Download Lupus Framework - Wilhelm Johannsen Centre for Functional

Wilhelm Johannsen Centre for Functional Genome Research
University of Copenhagen
Comprehensive annotated database of K channel mutations
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Holstebroe S , Heil B , Ludwig J , Sanders D , Hartung T , Drejer J , Lichtenberg-Fraté H , Tommerup N
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Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Denmark; 2Botanisches Institut, Universität Bonn,
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Germany; Physiologisch-chemisches Institut, Universität Tübingen, Germany; The Plant Laboratory, University of York, UK; S T Z InPut,
Konstantz, Germany; 6Neurosearch A/S, Ballerup, Denmark
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Workflow in the Lupus framework;
from XML to full featured web database
“Lupus”, a general scientific database framework
The database has been built using a customizable general purpose scientific
database framework constructed for this purpose. This framework allows very
rapid development of annotation databases commonly found in the community. The database is a hybrid between an object oriented database, a relational
SQL database and an XML database, drawing benefits from each domain’s
advantages. The support for XML import and export makes interaction with
other databases supporting XML fairly simple.
Building a database in lupus takes the following steps:
• Define the database in xml
• Use the Lupus model generator to translate the xml to sql tables and
corresponding java peer classes. These java classes can without changes
produce a full webinterface for submitting, browsing and searching the
defined data.
• Write java classes and jsp files to customize details of the presentation,
validation, storage and filtering your datamodel.
• Deploy and announce your database
More information about the Multiplex potassium channel project can be found
at: http://www.multiplex-network.de
For more information about the Lupus framework, please contact Søren
Holstebroe at [email protected]
<table name="Mutation" basetype="AnnotatedDataObject">
<string name="name" caption="Name" size="100" unique="yes" index="yes"/>
<stringlist name="aliases" caption="Aliases" index="yes"/>
<foreign name="gene" caption="Gene" foreignTable="Gene"/>
<selection name="mutationType" caption="Mutation type">
<option name="Insertion"/>
<option name="Deletion"/>
<option name="Single base"/>
<option name="Duplication"/>
<option name="Silent"/>
<option name="Indels"/>
<option name="Complex"/>
</selection>
<string name="dnaChange" caption="DNA change" size="100" />
<selection name="changeEffect" caption="Change effect">
<option name="Frameshift"/>
<option name="Replacement"/>
<option name="Splicing"/>
<option name="Deletion"/>
</selection>
<selection name="changeLocation" caption="Change location">
<option name="Dominant positive"/>
<option name="Dominant negative"/>
<option name="Recessive positive"/>
<option name="Recessive negative"/>
</selection>
<foreign name="classification" caption="Classification" foreignTable="Classification"/>
<foreign name="phenotype" caption="Phenotype" foreignTable="Phenotype"/>
<boolean name="isInherited" caption="Inherited"/>
<selection name="domination" caption="Domination">
<option name="cDNA"/>
<option name="Promoter"/>
<option name="Exon"/>
<option name="Intron"/>
<option name="Other"/>
</selection>
<integer name="studiedCases" caption="Studied cases"/>
<stringlist name="ethnicalBackground" caption="Ethnical background"/>
</table>
<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
<!DOCTYPE database SYSTEM "lupus.dtd">
<database name="Multiplex" basePackage="Multiplex.DataModel" >
<!-- Gene -->
<table name="Gene" basetype="AnnotatedDataObject" >
<string name="name" caption="Name" />
<stringlist name="aliases" caption="Aliases" />
<string name="chromPosition" caption="Chromosome position"/>
<foreign name="organism" caption="Organism" foreignTable="Organism" />
<relationlist name="channelList" caption="Channels" relationTable="GeneChannelRel"
foreignSide="right" selector="dropdown" />
</ table>
<!-- Strain -->
<table name="Strain" basetype="AnnotatedDataObject" >
<string name="name" caption="Strain name" size="100"/>
<foreign name="host" caption="Host strain" foreignTable="Strain" selector="search"/>
<string name="genotype" caption="Genotype compared with host strain"/>
<foreign name="construct" caption="Construct strain" foreignTable="Strain" selector="constructor"/>
<selection name="constructtype" caption="Construct type">
<option name="Centromeric" />
<option name="Episomal (multi-copy)"/>
<option name="Integrated"/>
</ selection >
<set name="verification" caption="Verification" >
<option name="PCR (3')"/>
<option name="PCR (5')"/>
<option name="Plasmid recovery"/>
<option name="Northern blot"/>
<option name="Southern blot"/>
</ set >
<set name="requiredSupplements" caption="Required supplements" type="dynamic">
