          <Entity name="Contig" keyType="name-string">          <Entity name="Contig" keyType="string">
171              <DisplayInfo theme="nmpdr" col="1" row="1" />              <DisplayInfo theme="nmpdr" col="1" row="1" />
172              <Notes>A contig is a contiguous run of residues. The contig's ID consists of the              <Notes>A contig is a contiguous run of residues. The contig's ID consists of the
173              genome ID followed by a name that identifies which contig this is for the parent genome. As              genome ID followed by a name that identifies which contig this is for the parent genome. As
# Line 104  Line 177 
177              contain the characters that represent the residues as well as data on the quality of              contain the characters that represent the residues as well as data on the quality of
178              the residue identification.</Notes>              the residue identification.</Notes>
179          </Entity>          </Entity>
180          <Entity name="Sequence" keyType="name-string">          <Entity name="Sequence" keyType="string">
181              <Notes>A sequence is a continuous piece of a contig. Contigs are split into              <Notes>A sequence is a continuous piece of a contig. Contigs are split into
182              sequences so that we don't have to have the entire contig in memory when we are              sequences so that we don't have to have the entire contig in memory when we are
183              manipulating it. The key of the sequence is the contig ID followed by the index of              manipulating it. The key of the sequence is the contig ID followed by the index of
184              the begin point.</Notes>              the begin point.</Notes>
185              <Fields>              <Fields>
186                  <Field name="sequence" type="text">                  <Field name="sequence" type="dna">
187                      <Notes>String consisting of the residues (base pairs). Each residue is described by a single                      <Notes>String consisting of the residues (base pairs). Each residue is described by a single
188                      character in the string.</Notes>                      character in the string.</Notes>
189                  </Field>                  </Field>
# Line 120  Line 193 
193                      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
194                      10^-30. A higher quality number indicates a better chance of a correct match. It is                      10^-30. A higher quality number indicates a better chance of a correct match. It is
195                      possible that the quality data is not known for a sequence. If that is the case, the                      possible that the quality data is not known for a sequence. If that is the case, the
196                      quality vector will contain the string =unknown=.</Notes>                      quality vector will contain the string "unknown".</Notes>
197                  </Field>                  </Field>
198              </Fields>              </Fields>
199          </Entity>          </Entity>
200          <Entity name="Keyword" keyType="name-string">          <Entity name="Keyword" keyType="string">
201              <Notes>A keyword is a word that can be used to search the feature table. This entity              <Notes>A keyword is a word that can be used to search the feature table. This entity
202              contains the keyword's stem, its phonetic form, and the number of features that              contains the keyword's stem, its phonetic form, and the number of features that
203              can be found by searching for the word.</Notes>              can be found by searching for the word.</Notes>
204              <Fields>              <Fields>
205                  <Field name="stem" type="name-string">                  <Field name="stem" type="string">
206                      <Notes>The stem of a keyword is a normalized form that is independent of parts                      <Notes>The stem of a keyword is a normalized form that is independent of parts
207                      of speech. The actual keywords stored in the database search index are stems.</Notes>                      of speech. The actual keywords stored in the database search index are stems.</Notes>
208                  </Field>                  </Field>
209                  <Field name="phonex" type="name-string">                  <Field name="phonex" type="string">
210                      <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the                      <Notes>A _phonex_ is a string that identifies the phonetic characteristics of the
211                      word stem. This can be used to find alternative spellings if an matching word is not                      word stem. This can be used to find alternative spellings if an matching word is not
212                      present.</Notes>                      present.</Notes>
# Line 154  Line 227 
227                  </Index>                  </Index>
228              </Indexes>              </Indexes>
229          </Entity>          </Entity>
230          <Entity name="ExternalDatabase" keyType="key-string">          <Entity name="ExternalDatabase" keyType="string">
231              <Notes>An external database identifies a biological database surveyed by PIR International              <Notes>An external database identifies a biological database surveyed by PIR International
232              as part of an effort to determine which features are essentially identical between bioinformatics              as part of an effort to determine which features are essentially identical between bioinformatics
