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revision 1.40, Wed Sep 27 12:58:18 2006 UTC revision 1.41, Fri Oct 13 21:46:45 2006 UTC
# Line 156  Line 156 
156                      <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>
157                      <DataGen>1</DataGen>                      <DataGen>1</DataGen>
158                  </Field>                  </Field>
159                  <Field name="assignment" type="text">                  <Field name="keywords" type="text" searchable="1">
160                      <Notes>This is the primary functional assignment for the feature.</Notes>                      <Notes>This is a list of search keywords for the feature. It includes the
161                        functional assignment, subsystem roles, and special properties.</Notes>
162                  </Field>                  </Field>
163                  <Field name="link" type="text" relation="FeatureLink">                  <Field name="link" type="text" relation="FeatureLink">
164                      <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
# Line 166  Line 167 
167                      <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} .
168                      "&amp;Number=" . IntGen(1,99)</DataGen>                      "&amp;Number=" . IntGen(1,99)</DataGen>
169                  </Field>                  </Field>
170                    <Field name="conservation" type="float" relation="FeatureConservation">
171                        <Notes>A number between 0 and 1 that indicates the degree to which this feature's DNA is
172                        conserved in related genomes. A value of 1 indicates perfect conservation. A value less
173                        than 1 is a reflect of the degree to which gap characters interfere in the alignment
174                        between the feature and its close relatives.</Notes>
175                    </Field>
176              </Fields>              </Fields>
177              <Indexes>              <Indexes>
178                  <Index>                  <Index>
# Line 441  Line 448 
448                  </Field>                  </Field>
449              </Fields>              </Fields>
450          </Entity>          </Entity>
451            <Entity name="DrugProject" keyType="name-string">
452                <Notes>A drug project is a coherent sent of drug target data that came through the
453                pipeline. In other words, data is put into the database one drug project at a time.
454                This makes it easier to manage the incoming data and to track where a particular
455                piece of data originated.</Notes>
456            </Entity>
457            <Entity name="DrugTopic" keyType="int">
458                <Notes>A drug topic organizes the data in a project relating to a single organism
459                group's features as they apply to a specific category of activity. Categories include
460                features essential to the organism's survival, those that are targets or inhibitors
461                of anti-biotics, and those associated with virulence. Thus, a drug topic consists
462                of data from a single project for features that make good drug targets for the same
463                reason. Drug topics have an artificial, internally-generated key.</Notes>
464                <Fields>
465                    <Field name="identifier" type="name-string">
466                        <Notes>The topic identifier, consisting usually of a generalized organism name
467                        (e.g. Staphylococcus) and the last name of the project's author. More than
468                        one topic may have the same identifier, which is why this isn't the key.</Notes>
469                    </Field>
470                    <Field name="function" type="name-string">
471                        <Notes>A short phrase describing the topic.</Notes>
472                    </Field>
473                    <Field name="URL" type="string">
474                        <Notes>A URL for the paper from which the topic was gathered.</Notes>
475                    </Field>
476                    <Field name="category" type="key-string">
477                        <Notes>The code for this topic's activity category.</Notes>
478                    </Field>
479                </Fields>
480                <Indexes>
481                    <Index>
482                        <Notes>This index enables the application to find all topics with a specified
483                        category, ordered by function.</Notes>
484                        <IndexFields>
485                            <IndexField name="category" order="ascending" />
486                            <IndexField name="function" order="ascending" />
487                        </IndexFields>
488                    </Index>
489                    <Index>
490                        <Notes>This index enables the application to find all topics with a specified
491                        identifier, ordered by category.</Notes>
492                        <IndexFields>
493                            <IndexField name="identifier" order="ascending" />
494                            <IndexField name="category" order="ascending" />
495                        </IndexFields>
496                    </Index>
497                </Indexes>
498            </Entity>
499            <Entity name="PDB" keyType="key-string">
500                <Notes>A PDB is a database of protein structure and related information of use
501                in drug targeting. The purpose of drug targeting is to analyze the ability
502                of drug molecules, or ligands, to bond to proteins. A PDB for a protein already
503                attached to a ligand is called a bound PDB. A PDB for the protein by itself is
504                called a free PDB. The key of the PDB is its code name on the Protein Data
505                Bank web site.</Notes>
506                <Fields>
