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revision 1.25, Sat May 27 02:02:47 2006 UTC revision 1.44, Sat Oct 21 06:43:10 2006 UTC
# Line 36  Line 36 
36                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),                      <DataGen pass="2">join('; ', (RandParam('bacteria', 'archaea', 'eukaryote', 'virus', 'environmental'),
37                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>                                                    ListGen('PKVKVKVK', 5), $this->{genus}, $this->{species}))</DataGen>
38                  </Field>                  </Field>
39                    <Field name="primary-group" type="name-string">
40                        <Notes>The primary NMPDR group for this organism. There is always exactly one NMPDR group
41                        (either based on the organism name or the default value "Supporting"), whereas there can be
42                        multiple named groups or even none.</Notes>
43                    </Field>
44                  <Field name="group-name" type="name-string" relation="GenomeGroups">                  <Field name="group-name" type="name-string" relation="GenomeGroups">
45                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular                      <Notes>The group identifies a special grouping of organisms that would be displayed on a particular
46                      page or of particular interest to a research group or web site. A single genome can belong to multiple                      page or of particular interest to a research group or web site. A single genome can belong to multiple
# Line 43  Line 48 
48                  </Field>                  </Field>
49              </Fields>              </Fields>
50              <Indexes>              <Indexes>
51                  <Index>                  <Index Unique="false">
52                      <Notes>This index allows the applications to find all genomes associated with                      <Notes>This index allows the applications to find all genomes associated with
53                      a specific access code, so that a complete list of the genomes users can view                      a specific access code, so that a complete list of the genomes users can view
54                      may be generated.</Notes>                      may be generated.</Notes>
# Line 55  Line 60 
60                      </IndexFields>                      </IndexFields>
61                  </Index>                  </Index>
62                  <Index Unique="false">                  <Index Unique="false">
63                        <Notes>This index allows the applications to find all genomes associated with
64                        a specific primary (NMPDR) group.</Notes>
65                        <IndexFields>
66                            <IndexField name="primary-group" order="ascending" />
67                            <IndexField name="genus" order="ascending" />
68                            <IndexField name="species" order="ascending" />
69                            <IndexField name="unique-characterization" order="ascending" />
70                        </IndexFields>
71                    </Index>
72                    <Index Unique="false">
73                      <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
74                      species.</Notes>                      species.</Notes>
75                      <IndexFields>                      <IndexFields>
# Line 137  Line 152 
152                      the feature's initial residues.</Notes>                      the feature's initial residues.</Notes>
153                      <DataGen testCount="0"></DataGen>                      <DataGen testCount="0"></DataGen>
154                  </Field>                  </Field>
155                    <Field name="assignment" type="text">
156                        <Notes>Default functional assignment for this feature.</Notes>
157                    </Field>
158                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
159                      <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>
160                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
161                  </Field>                  </Field>
162                    <Field name="keywords" type="text" searchable="1">
163                        <Notes>This is a list of search keywords for the feature. It includes the
164                        functional assignment, subsystem roles, and special properties.</Notes>
165                    </Field>
166                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
167                      <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
168                      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
# Line 148  Line 170 
170                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .                      <DataGen testCount="3">'http://www.conservativecat.com/Ferdy/TestTarget.php?Source=' . $this->{id} .
171                      "&amp;Number=" . IntGen(1,99)</DataGen>                      "&amp;Number=" . IntGen(1,99)</DataGen>
172                  </Field>                  </Field>
173                    <Field name="conservation" type="float" relation="FeatureConservation">
174                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
175                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
176                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
177                        between the feature and its close relatives.</Notes>
178                    </Field>
179              </Fields>              </Fields>
180              <Indexes>              <Indexes>
181                  <Index>                  <Index>
# Line 159  Line 187 
187                  </Index>                  </Index>
188              </Indexes>              </Indexes>
189          </Entity>          </Entity>
190            <Entity name="SynonymGroup" keyType="id-string">
191                <Notes>A [i]synonym group[/i] represents a group of features. Substantially identical features
192                are mapped to the same synonym group, and this information is used to expand similarities.</Notes>
193            </Entity>
194          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
195              <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.
