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revision 1.45, Fri Nov 3 00:44:01 2006 UTC revision 1.47, Mon Jan 22 20:24:53 2007 UTC
# Line 452  Line 452 
452                  </Field>                  </Field>
453              </Fields>              </Fields>
454          </Entity>          </Entity>
         <Entity name="DrugProject" keyType="name-string">  
             <Notes>A drug project is a coherent sent of drug target data that came through the  
             pipeline. In other words, data is put into the database one drug project at a time.  
             This makes it easier to manage the incoming data and to track where a particular  
             piece of data originated.</Notes>  
         </Entity>  
         <Entity name="DrugTopic" keyType="int">  
             <Notes>A drug topic organizes the data in a project relating to a single organism  
             group's features as they apply to a specific category of activity. Categories include  
             features essential to the organism's survival, those that are targets or inhibitors  
             of anti-biotics, and those associated with virulence. Thus, a drug topic consists  
             of data from a single project for features that make good drug targets for the same  
             reason. Drug topics have an artificial, internally-generated key.</Notes>  
             <Fields>  
                 <Field name="identifier" type="name-string">  
                     <Notes>The topic identifier, consisting usually of a generalized organism name  
                     (e.g. Staphylococcus) and the last name of the project's author. More than  
                     one topic may have the same identifier, which is why this isn't the key.</Notes>  
                 </Field>  
                 <Field name="tag" type="name-string">  
                     <Notes>A short phrase describing the topic.</Notes>  
                 </Field>  
                 <Field name="URL" type="string">  
                     <Notes>A URL for the paper from which the topic was gathered.</Notes>  
                 </Field>  
                 <Field name="category" type="key-string">  
                     <Notes>The code for this topic's activity category.</Notes>  
                 </Field>  
             </Fields>  
             <Indexes>  
                 <Index>  
                     <Notes>This index enables the application to find all topics with a specified  
                     category, ordered by tag.</Notes>  
                     <IndexFields>  
                         <IndexField name="category" order="ascending" />  
                         <IndexField name="tag" order="ascending" />  
                     </IndexFields>  
                 </Index>  
                 <Index>  
                     <Notes>This index enables the application to find all topics with a specified  
                     identifier, ordered by category.</Notes>  
                     <IndexFields>  
                         <IndexField name="identifier" order="ascending" />  
                         <IndexField name="category" order="ascending" />  
                     </IndexFields>  
                 </Index>  
             </Indexes>  
         </Entity>  
         <Entity name="PDB" keyType="key-string">  
             <Notes>A PDB is a database of protein structure and related information of use  
             in drug targeting. The purpose of drug targeting is to analyze the ability  
             of drug molecules, or ligands, to bond to proteins. A PDB for a protein already  
             attached to a ligand is called a bound PDB. A PDB for the protein by itself is  
             called a free PDB. The key of the PDB is its code name on the Protein Data  
             Bank web site.</Notes>  
             <Fields>  
                 <Field name="type" type="id-string">  
                     <Notes>The type of PDB: "bound" or "free".</Notes>  
                 </Field>  
                 <Field name="title" type="string">  
                     <Notes>The descriptive title of this PDB.</Notes>  
                 </Field>  
             </Fields>  
         </Entity>  
         <Entity name="Ligand" keyType="string">  
             <Notes>A ligand is a molecule that can bind to a PDB. The CLIBE analysis  
             for a PDB is an attribute of the relationship between a PDB and a ligand.</Notes>  
         </Entity>  
455      </Entities>      </Entities>
456      <Relationships>      <Relationships>
         <Relationship name="BindsWith" from="PDB" to="Ligand" arity="MM">  
             <Notes>This relationship describes the energy required for a ligand to bind  
             to the protein described by a PDB. The total energy required to bind  
             the ligand to the protein is described in this relationship by four  
             quantities. A negative value is energy released; a positive value is  
             energy required.</Notes>  