233              organizations. Each feature in the database will have zero or more corresponding IDs that are              organizations. Each feature in the database will have zero or more corresponding IDs that are
234              captured from the PIR data. Each corresponding ID is represented in a relationship between an external              captured from the PIR data. Each corresponding ID is represented in a relationship between an external
235              database and the feature itself.</Notes>              database and the feature itself.</Notes>
236          </Entity>          </Entity>
237          <Entity name="Feature" keyType="id-string">          <Entity name="Feature" keyType="string">
238              <DisplayInfo theme="nmpdr" col="3" row="3" />              <DisplayInfo theme="nmpdr" col="3" row="3" />
239              <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features              <Notes>A feature (sometimes also called a "gene" is a part of a genome that is of special interest. Features
240              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
241              one genome. Features can be assigned to roles via spreadsheet cells,              one genome. Features can be assigned to roles via spreadsheet cells,
242              and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>              and are the targets of annotation. Each feature in the database has a unique FigId.</Notes>
243              <Fields>              <Fields>
244                  <Field name="feature-type" type="id-string">                  <Field name="feature-type" type="string">
245                      <Notes>Code indicating the type of this feature. Among the codes currently                      <Notes>Code indicating the type of this feature. Among the codes currently
246                      supported are =peg= for a [[protein encoding gene]], =bs= for a                      supported are "peg" for a protein encoding gene, "bs" for a
247                      binding site, =opr= for an operon, and so forth.</Notes>                      binding site, "opr" for an operon, and so forth.</Notes>
248                  </Field>                  </Field>
249                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
250                      <Notes>_(optional)_ A translation of this feature's residues into character                      <Notes>(optional) A translation of this feature's residues into
251                      codes, formed by concatenating the pieces of the feature together. For a                      protein character codes, formed by concatenating the pieces
252                      [[protein encoding gene]], the translation contains protein characters. For other types                      of the feature together. Only protein encoding genes have
253                      it contains DNA characters.</Notes>                      translations.</Notes>
254                  </Field>                  </Field>
255                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
256                      <Notes>Upstream sequence for the feature. This includes residues preceding the feature as                      <Notes>Upstream sequence for the feature. This includes residues preceding the feature as
# Line 186  Line 259 
259                  <Field name="assignment" type="text">                  <Field name="assignment" type="text">
260                      <Notes>Default functional assignment for this feature.</Notes>                      <Notes>Default functional assignment for this feature.</Notes>
261                  </Field>                  </Field>
262                  <Field name="assignment-maker" type="name-string">                  <Field name="assignment-maker" type="string">
263                      <Notes>name of the user who made the functional assignment</Notes>                      <Notes>name of the user who made the functional assignment</Notes>
264                  </Field>                  </Field>
265                  <Field name="assignment-quality" type="char">                  <Field name="assignment-quality" type="char">
# Line 200  Line 273 
273                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
274                      <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The                      <Notes>Web hyperlink for this feature. A feature can have no hyperlinks or it can have many. The
275                      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
276                      are coded as raw HTML, using &lt;a href="_link_"&gt;_text_&lt;/a&gt; notation.</Notes>                      are coded as raw HTML.</Notes>
277                  </Field>                  </Field>
278                  <Field name="conservation" type="float" relation="FeatureConservation">                  <Field name="essential" type="link" relation="FeatureEssential" special="property_search">
                     <Notes>_(optional)_ A number between 0 and 1 that indicates the degree to which this feature's DNA is  
                     conserved in related genomes. A value of 1 indicates perfect conservation. A value less  
                     than 1 is a reflection of the degree to which gap characters interfere in the alignment  
                     between the feature and its close relatives.</Notes>  
                 </Field>  
                 <Field name="essential" type="text" relation="FeatureEssential" special="property_search">  
279                      <Notes>A value indicating the essentiality of the feature, coded as HTML. In most                      <Notes>A value indicating the essentiality of the feature, coded as HTML. In most
280                      cases, this will be a word describing whether the essentiality is confirmed (essential)                      cases, this will be a word describing whether the essentiality is confirmed (essential)