196              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>
# Line 194  Line 226 
226                      <Notes>Text of the annotation.</Notes>                      <Notes>Text of the annotation.</Notes>
227                  </Field>                  </Field>
228              </Fields>              </Fields>
229                <Indexes>
230                    <Index>
231                        <Notes>This index allows the user to find recent annotations.</Notes>
232                        <IndexFields>
233                            <IndexField name="time" order="descending" />
234                        </IndexFields>
235                    </Index>
236                </Indexes>
237          </Entity>          </Entity>
238          <Entity name="Reaction" keyType="key-string">          <Entity name="Reaction" keyType="key-string">
239              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID              <Notes>A [i]reaction[/i] is a chemical process catalyzed by a protein. The reaction ID
# Line 264  Line 304 
304                  <Field name="notes" type="text">                  <Field name="notes" type="text">
305                      <Notes>Descriptive notes about the subsystem.</Notes>                      <Notes>Descriptive notes about the subsystem.</Notes>
306                  </Field>                  </Field>
307                    <Field name="classification" type="string" relation="SubsystemClass">
308                        <Notes>Classification string, colon-delimited. This string organizes the
309                        subsystems into a hierarchy.</Notes>
310                    </Field>
311              </Fields>              </Fields>
312          </Entity>          </Entity>
313          <Entity name="RoleSubset" keyType="string">          <Entity name="RoleSubset" keyType="string">
# Line 358  Line 402 
402                      </Field>                      </Field>
403                  </Fields>                  </Fields>
404          </Entity>          </Entity>
405          <Entity name="Coupling" keyType="hash-string">          <Entity name="Coupling" keyType="id-string">
406              <Notes>A coupling is a relationship between two features. The features are              <Notes>A coupling is a relationship between two features. The features are
407              physically close on the contig, and there is evidence that they generally              physically close on the contig, and there is evidence that they generally
408              belong together. The key of this entity is formed by combining the coupled              belong together. The key of this entity is formed by combining the coupled
# Line 374  Line 418 
418                  </Field>                  </Field>
419              </Fields>              </Fields>
420          </Entity>          </Entity>
421          <Entity name="PCH" keyType="hash-string">          <Entity name="PCH" keyType="counter">
422              <Notes>A PCH (physically close homolog) connects a clustering (which is a              <Notes>A PCH (physically close homolog) connects a clustering (which is a
423              pair of physically close features on a contig) to a second pair of physically              pair of physically close features on a contig) to a second pair of physically
424              close features that are similar to the first. Essentially, the PCH is a              close features that are similar to the first. Essentially, the PCH is a
# Line 382  Line 426 
426              are similar to the second clustering's features. The simplest model for              are similar to the second clustering's features. The simplest model for
427              this would be to simply relate clusterings to each other; however, not all              this would be to simply relate clusterings to each other; however, not all
428              physically close pairs qualify as clusterings, so we relate a clustering to              physically close pairs qualify as clusterings, so we relate a clustering to
429              a pair of features. The key is the clustering key followed by the IDs              a pair of features. The key a unique ID number.</Notes>
             of the features in the second pair.</Notes>  
430              <Fields>              <Fields>
431                  <Field name="used" type="boolean">                  <Field name="used" type="boolean">
432                      <Notes>TRUE if this PCH is used in scoring the attached clustering,                      <Notes>TRUE if this PCH is used in scoring the attached clustering,
# Line 394  Line 437 
437                  </Field>                  </Field>
438              </Fields>              </Fields>
439          </Entity>          </Entity>
440            <Entity name="Family" keyType="id-string">
441                <Notes>A family is a group of homologous PEGs believed to have the same function. Protein
442                families provide a mechanism for verifying the accuracy of functional assignments
443                and are also used in determining phylogenetic trees.</Notes>
444                <Fields>
445                    <Field name="function" type="text">
446                        <Notes>The functional assignment expected for all PEGs in this family.</Notes>
447                    </Field>
448                    <Field name="size" type="int">
449                        <Notes>The number of proteins in this family. This may be larger than the
450                        number of PEGs included in the family, since the family may also contain external
451                        IDs.</Notes>
452                    </Field>
453                </Fields>
454            </Entity>
455            <Entity name="DrugProject" keyType="name-string">
456                <Notes>A drug project is a coherent sent of drug target data that came through the
457                pipeline. In other words, data is put into the database one drug project at a time.
