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revision 1.49, Fri May 11 06:37:38 2007 UTC revision 1.50, Mon Jul 16 19:59:33 2007 UTC
# Line 42  Line 42 
42                      (either based on the organism name or the default value "Supporting"), whereas there can be                      (either based on the organism name or the default value "Supporting"), whereas there can be
43                      multiple named groups or even none.</Notes>                      multiple named groups or even none.</Notes>
44                  </Field>                  </Field>
                 <Field name="group-name" type="name-string" relation="GenomeGroups">  
                     <Notes>The group identifies a special grouping of organisms that would be displayed on a particular  
                     page or of particular interest to a research group or web site. A single genome can belong to multiple  
                     such groups or none at all.</Notes>  
                 </Field>  
45              </Fields>              </Fields>
46              <Indexes>              <Indexes>
47                  <Index>                  <Index>
# Line 81  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>
# Line 129  Line 129 
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>
134                  </Field>                  </Field>
                 <Field name="alias" type="medium-string" relation="FeatureAlias">  
                     <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>  
                 </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
# Line 170  Line 167 
167                  <Field name="conservation" type="float" relation="FeatureConservation">                  <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                      <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                      conserved in related genomes. A value of 1 indicates perfect conservation. A value less
170                      than 1 is a reflect of the degree to which gap characters interfere in the alignment                      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>                      between the feature and its close relatives.</Notes>
172                  </Field>                  </Field>
173                  <Field name="essential" type="text" relation="FeatureEssential" special="property_search">                  <Field name="essential" type="text" relation="FeatureEssential" special="property_search">
# Line 186  Line 183 
183                      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
184                      will have no values; otherwise, it may have multiple values.</Notes>                      will have no values; otherwise, it may have multiple values.</Notes>
185                  </Field>                  </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">                  <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                      <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,                      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                      this field will have no values. Otherwise, it will have an epitope name and/or
194                      sequence, hyperlinked to the database.</Notes>                      sequence, hyperlinked to the database.</Notes>
195                  </Field>                  </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>
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">          <Entity name="SynonymGroup" keyType="id-string">
218              <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features              <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>              are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
# Line 210  Line 221 
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="EC" type="string" relation="RoleEC">          <Entity name="RoleEC" keyType="string">
226                      <Notes>EC code for this role.</Notes>              <Notes>EC code for a role.</Notes>
                 </Field>  
                 <Field name="abbr" type="name-string">  
                     <Notes>Abbreviated name for the role, generally non-unique, but useful  
                     in column headings for HTML tables.</Notes>  
                 </Field>  
             </Fields>  
             <Indexes>  
                 <Index>  
                     <Notes>This index allows the user to find the role corresponding to  
                     an EC number.</Notes>  
                     <IndexFields>  
                         <IndexField name="EC" order="ascending" />  
                     </IndexFields>  
                 </Index>  
             </Indexes>  
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
# Line 267  Line 263 
263              <Notes>A [i]compound[/i] is a chemical that participates in a reaction.              <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>              All compounds have a unique ID and may also have one or more names.</Notes>
265              <Fields>              <Fields>
266                  <Field name="name-priority" type="int" relation="CompoundName">                  <Field name="label" type="string">
                     <Notes>Priority of a compound name. The name with the loweset  
                     priority is the main name of this compound.</Notes>  
                 </Field>  
                 <Field name="name" type="name-string" relation="CompoundName">  
                     <Notes>Descriptive name for the compound. A compound may  
                     have several names.</Notes>  
                 </Field>  
                 <Field name="cas-id" type="name-string" relation="CompoundCAS">  
                     <Notes>Chemical Abstract Service ID for this compound (optional).</Notes>  
                 </Field>  
                 <Field name="label" type="name-string">  
267                      <Notes>Name used in reaction display strings.                      <Notes>Name used in reaction display strings.
268                      It is the same as the name possessing a priority of 1, but it is placed                      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>                      here to speed up the query used to create the display strings.</Notes>
270                  </Field>                  </Field>
271              </Fields>              </Fields>
272              <Indexes>          </Entity>
273                  <Index>          <Entity name="CompoundName" keyType="string">
274                      <Notes>This index allows the user to find the compound corresponding to              <Notes>A [i]compound name[/i] is a common name for the chemical represented by a
275                      the specified name.</Notes>              compound.</Notes>
276                      <IndexFields>          </Entity>
277                          <IndexField name="name" order="ascending" />          <Entity name="CompoundCAS" keyType="name-string">
278                      </IndexFields>              <Notes>This entity represents the Chemical Abstract Service ID for a compound. Each
279                  </Index>              Compound has at most one CAS ID.</Notes>
                 <Index>  
                     <Notes>This index allows the user to find the compound corresponding to  
                     the specified CAS ID.</Notes>  
                     <IndexFields>  
                         <IndexField name="cas-id" order="ascending" />  
                     </IndexFields>  
                 </Index>  
                 <Index>  
                     <Notes>This index allows the user to access the compound names in  
                     priority order.</Notes>  
                     <IndexFields>  
                         <IndexField name="id" order="ascending" />  
                         <IndexField name="name-priority" order="ascending" />  
                     </IndexFields>  
                 </Index>  
             </Indexes>  
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
# Line 416  Line 385 
385                      </Field>                      </Field>
386                  </Fields>                  </Fields>
387          </Entity>          </Entity>
         <Entity name="Coupling" keyType="id-string">  
             <Notes>A coupling is a relationship between two features. The features are  
             physically close on the contig, and there is evidence that they generally  