281                      or potential (potential-essential), hyperlinked to the document from which the                      or potential (potential-essential), hyperlinked to the document from which the
282                      essentiality was curated. If a feature is not essential, this field will have no                      essentiality was curated. If a feature is not essential, this field will have no
283                      values; otherwise, it may have multiple values.</Notes>                      values; otherwise, it may have multiple values.</Notes>
284                  </Field>                  </Field>
285                  <Field name="virulent" type="text" relation="FeatureVirulent" special="property_search">                  <Field name="virulent" type="link" relation="FeatureVirulent" special="property_search">
286                      <Notes>A value indicating the virulence of the feature, coded as HTML. In most                      <Notes>A value indicating the virulence of the feature, coded as HTML. In most
287                      cases, this will be a phrase or SA number hyperlinked to the document from which                      cases, this will be a phrase or SA number hyperlinked to the document from which
288                      the virulence information was curated. If the feature is not virulent, this field                      the virulence information was curated. If the feature is not virulent, this field
289                      will have no values; otherwise, it may have multiple values.</Notes>                      will have no values; otherwise, it may have multiple values.</Notes>
290                  </Field>                  </Field>
291                  <Field name="iedb" type="text" relation="FeatureIEDB" special="property_search">                  <Field name="iedb" type="link" relation="FeatureIEDB" special="property_search">
292                      <Notes>A value indicating whether or not the feature can be found in the                      <Notes>A value indicating whether or not the feature can be found in the
293                      Immune Epitope Database. If the feature has not been matched to that database,                      Immune Epitope Database. If the feature has not been matched to that database,
294                      this field will have no values. Otherwise, it will have an epitope name and/or                      this field will have no values. Otherwise, it will have an epitope name and/or
# Line 230  Line 297 
297                  <Field name="location-string" type="text">                  <Field name="location-string" type="text">
298                      <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location                      <Notes>Location of the feature, expressed as a comma-delimited list of Sprout location
299                      strings. This gives us a fast mechanism for extracting the feature location. Otherwise,                      strings. This gives us a fast mechanism for extracting the feature location. Otherwise,
300                      we have to painstakingly paste together the [[#IsLocatedIn]] records, which are themselves                      we have to painstakingly paste together the IsLocatedIn records, which are themselves
301                      designed to help look for features in a particular region rather than to find the location                      designed to help look for features in a particular region rather than to find the location
302                      of a feature.</Notes>                      of a feature.</Notes>
303                  </Field>                  </Field>
304                  <Field name="signal-peptide" type="name-string">                  <Field name="signal-peptide" type="string">
305                      <Notes>The signal peptide location for this feature. This is expressed as start and end                      <Notes>The signal peptide location for this feature. This is expressed as start and end
306                      numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal                      numbers with a hyphen for the relevant amino acids. So, "1-22" would indicate a signal
307                      peptide at the beginning of the feature's protein and extending through 22 amino acid                      peptide at the beginning of the feature's protein and extending through 22 amino acid
# Line 272  Line 339 
339                  <Field name="in-genbank" type="boolean">                  <Field name="in-genbank" type="boolean">
340                      <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>                      <Notes>TRUE if a feature can be found in GenBank, else FALSE</Notes>
341                  </Field>                  </Field>
342                    <Field name="conserved-neighbors" type="int">
343                        <Notes>number of coupled features</Notes>
344                    </Field>
345                    <Field name="transmembrane-domain-count" type="int">
346                        <Notes>number of sections in the feature's protein that
347                        become embedded in the cell membrane</Notes>
348                    </Field>
349                    <Field name="ec" type="string" relation="FeatureEC">
350                        <Notes>An EC number associated with this feature.</Notes>
351                    </Field>
352              </Fields>              </Fields>
353                <Indexes>
354                    <Index>
355                        <Notes>This index supports looking up features by EC
356                        number.</Notes>
357                        <IndexFields>