<option name="LEU"/>
<option name="TRP"/>
<option name="URA" />
<option name="HIS" />
</ set >
<tupplelist name="mediumList" caption="Medium list" tableName="StrainMedium" basetype="TuppleData" >
<string name="medium" caption="Medium" size="100"/>
<double name="kConcentration" caption="K Concentration"/>
<double name="pH" caption="pH"/>
</ tupplelist>
<set name="expressionCassetteMarkers" caption="Selectable marker of expression cassette in yeast" type="dynamic">
<option name="G418"/>
<option name="LEU"/>
<option name="URA" />
<option name="HIS" />
<option name="TRP"/>
</ set >
<section caption="Fluorescence control images">
<image name="protoplastLocalizationImage" caption="Protoplast localization"/>
<image name="cellularLocalizationImage" caption="Cellular localization"/>
</ section >
<imagelist name="images" caption="Additional images"/>
</ table>
XML Description
// This class was created automatically by DMGenerator
// DO NOT MANUALLY EDIT, only edit inherited classes
// Created on: Apr 25, 2003 11:10:10 AM
package Multiplex.DataModel.Base;
import Multiplex.DataModel.*;
import Lupus.DataModel.Param.*;
import Lupus.DataModel.*;
import java.util.AbstractCollection;
abstract public class BaseMutation extends AnnotatedDataObject {
public static final String NAME = "Mutation";
public static final String PARAM_NAME = "name";
public static final String PARAM_NAME_CAPTION = "Name";
public static final String PARAM_ALIASES = "aliases";
public static final String PARAM_ALIASES_CAPTION = "Aliases";
public static final String PARAM_GENE = "gene";
public static final String PARAM_GENE_CAPTION = "Gene";
public static final String PARAM_MUTATIONTYPE = "mutationType";public static final String [] MUTATIONTYPETYPES =
{"Insertion","Deletion","Single base","Duplication","Silent","Indels","Complex"};
<!-- Electrophysiological data -->
<table name="ElectrophysiologicalData" basetype="AnnotatedDataObject" >
<foreign name="strain" caption="Strain" foreignTable="Strain" selector="search"/>
<section caption="Recording conditions">
<double name="temperature" caption="Temperature"/>
<double name="holdingPotential" caption="Holding potential"/>
<double name="pipetteKConcentration" caption="Pipette K Concentration"/>
<double name="pipettePh" caption="Pipette pH"/>
<double name="bathKConcentration" caption="Bath K concentration"/>
<double name="bathPh" caption="Bath pH"/>
<selection name="configuration" caption="Configuration">
<option name="Whole-cell" />
<option name="Cell-attached"/>
<option name="Inside-out"/>
<option name="Outside-out"/>
</ selection >
</ section >
public static final String PARAM_MUTATIONTYPE_CAPTION = "Mutation type";
public static final String PARAM_DNACHANGE = "dnaChange";
public static final String PARAM_DNACHANGE_CAPTION = "DNA change";
public static final String PARAM_CHANGEEFFECT = "changeEffect";public static final String [] CHANGEEFFECTTYPES =
{"Frameshift","Replacement","Splicing","Deletion"};
public static final String PARAM_CHANGEEFFECT_CAPTION = "Change effect";
public static final String PARAM_CHANGELOCATION = "changeLocation";public static final String [] CHANGELOCATIONTYPES =
{"Dominant positive","Dominant negative","Recessive positive","Recessive negative"};
Database
Generator
<subtitle caption="Experimental data"/>
<double name="maxCellConductance" caption="Max whole cell conductance [nS]"/>
<double name="halfMaxActivation" caption="Half max activation"/>
<double name="activationTimeConst" caption="Activation time constant [ms]"/>
<double name="activationTimeConstVolt" caption="Activation time constant at [mV]"/>
<double name="inactivationTimeConst" caption="Inactivation time constant [ms]"/>
<double name="inactivationTimeConstVolt" caption="Inactivation time constant at [mV]"/>
<double name="deactivationTimeConst" caption="Deactivation time constant [ms]"/>
<double name="deactivationTimeConstVolt" caption="Deactivation time constant at [mV]"/>
public static final String PARAM_CHANGELOCATION_CAPTION = "Change location";
public static final String PARAM_CLASSIFICATION = "classification";
public static final String PARAM_CLASSIFICATION_CAPTION = "Classification";
public static final String PARAM_PHENOTYPE = "phenotype";
public static final String PARAM_PHENOTYPE_CAPTION = "Phenotype";
public static final String PARAM_ISINHERITED = "isInherited";
public static final String PARAM_ISINHERITED_CAPTION = "Inherited";
public static final String PARAM_DOMINATION = "domination";public static final String [] DOMINATIONTYPES =
{"cDNA","Promoter","Exon","Intron","Other"};
<foreign name="compound" caption="Compound" foreignTable="Compound" />
<double name="compoundConcentration" caption="Compound concentration or range [myM]"/>
<selection name="effect" caption="Effect">
<option name="Block"/>
<option name="Stimulation" />
<option name="No effect"/>
</ selection >
Lupus
Framework
<double name="pka" caption="pKa"/>