             <Fields>  
                 <Field name="URL" type="string">  
                     <Notes>URL for viewing the CLIBE data for this binding relationship.</Notes>  
                 </Field>  
                 <Field name="vanderwaals-energy" type="float">  
                     <Notes>kCal/mol of energy due to Van der Waals force.</Notes>  
                 </Field>  
                 <Field name="hbond-energy" type="float">  
                     <Notes>kCal/mol of energy due to hydrogen bonding.</Notes>  
                 </Field>  
                 <Field name="ionic-energy" type="float">  
                     <Notes>kCal/mol of energy due to ionic bonding.</Notes>  
                 </Field>  
                 <Field name="solvation-energy" type="float">  
                     <Notes>kCal/mol of energy due to attraction to the solvent in which  
                     the ligand is immersed.</Notes>  
                 </Field>  
             </Fields>  
         </Relationship>  
         <Relationship name="ContainsAnalysisOf" from="DrugTopic" to="PDB" arity="MM">  
             <Notes>This relationship describes the analysis of a free PDB as produced from a  
             particular topic.</Notes>  
             <Fields>  
                 <Field name="pass-asp-info" type="int">  
                     <Notes>The number of Active Site Points at which ligands can bind to  
                     the protein.</Notes>  
                 </Field>  
                 <Field name="ramsol-file" type="string">  
                     <Notes>The URL of a file that can be downloaded by the user and  
                     passed to the Ramsol program for viewing the protein.</Notes>  
                 </Field>  
                 <Field name="pass-weight" type="float">  
                     <Notes>A score for the largest pocket into which a ligand can bind. A  
                     higher score makes for a better target.</Notes>  
                 </Field>  
                 <Field name="pass-file" type="string">  
                     <Notes>The URL for a GIF file that shows the active sites on the protein.</Notes>  
                 </Field>  
             </Fields>  
         </Relationship>  
         <Relationship name="IncludesBound" from="DrugTopic" to="PDB" arity="MM">  
             <Note>This relationship connects a drug topic to its bound PDBs. (A separate  
             relationship is used to connect the free PDBs.)</Note>  
         </Relationship>  
         <Relationship name="IsBoundIn" from="PDB" to="PDB" arity="MM">  
             <Note>This relationship connects free PDBs to their bound counterparts.</Note>  
         </Relationship>  
         <Relationship name="DescribesProteinForFeature" from="PDB" to="Feature" arity="MM">  
             <Notes>This relationship connects a feature to a protein database (PDB) that  
             is relevant for determining drugs that target the feature.</Notes>  
             <Fields>  
                 <Field name="score" type="float">  
                     <Notes>The BLAST score for the feature as it relates to the PDB's  
                     protein, expressed as a small positive number. Generally only a  
                     very low BLAST score (1e-15 or less) indicates a good match.</Notes>  
                 </Field>  
                 <Field name="distance" type="float">  
                     <Notes>A distance value indicating how far the PDB's protein is  
                     from the feature's protein. A distance of 0 indicates a perfect  
                     match.</Notes>  
                 </Field>  
             </Fields>  
             <FromIndex>  
                 <Notes>This index yields the Features for a PDB in order from best  
                 score to worst.</Notes>  
                 <IndexFields>  
                     <IndexField name="score" order="ascending" />  
                 </IndexFields>  
             </FromIndex>  
             <ToIndex>  
                 <Notes>This index yields the Features for a PDB in order from best  
                 score to worst.</Notes>  
                 <IndexFields>  
                     <IndexField name="score" order="ascending" />  
                 </IndexFields>  
             </ToIndex>  
         </Relationship>  
         <Relationship name="ContainsTopic" from="DrugProject" to="DrugTopic" arity="1M">  
             <Notes>This relationship connects a drug target project to all of its  
             topics.</Notes>  
         </Relationship>  
457          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">          <Relationship name="IsFamilyForFeature" from="Family" to="Feature" arity="MM">
458              <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
459              each PEG to all of its protein families.</Notes>              each PEG to all of its protein families.</Notes>

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