458                This makes it easier to manage the incoming data and to track where a particular
459                piece of data originated.</Notes>
460            </Entity>
461            <Entity name="DrugTopic" keyType="int">
462                <Notes>A drug topic organizes the data in a project relating to a single organism
463                group's features as they apply to a specific category of activity. Categories include
464                features essential to the organism's survival, those that are targets or inhibitors
465                of anti-biotics, and those associated with virulence. Thus, a drug topic consists
466                of data from a single project for features that make good drug targets for the same
467                reason. Drug topics have an artificial, internally-generated key.</Notes>
468                <Fields>
469                    <Field name="identifier" type="name-string">
470                        <Notes>The topic identifier, consisting usually of a generalized organism name
471                        (e.g. Staphylococcus) and the last name of the project's author. More than
472                        one topic may have the same identifier, which is why this isn't the key.</Notes>
473                    </Field>
474                    <Field name="tag" type="name-string">
475                        <Notes>A short phrase describing the topic.</Notes>
476                    </Field>
477                    <Field name="URL" type="string">
478                        <Notes>A URL for the paper from which the topic was gathered.</Notes>
479                    </Field>
480                    <Field name="category" type="key-string">
481                        <Notes>The code for this topic's activity category.</Notes>
482                    </Field>
483                </Fields>
484                <Indexes>
485                    <Index>
486                        <Notes>This index enables the application to find all topics with a specified
487                        category, ordered by tag.</Notes>
488                        <IndexFields>
489                            <IndexField name="category" order="ascending" />
490                            <IndexField name="tag" order="ascending" />
491                        </IndexFields>
492                    </Index>
493                    <Index>
494                        <Notes>This index enables the application to find all topics with a specified
495                        identifier, ordered by category.</Notes>
496                        <IndexFields>
497                            <IndexField name="identifier" order="ascending" />
498                            <IndexField name="category" order="ascending" />
499                        </IndexFields>
500                    </Index>
501                </Indexes>
502            </Entity>
503            <Entity name="PDB" keyType="key-string">
504                <Notes>A PDB is a database of protein structure and related information of use
505                in drug targeting. The purpose of drug targeting is to analyze the ability
506                of drug molecules, or ligands, to bond to proteins. A PDB for a protein already
507                attached to a ligand is called a bound PDB. A PDB for the protein by itself is
508                called a free PDB. The key of the PDB is its code name on the Protein Data
509                Bank web site.</Notes>
510                <Fields>
511                    <Field name="type" type="id-string">
512                        <Notes>The type of PDB: "bound" or "free".</Notes>
513                    </Field>
514                    <Field name="title" type="string">
515                        <Notes>The descriptive title of this PDB.</Notes>
516                    </Field>
517                </Fields>
518            </Entity>
519            <Entity name="Ligand" keyType="string">
520                <Notes>A ligand is a molecule that can bind to a PDB. The CLIBE analysis
521                for a PDB is an attribute of the relationship between a PDB and a ligand.</Notes>
522            </Entity>
523      </Entities>      </Entities>
524      <Relationships>      <Relationships>
525            <Relationship name="BindsWith" from="PDB" to="Ligand" arity="MM">
526                <Notes>This relationship describes the energy required for a ligand to bind
527                to the protein described by a PDB. The total energy required to bind
528                the ligand to the protein is described in this relationship by four
529                quantities. A negative value is energy released; a positive value is
530                energy required.</Notes>
531                <Fields>
532                    <Field name="URL" type="string">
533                        <Notes>URL for viewing the CLIBE data for this binding relationship.</Notes>
534                    </Field>
535                    <Field name="vanderwaals-energy" type="float">
536                        <Notes>kCal/mol of energy due to Van der Waals force.</Notes>
537                    </Field>
538                    <Field name="hbond-energy" type="float">
539                        <Notes>kCal/mol of energy due to hydrogen bonding.</Notes>
540                    </Field>
541                    <Field name="ionic-energy" type="float">
542                        <Notes>kCal/mol of energy due to ionic bonding.</Notes>
543                    </Field>
544                    <Field name="solvation-energy" type="float">
545                        <Notes>kCal/mol of energy due to attraction to the solvent in which
546                        the ligand is immersed.</Notes>
547                    </Field>
548                </Fields>
549            </Relationship>
550            <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="1M">
551                <Notes>This relationship describes the analysis of a free PDB as produced from a
552                particular topic.</Notes>
553                <Fields>
554                    <Field name="pass-asp-info" type="int">
555                        <Notes>The number of Active Site Points at which ligands can bind to
556                        the protein.</Notes>
557                    </Field>
558                    <Field name="ramsol-file" type="string">
559                        <Notes>The URL of a file that can be downloaded by the user and
560                        passed to the Ramsol program for viewing the protein.</Notes>
561                    </Field>
562                    <Field name="pass-weight" type="float">
563                        <Notes>A score for the largest pocket into which a ligand can bind. A
564                        higher score makes for a better target.</Notes>
565                    </Field>
566                    <Field name="pass-file" type="string">
567                        <Notes>The URL for a GIF file that shows the active sites on the protein.</Notes>
568                    </Field>
569                </Fields>
570            </Relationship>
571            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="1M">
572                <Note>This relationship connects a free PDB to its bound counterparts.</Note>
573            </Relationship>