358                            <IndexField name="ec" order="ascending" />
359                        </IndexFields>
360                    </Index>
361                </Indexes>
362          </Entity>          </Entity>
363          <Entity name="FeatureAlias" keyType="medium-string">          <Entity name="FeatureAlias" keyType="string">
364              <Notes>Alternative names for features. A feature can have many aliases. In general,              <Notes>Alternative names for features. A feature can have many aliases. In general,
365              each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>              each alias corresponds to only one feature, but there are many exceptions to this rule.</Notes>
366          </Entity>          </Entity>
367          <Entity name="SproutUser" keyType="name-string">          <Entity name="SproutUser" keyType="string">
368              <Notes>A user is a person who can make annotations and view data in the database. The              <Notes>A user is a person who can make annotations and view data in the database. The
369              user object is keyed on the user's login name.</Notes>              user object is keyed on the user's login name.</Notes>
370              <Fields>              <Fields>
# Line 287  Line 373 
373                  </Field>                  </Field>
374              </Fields>              </Fields>
375          </Entity>          </Entity>
376          <Entity name="SynonymGroup" keyType="id-string">          <Entity name="SynonymGroup" keyType="string">
377              <Notes>A synonym group represents a group of features. Features that represent substantially              <Notes>A synonym group represents a group of features. Features that represent substantially
378              identical proteins or DNA sequences are mapped to the same synonym group, and this information is              identical proteins or DNA sequences are mapped to the same synonym group, and this information is
379              used to expand similarities.</Notes>              used to expand similarities.</Notes>
# Line 300  Line 386 
386          <Entity name="RoleEC" keyType="string">          <Entity name="RoleEC" keyType="string">
387              <Notes>EC code for a role.</Notes>              <Notes>EC code for a role.</Notes>
388          </Entity>          </Entity>
389          <Entity name="Annotation" keyType="name-string">          <Entity name="Annotation" keyType="string">
390              <DisplayInfo theme="seed" col="1" row="3" />              <DisplayInfo theme="seed" col="1" row="3" />
391              <Notes>An annotation contains supplementary information about a feature. The most              <Notes>An annotation contains supplementary information about a feature. The most
392              important type of annotation is the assignment of a [[functional role]]; however,              important type of annotation is the assignment of a functional role; however,
393              other types of annotations are also possible.</Notes>              other types of annotations are also possible.</Notes>
394              <Fields>              <Fields>
395                  <Field name="time" type="date">                  <Field name="time" type="date">
# Line 322  Line 408 
408                  </Index>                  </Index>
409              </Indexes>              </Indexes>
410          </Entity>          </Entity>
411          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="string">
412              <DisplayInfo  theme="web" col="7" row="5" />              <DisplayInfo  theme="web" col="7" row="5" />
413              <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID              <Notes>A reaction is a chemical process catalyzed by a protein. The reaction ID
414              is generally a small number preceded by a letter.</Notes>              is generally a small number preceded by a letter.</Notes>
# Line 336  Line 422 
422                  </Field>                  </Field>
423              </Fields>              </Fields>
424          </Entity>          </Entity>
425          <Entity name="Compound" keyType="name-string">          <Entity name="Compound" keyType="string">
426              <DisplayInfo  theme="web" col="7" row="7" />              <DisplayInfo  theme="web" col="7" row="7" />
427              <Notes>A compound is a chemical that participates in a reaction.              <Notes>A compound is a chemical that participates in a reaction.
428              All compounds have a unique ID and may also have one or more names.</Notes>              All compounds have a unique ID and may also have one or more names.</Notes>
# Line 352  Line 438 
438              <Notes>A compound name is a common name for the chemical represented by a              <Notes>A compound name is a common name for the chemical represented by a
439              compound.</Notes>              compound.</Notes>
440          </Entity>          </Entity>
441          <Entity name="CompoundCAS" keyType="name-string">          <Entity name="CompoundCAS" keyType="string">
442              <Notes>This entity represents the Chemical Abstract Service ID for a              <Notes>This entity represents the Chemical Abstract Service ID for a
443              compound. Each Compound has at most one CAS ID.</Notes>              compound. Each Compound has at most one CAS ID.</Notes>
444          </Entity>          </Entity>
# Line 399  Line 485 
485              <Notes>Part of the process of subsystem annotation of features              <Notes>Part of the process of subsystem annotation of features
486              is creating a spreadsheet of genomes and roles to which features are assigned.              is creating a spreadsheet of genomes and roles to which features are assigned.