507                    <Field name="type" type="id-string">
508                        <Notes>The type of PDB: "bound" or "free".</Notes>
509                    </Field>
510                    <Field name="title" type="string">
511                        <Notes>The descriptive title of this PDB.</Notes>
512                    </Field>
513                </Fields>
514            </Entity>
515            <Entity name="Ligand" keyType="string">
516                <Notes>A ligand is a molecule that can bind to a PDB. The CLIBE analysis
517                for a PDB is an attribute of the relationship between a PDB and a ligand.</Notes>
518            </Entity>
519      </Entities>      </Entities>
520      <Relationships>      <Relationships>
521            <Relationship name="BindsWith" from="PDB" to="Ligand" arity="MM">
522                <Notes>This relationship describes the energy required for a ligand to bind
523                to the protein described by a PDB. The total energy required to bind
524                the ligand to the protein is described in this relationship by four
525                quantities. A negative value is energy released; a positive value is
526                energy required.</Notes>
527                <Fields>
528                    <Field name="URL" type="string">
529                        <Notes>URL for viewing the CLIBE data for this binding relationship.</Notes>
530                    </Field>
531                    <Field name="vanderwaals-energy" type="float">
532                        <Notes>kCal/mol of energy due to Van der Waals force.</Notes>
533                    </Field>
534                    <Field name="hbond-energy" type="float">
535                        <Notes>kCal/mol of energy due to hydrogen bonding.</Notes>
536                    </Field>
537                    <Field name="ionic-energy" type="float">
538                        <Notes>kCal/mol of energy due to ionic bonding.</Notes>
539                    </Field>
540                    <Field name="solvation-energy" type="float">
541                        <Notes>kCal/mol of energy due to attraction to the solvent in which
542                        the ligand is immersed.</Notes>
543                    </Field>
544                </Fields>
545            </Relationship>
546            <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="1M">
547                <Notes>This relationship describes the analysis of a free PDB as produced from a
548                particular topic.</Notes>
549                <Fields>
550                    <Field name="pass-asp-info" type="int">
551                        <Notes>The number of Active Site Points at which ligands can bind to
552                        the protein.</Notes>
553                    </Field>
554                    <Field name="ramsol-file" type="string">
555                        <Notes>The URL of a file that can be downloaded by the user and
556                        passed to the Ramsol program for viewing the protein.</Notes>
557                    </Field>
558                    <Field name="pass-weight" type="float">
559                        <Notes>A score for the largest pocket into which a ligand can bind. A
560                        higher score makes for a better target.</Notes>
561                    </Field>
562                    <Field name="pass-file" type="string">
563                        <Notes>The URL for a GIF file that shows the active sites on the protein.</Notes>
564                    </Field>
565                </Fields>
566            </Relationship>
567            <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="1M">
568                <Note>This relationship connects a free PDB to its bound counterparts.</Note>
569            </Relationship>
570            <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">
571                <Notes>This relationship connects a feature to a protein database (PDB) that
572                is relevant for determining drugs that target the feature.</Notes>
573                <Fields>
574                    <Field name="score" type="float">
575                        <Notes>The BLAST score for the feature as it relates to the PDB's
576                        protein, expressed as a small positive number. Generally only a
577                        very low BLAST score (1e-15 or less) indicates a good match.</Notes>
578                    </Field>
579                    <Field name="distance" type="float">
580                        <Notes>A distance value indicating how far the PDB's protein is
581                        from the feature's protein. A distance of 0 indicates a perfect
582                        match.</Notes>
583                    </Field>
584                </Fields>
585                <FromIndex>
586                    <Notes>This index yields the Features for a PDB in order from best
587                    score to worst.</Notes>
588                    <IndexFields>
589                        <IndexField name="score" order="ascending" />
590                    </IndexFields>
591                </FromIndex>
592                <ToIndex>
593                    <Notes>This index yields the Features for a PDB in order from best
594                    score to worst.</Notes>
595                    <IndexFields>
596                        <IndexField name="score" order="ascending" />
597                    </IndexFields>
598                </ToIndex>
599            </Relationship>
600            <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">
601                <Notes>This relationship connects a drug target project to all of its
602                topics.</Notes>
603            </Relationship>
604          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
605              <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
606              each PEG to all of its protein families.</Notes>              each PEG to all of its protein families.</Notes>

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