574            <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
575                <Notes>This relationship connects a feature to a protein database (PDB) that
576                is relevant for determining drugs that target the feature.</Notes>
577                <Fields>
578                    <Field name="score" type="float">
579                        <Notes>The BLAST score for the feature as it relates to the PDB's
580                        protein, expressed as a small positive number. Generally only a
581                        very low BLAST score (1e-15 or less) indicates a good match.</Notes>
582                    </Field>
583                    <Field name="distance" type="float">
584                        <Notes>A distance value indicating how far the PDB's protein is
585                        from the feature's protein. A distance of 0 indicates a perfect
586                        match.</Notes>
587                    </Field>
588                </Fields>
589                <FromIndex>
590                    <Notes>This index yields the Features for a PDB in order from best
591                    score to worst.</Notes>
592                    <IndexFields>
593                        <IndexField name="score" order="ascending" />
594                    </IndexFields>
595                </FromIndex>
596                <ToIndex>
597                    <Notes>This index yields the Features for a PDB in order from best
598                    score to worst.</Notes>
599                    <IndexFields>
600                        <IndexField name="score" order="ascending" />
601                    </IndexFields>
602                </ToIndex>
603            </Relationship>
604            <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">
605                <Notes>This relationship connects a drug target project to all of its
606                topics.</Notes>
607            </Relationship>
608            <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
609                <Notes>This relationship connects a protein family to all of its PEGs and connects
610                each PEG to all of its protein families.</Notes>
611            </Relationship>
612          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">          <Relationship name="ParticipatesInCoupling" from="Feature" to="Coupling" arity="MM">
613              <Notes>This relationship connects a feature to all the functional couplings              <Notes>This relationship connects a feature to all the functional couplings
614              in which it participates. A functional coupling is a recognition of the fact              in which it participates. A functional coupling is a recognition of the fact
# Line 416  Line 629 
629                  </IndexFields>                  </IndexFields>
630              </ToIndex>              </ToIndex>
631          </Relationship>          </Relationship>
632            <Relationship name="IsSynonymGroupFor" from="SynonymGroup" to="Feature" arity="1M">
633                <Notes>This relation connects a synonym group to the features that make it
634                up.</Notes>
635            </Relationship>
636          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">          <Relationship name="HasFeature" from="Genome" to="Feature" arity="1M">
637              <Notes>This relationship connects a genome to all of its features. This              <Notes>This relationship connects a genome to all of its features. This
638              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 427  Line 644 
644                      <Notes>Feature type (eg. peg, rna)</Notes>                      <Notes>Feature type (eg. peg, rna)</Notes>
645                  </Field>                  </Field>
646              </Fields>              </Fields>
647              <ToIndex>              <FromIndex>
648                  <Notes>This index enables the application to view the features of a                  <Notes>This index enables the application to view the features of a
649                  Genome sorted by type.</Notes>                  Genome sorted by type.</Notes>
650                  <IndexFields>                  <IndexFields>
651                      <IndexField name="type" order="ascending" />                      <IndexField name="type" order="ascending" />
652                  </IndexFields>                  </IndexFields>
653              </ToIndex>              </FromIndex>
654          </Relationship>          </Relationship>
655          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">          <Relationship name="IsEvidencedBy" from="Coupling" to="PCH" arity="1M">
656              <Notes>This relationship connects a functional coupling to the physically              <Notes>This relationship connects a functional coupling to the physically
# Line 660  Line 877 
877                  </IndexFields>                  </IndexFields>
878              </ToIndex>              </ToIndex>
879          </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>  
880          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">          <Relationship name="HasProperty" from="Feature" to="Property" arity="MM">
881              <Notes>This relationship connects a feature to its known property values.              <Notes>This relationship connects a feature to its known property values.
882              The relationship contains text data that indicates the paper or organization              The relationship contains text data that indicates the paper or organization
# Line 747  Line 942 
942              chemical reactions. A single reaction can be triggered by many roles,              chemical reactions. A single reaction can be triggered by many roles,
943              and a role can trigger many reactions.</Notes>              and a role can trigger many reactions.</Notes>
944          </Relationship>          </Relationship>
945            <Relationship name="HasRoleInSubsystem" from="Feature" to="Subsystem" arity="MM">
946                <Notes>This relationship connects a feature to the subsystems in which it
947                participates. This is technically redundant information, but it is used
948                so often that it deserves its own table.</Notes>
949                <Fields>
950                    <Field name="genome" type="name-string">
951                        <Notes>ID of the genome containing the feature</Notes>
952                    </Field>
953                    <Field name="type" type="key-string">
954                        <Notes>Feature type (eg. peg, rna)</Notes>
955                    </Field>
956                </Fields>
957                <ToIndex>
958                    <Notes>This index enables the application to view the features of a
959                    subsystem sorted by genome and feature type.</Notes>
960                    <IndexFields>
961                        <IndexField name="genome" order="ascending" />
962                        <IndexField name="type" order="ascending" />
963                    </IndexFields>
964                </ToIndex>
965            </Relationship>
966      </Relationships>      </Relationships>
967  </Database>  </Database>

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