487              A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>              A spreadsheet cell represents one of the positions on the spreadsheet.</Notes>
488                <Fields>
489                    <Field name="column-number" type="int">
490                        <Notes>Column number of this cell. This value is put here to
491                        improve the performance of an essential query.</Notes>
492                    </Field>
493                </Fields>
494          </Entity>          </Entity>
495          <Entity name="Property" keyType="int">          <Entity name="Property" keyType="int">
496              <Notes>A property is a type of assertion that could be made about the properties of              <Notes>A property is a type of assertion that could be made about the properties of
# Line 407  Line 499 
499              pairs, even some that notionally contradict each other. For example, there can be evidence              pairs, even some that notionally contradict each other. For example, there can be evidence
500              that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>              that a feature is essential to the organism's survival and evidence that it is superfluous.</Notes>
501              <Fields>              <Fields>
502                  <Field name="property-name" type="name-string">                  <Field name="property-name" type="string">
503                      <Notes>Name of this property.</Notes>                      <Notes>Name of this property.</Notes>
504                  </Field>                  </Field>
505                  <Field name="property-value" type="string">                  <Field name="property-value" type="text">
506                      <Notes>Value associated with this property. For each property                      <Notes>Value associated with this property. For each property
507                      name, there must by a property record for all of its possible                      name, there must by a property record for all of its possible
508                      values.</Notes>                      values.</Notes>
# Line 427  Line 519 
519                  </Index>                  </Index>
520              </Indexes>              </Indexes>
521          </Entity>          </Entity>
522          <Entity name="Diagram" keyType="name-string">          <Entity name="Diagram" keyType="string">
523              <DisplayInfo theme="web" col="7" row="1" />              <DisplayInfo theme="web" col="7" row="1" />
524              <Notes>A functional diagram describes a network of chemical reactions, often comprising a single              <Notes>A functional diagram describes a network of chemical reactions, often comprising a single
525              subsystem. A diagram is identified by a short name and contains a longer descriptive name.              subsystem. A diagram is identified by a short name and contains a longer descriptive name.
# Line 440  Line 532 
532                  </Field>                  </Field>
533              </Fields>              </Fields>
534          </Entity>          </Entity>
535          <Entity name="PDB" keyType="id-string">          <Entity name="PDB" keyType="string">
536              <DisplayInfo theme="web" col="3" row="5" />              <DisplayInfo theme="web" col="3" row="5" />
537              <Notes>A PDB is a protein data bank entry containing information that can be used              <Notes>A PDB is a protein data bank entry containing information that can be used
538              to determine the shape of the protein and the energies required to dock with it.              to determine the shape of the protein and the energies required to dock with it.
# Line 459  Line 551 
551                  </Index>                  </Index>
552              </Indexes>              </Indexes>
553          </Entity>          </Entity>
554          <Entity name="Ligand" keyType="id-string">          <Entity name="Ligand" keyType="string">
555              <DisplayInfo theme="web" col="3" row="7" />              <DisplayInfo theme="web" col="3" row="7" />
556              <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.              <Notes>A Ligand is a chemical of interest in computing docking energies against a PDB.
557              The ID of the ligand is an 8-digit ID number in the [[http://zinc.docking.org ZINC database]].</Notes>              The ID of the ligand is an 8-digit ID number in the ZINC database.</Notes>
558              <Fields>              <Fields>
559                  <Field name="name" type="long-string">                  <Field name="name" type="long-string">
560                      <Notes>Chemical name of this ligand.</Notes>                      <Notes>Chemical name of this ligand.</Notes>
561                  </Field>                  </Field>
562              </Fields>              </Fields>
563          </Entity>          </Entity>
564          <Entity name="CellLocation" keyType="key-string">          <Entity name="CellLocation" keyType="string">
565              <Notes>A section of the cell in which a protein might be found. This includes the cell wall or              <Notes>A section of the cell in which a protein might be found. This includes the cell wall or
566              membrane, outside the cell, inside the cell, and so forth.</Notes>              membrane, outside the cell, inside the cell, and so forth.</Notes>
567          </Entity>          </Entity>
# Line 481  Line 573 
573          </Entity>          </Entity>
574      </Entities>      </Entities>
575      <Relationships>      <Relationships>
576          <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM">          <Relationship name="IsPathogenicIn" from="Genome" to="Host" arity="MM">
577                <Notes>This relationship connects a genome to a host in which it is
578                pathogenic. Many genomes do not have a pathogenic host; some have
579                multiple hosts.</Notes>
580            </Relationship>
581            <Relationship name="IsFamilyForFeature" from="ProteinFamily" to="Feature"
582                          arity="MM" converse="IsInFamily">
583                <Notes>This relationship connects a feature to its protein
584                families.</Notes>
585                <Fields>
586                    <Field name="range" type="string">
587                        <Notes>Location in the feature of the matching protein.</Notes>
588                    </Field>
589                </Fields>
590            </Relationship>
591            <Relationship name="Catalyzes" from="Role" to="Reaction" arity="MM"
592                          converse="IsCatalyzedBy">
593              <DisplayInfo theme="web" />              <DisplayInfo theme="web" />
594              <Notes>This relationship connects a role to the reactions it catalyzes.              <Notes>This relationship connects a role to the reactions it catalyzes.