             belong together. The key of this entity is formed by combining the coupled  
             feature IDs with a space.</Notes>  
             <Fields>  
                 <Field name="score" type="int">  
                     <Notes>A number based on the set of PCHs (pairs of close homologs). A PCH  
                     indicates that two genes near each other on one genome are very similar to  
                     genes near each other on another genome. The score only counts PCHs for which  
                     the genomes are very different. (In other words, we have a pairing that persists  
                     between different organisms.) A higher score implies a stronger meaning to the  
                     clustering.</Notes>  
                 </Field>  
             </Fields>  
         </Entity>  
         <Entity name="PCH" keyType="counter">  
             <Notes>A PCH (physically close homolog) connects a clustering (which is a  
             pair of physically close features on a contig) to a second pair of physically  
             close features that are similar to the first. Essentially, the PCH is a  
             relationship between two clusterings in which the first clustering's features  
             are similar to the second clustering's features. The simplest model for  
             this would be to simply relate clusterings to each other; however, not all  
             physically close pairs qualify as clusterings, so we relate a clustering to  
             a pair of features. The key a unique ID number.</Notes>  
             <Fields>  
                 <Field name="used" type="boolean">  
                     <Notes>TRUE if this PCH is used in scoring the attached clustering,  
                     else FALSE. If a clustering has a PCH for a particular genome and many  
                     similar genomes are present, then a PCH will probably exist for the  
                     similar genomes as well. When this happens, only one of the PCHs will  
                     be scored: the others are considered duplicates of the same evidence.</Notes>  
                 </Field>  
             </Fields>  
         </Entity>  
388          <Entity name="Family" keyType="id-string">          <Entity name="Family" keyType="id-string">
389              <Notes>A family is a group of homologous PEGs believed to have the same function. Protein              <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
390              families provide a mechanism for verifying the accuracy of functional assignments              families provide a mechanism for verifying the accuracy of functional assignments
# Line 495  Line 429 
429          </Entity>          </Entity>
430      </Entities>      </Entities>
431      <Relationships>      <Relationships>
432            <Relationship name="IsPresentOnProteinOf" from="CDD" to="Feature" arity="MM">
433                <Notes>This relationship connects a feature to its CDD protein domains. The
434                match score is included as intersection data.</Notes>
435                <Fields>
436                    <Field name="score" type="float">
437                        <Notes>This is the match score between the feature and the CDD. A
438                        lower score is a better match.</Notes>
439                    </Field>
440                </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">          <Relationship name="IsProteinForFeature" from="PDB" to="Feature" arity="MM">
478              <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>              <Notes>Relates a PDB to features that produce highly similar proteins.</Notes>
479              <Fields>              <Fields>
# Line 573  Line 552 
552              <Notes>This relationship connects a protein family to all of its PEGs and connects              <Notes>This relationship connects a protein family to all of its PEGs and connects
553              each PEG to all of its protein families.</Notes>              each PEG to all of its protein families.</Notes>
554          </Relationship>          </Relationship>
555          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="MM">
             <Notes>This relationship connects a feature to all the functional couplings  
             in which it participates. A functional coupling is a recognition of the fact  
             that the features are close to each other on a chromosome, and similar  
             features in other genomes also tend to be close.</Notes>  
             <Fields>  
                 <Field name="pos" type="int">  
                     <Notes>Ordinal position of the feature in the coupling. Currently,  
                     this is either "1" or "2".</Notes>  
                 </Field>  
             </Fields>  
             <ToIndex>  
                 <Notes>This index enables the application to view the features of  
                 a coupling in the proper order. The order influences the way the  
                 PCHs are examined.</Notes>  
                 <IndexFields>  
                     <IndexField name="pos" order="ascending" />  
                 </IndexFields>  
             </ToIndex>  
         </Relationship>  
         <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">  
556              <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
557              up.</Notes>              up.</Notes>
558          </Relationship>          </Relationship>
# Line 616  Line 575 
575                  </IndexFields>                  </IndexFields>
576              </FromIndex>              </FromIndex>
577          </Relationship>          </Relationship>
         <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">  
             <Notes>This relationship connects a functional coupling to the physically  
             close homologs (PCHs) which affirm that the coupling is meaningful.</Notes>  
         </Relationship>  
         <Relationship name="UsesAsEvidence" from="PCH" to="Feature" arity="MM">  
             <Notes>This relationship connects a PCH to the features that represent its  
             evidence. Each PCH is connected to a parent coupling that relates two features  
             on a specific genome. The PCH's evidence that the parent coupling is functional  
             is the existence of two physically close features on a different genome that  
             correspond to the features in the coupling. Those features are found on the  
             far side of this relationship.</Notes>  
             <Fields>  
                 <Field name="pos" type="int">  
                     <Notes>Ordinal position of the feature in the coupling that corresponds  
                     to our target feature. There is a one-to-one correspondence between the  
                     features connected to the PCH by this relationship and the features  
                     connected to the PCH's parent coupling. The ordinal position is used  
                     to decode that relationship. Currently, this field is either "1" or  
                     "2".</Notes>  
                 </Field>  
             </Fields>  
             <FromIndex>  
                 <Notes>This index enables the application to view the features of  
                 a PCH in the proper order.</Notes>  
                 <IndexFields>  
                     <IndexField name="pos" order="ascending" />  
                 </IndexFields>  
             </FromIndex>  
         </Relationship>  
578          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">          <Relationship name="HasContig" from="Genome" to="Contig" arity="1M">
579              <Notes>This relationship connects a genome to the contigs that contain the actual genetic              <Notes>This relationship connects a genome to the contigs that contain the actual genetic
580              information.</Notes>              information.</Notes>
# Line 707  Line 637 
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>              <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">                  <Field name="column-number" type="int">
645                      <Notes>Column number for this role in the specified subsystem's                      <Notes>Column number for this role in the specified subsystem's
646                      spreadsheet.</Notes>                      spreadsheet.</Notes>

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