595              The purpose of a role is to create proteins that trigger certain              The purpose of a role is to create proteins that trigger certain
# Line 608  Line 716 
716              good chance of disabling the protein. At the current time, only the best              good chance of disabling the protein. At the current time, only the best
717              docking results are kept.</Notes>              docking results are kept.</Notes>
718              <Fields>              <Fields>
719                  <Field name="reason" type="id-string">                  <Field name="reason" type="string">
720                      <Notes>Indication of the reason for determining the docking result.                      <Notes>Indication of the reason for determining the docking result.
721                      A value of =Random= indicates the docking was attempted as a part                      A value of =Random= indicates the docking was attempted as a part
722                      of a random survey used to determine the docking characteristics of the                      of a random survey used to determine the docking characteristics of the
# Line 616  Line 724 
724                      a low-energy docking result was predicted for the ligand with respect                      a low-energy docking result was predicted for the ligand with respect
725                      to the PDB.</Notes>                      to the PDB.</Notes>
726                  </Field>                  </Field>
727                  <Field name="tool" type="id-string">                  <Field name="tool" type="string">
728                      <Notes>Name of the tool used to produce the docking result.</Notes>                      <Notes>Name of the tool used to produce the docking result.</Notes>
729                  </Field>                  </Field>
730                  <Field name="total-energy" type="float">                  <Field name="total-energy" type="float">
# Line 649  Line 757 
757              essentially identical features. The name used in the external database is stored              essentially identical features. The name used in the external database is stored
758              in the relationship as intersection data.</Notes>              in the relationship as intersection data.</Notes>
759              <Fields>              <Fields>
760                  <Field name="alias" type="name-string">                  <Field name="alias" type="string">
761                      <Notes>ID of the feature in the specified external database.</Notes>                      <Notes>ID of the feature in the specified external database.</Notes>
762                  </Field>                  </Field>
763              </Fields>              </Fields>
# Line 666  Line 774 
774              <Notes>This relation connects a synonym group to the features that make it              <Notes>This relation connects a synonym group to the features that make it
775              up.</Notes>              up.</Notes>
776          </Relationship>          </Relationship>
777          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M" converse="IsInGenome">
778              <DisplayInfo theme="nmpdr" caption="Has\nFeature" />              <DisplayInfo theme="nmpdr" caption="Has\nFeature" />
779              <Notes>This relationship connects a genome to all of its features. This              <Notes>This relationship connects a genome to all of its features. This
780              relationship is redundant in a sense, because the genome ID is part              relationship is redundant in a sense, because the genome ID is part
# Line 674  Line 782 
782              convenient because you can drag in filtering information for a feature's              convenient because you can drag in filtering information for a feature's
783              genome.</Notes>              genome.</Notes>
784              <Fields>              <Fields>
785                  <Field name="type" type="key-string">                  <Field name="type" type="string">
786                      <Notes>Feature type (eg. peg, rna)</Notes>                      <Notes>Feature type (eg. peg, rna)</Notes>
787                  </Field>                  </Field>
788              </Fields>              </Fields>
# Line 731  Line 839 
839              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
840              connected to the genome features through the *SSCell* object.</Notes>              connected to the genome features through the *SSCell* object.</Notes>
841              <Fields>              <Fields>
842                  <Field name="variant-code" type="key-string">                  <Field name="variant-code" type="string">
843                      <Notes>Code indicating the subsystem variant to which this                      <Notes>Code indicating the subsystem variant to which this
844                      genome belongs. Each subsystem can have multiple variants. A variant                      genome belongs. Each subsystem can have multiple variants. A variant
845                      code of =-1= indicates that the genome does not have a functional                      code of -1 indicates that the genome does not have a functional
846                      variant of the subsystem. A variant code of =0= indicates that                      variant of the subsystem. A variant code of 0 indicates that
847                      the genome's participation is considered iffy.</Notes>                      the genome's participation is considered iffy.</Notes>
848                  </Field>                  </Field>
849              </Fields>              </Fields>
# Line 748  Line 856 
856                  </IndexFields>                  </IndexFields>
857              </ToIndex>              </ToIndex>
858          </Relationship>          </Relationship>
859          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM">          <Relationship name="OccursInSubsystem" from="Role" to="Subsystem" arity="MM" converse="Uses">
860              <DisplayInfo caption="Uses" theme="seed" />              <DisplayInfo caption="Uses" theme="seed" />
861              <Notes>This relationship connects roles to the subsystems that implement them.</Notes>              <Notes>This relationship connects roles to the subsystems that implement them.</Notes>
862              <Fields>              <Fields>
863                  <Field name="abbr" type="name-string">                  <Field name="abbr" type="string">
864                      <Notes>Abbreviated name for the role, generally non-unique, but useful                      <Notes>Abbreviated name for the role, generally non-unique, but useful
865                      in column headings for HTML tables.</Notes>                      in column headings for HTML tables.</Notes>
866                  </Field>                  </Field>
# Line 818  Line 926 
926                      compound left of the arrow and a value of TRUE still puts it to the                      compound left of the arrow and a value of TRUE still puts it to the
927                      right.</Notes>                      right.</Notes>
928                  </Field>                  </Field>
929                  <Field name="stoichiometry" type="key-string">                  <Field name="stoichiometry" type="string">
930                      <Notes>Number of molecules of the compound that participate in a                      <Notes>Number of molecules of the compound that participate in a
931                      single instance of the reaction. For example, if a reaction                      single instance of the reaction. For example, if a reaction
932                      produces two water molecules, the stoichiometry of water for the                      produces two water molecules, the stoichiometry of water for the
# Line 833  Line 941 
941                      case this value would be FALSE for all of the relevant                      case this value would be FALSE for all of the relevant
942                      compounds.</Notes>                      compounds.</Notes>
943                  </Field>                  </Field>
944                  <Field name="loc" type="key-string">                  <Field name="loc" type="string">
945                      <Notes>An optional character string that indicates the relative                      <Notes>An optional character string that indicates the relative
946                      position of this compound in the reaction's chemical formula. The                      position of this compound in the reaction's chemical formula. The
947                      location affects the way the compounds present as we cross the                      location affects the way the compounds present as we cross the
# Line 971  Line 1079 
1079              participates. This is technically redundant information, but it is used              participates. This is technically redundant information, but it is used
1080              so often that it gets its own table for performance reasons.</Notes>              so often that it gets its own table for performance reasons.</Notes>
1081              <Fields>              <Fields>
1082                  <Field name="genome" type="name-string">                  <Field name="genome" type="string">
1083                      <Notes>ID of the genome containing the feature</Notes>                      <Notes>ID of the genome containing the feature</Notes>
1084                  </Field>                  </Field>
1085                  <Field name="type" type="key-string">                  <Field name="type" type="string">
1086                      <Notes>Feature type (eg. peg, rna)</Notes>                      <Notes>Feature type (eg. peg, rna)</Notes>
1087                  </Field>                  </Field>
1088              </Fields>              </Fields>
# Line 1003  Line 1111 
1111          </Shape>          </Shape>
1112          <Shape type="arrow" name="WebServices" from="Sims" to="Feature">          <Shape type="arrow" name="WebServices" from="Sims" to="Feature">
1113              <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />              <DisplayInfo caption=" " theme="nmpdr" col="2.5" row="4" />
1114                <Notes>HTTP services are used to transmit data between the servers and the
1115                NMPDR.</Notes>
1116          </Shape>          </Shape>
1117      </Shapes>      </Shapes>
1118  </Database>  </Database>

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