<double name="kHalfVolt" caption="K0.5 at [mV]"/>
<boolean name="blockVoltDep" caption="Voltage-dependence of Block"/>
<image name="voltageProtocol" caption="Voltage protocol image"/>
<image name="currentTraces" caption="Current traces image"/>
</ table>
<!-Plasmid
-->
<table name="Plasmid" basetype="AnnotatedDataObject" >
<string name="name" caption="Plasmid name" size="100"/>
<selection name="bactSelection" caption="Selection for bacteria">
<option name="Amp"/>
<option name="Kan"/>
<option name="Zeo"/>
<option name="n/a" />
</ selection >
<selection name="yeastSelection" caption="Selection for yeast">
<option name="G418" id="1"/>
<option name="Leu" id="2"/>
<option name="Ura" id="3"/>
<option name="His" id="4"/>
<option name="Trp" id="5"/>
<option name="n/a" id="6"/>
</ selection >
<selection name="bactPromotor" caption="Promotor for bacteria">
<option name="lac"/>
<option name="laq" />
<option name="mal"/>
<option name="n/a" />
</ selection >
public static final String PARAM_DOMINATION_CAPTION = "Domination";
public static final String PARAM_STUDIEDCASES = "studiedCases";
public static final String PARAM_STUDIEDCASES_CAPTION = "Studied cases";
public static final String PARAM_ETHNICALBACKGROUND = "ethnicalBackground";
public static final String PARAM_ETHNICALBACKGROUND_CAPTION = "Ethnical background";
protected StringParam name = new StringParam(PARAM_NAME,"Name");
protected StringListParam aliases = new StringListParam(PARAM_ALIASES,"Aliases");
protected ForeignDropDownParam gene = new ForeignDropDownParam(PARAM_GENE,"Gene", MultiplexAbstractFactory.getInstance().getGeneFactory());
protected TypeParam mutationType = new TypeParam(PARAM_MUTATIONTYPE,"Mutation type",MUTATIONTYPETYPES);
protected StringParam dnaChange = new StringParam(PARAM_DNACHANGE,"DNA change");
protected TypeParam changeEffect = new TypeParam(PARAM_CHANGEEFFECT,"Change effect",CHANGEEFFECTTYPES);
protected TypeParam changeLocation = new TypeParam(PARAM_CHANGELOCATION,"Change location",CHANGELOCATIONTYPES);
protected ForeignDropDownParam classification = new ForeignDropDownParam(PARAM_CLASSIFICATION,"Classification", MultiplexAbstractFactory.getInstance().getClassificationFactory());
protected ForeignDropDownParam phenotype = new ForeignDropDownParam(PARAM_PHENOTYPE,"Phenotype", MultiplexAbstractFactory.getInstance().getPhenotypeFactory());
protected BooleanParam isInherited = new BooleanParam(PARAM_ISINHERITED,"Inherited");
protected TypeParam domination = new TypeParam(PARAM_DOMINATION,"Domination",DOMINATIONTYPES);
protected IntegerParam studiedCases = new IntegerParam(PARAM_STUDIEDCASES,"Studied cases");
protected StringListParam ethnicalBackground = new StringListParam(PARAM_ETHNICALBACKGROUND,"Ethnical background");
public BaseMutation() {
super();
name.setUnique(true);
addParam(name);
addParam(aliases);
addParam(gene);
addParam(mutationType);
addParam(dnaChange);
addParam(changeEffect);
addParam(changeLocation);
addParam(classification);
addParam(phenotype);
addParam(isInherited);
addParam(domination);
addParam(studiedCases);
addParam(ethnicalBackground);
}
public String getDbTableName() {
return NAME;
}
Java Base
Datamodel
Inherit
The multiplex project
An extensive number of disease causing mutations in human K+ channels
have been identified. In order to assist further research and provide a public
comprehensive knowledgebase, we have constructed a web-based database
aiming to assemble all available molecular and clinical information regarding
K+ channel mutations. The clinical information will be supplemented by
pharmacological data and eletrocardiograms.
A concurrent project is constructing a plasmid library of all available
mutations enabling cloning in a yeast model. The cloned yeast will undergo
electrophysiological experiments and will be used as model organism for
prevalidation of novel alternative pharma/-toxicological screening. The
database will integrate and support experimental results, protocols and
technology transfers from this part of the project.
In order to gather and construct a comprehensive dataset, the database will try
to automatically collect and categorize public information from the Internet
using simple data mining methods for a selected number of public databases.
To obtain a large degree of flexibility, we have designed a very general
framework for the database, which easily could be used as platform for other
databases as well.
SQL
Tables
public String getName() {
return (String) name.get();
}
public String getAliases() {
return (String) aliases.get();
}
public Gene getGene() {
return (Gene) gene.get();
}
public Integer getMutationType() {
return (Integer) mutationType.get();
}
public String getDnaChange() {
return (String) dnaChange.get();
}
public Integer getChangeEffect() {
return (Integer) changeEffect.get();
}
public Integer getChangeLocation() {
return (Integer) changeLocation.get();
}
public Classification getClassification() {
return (Classification) classification.get();
Customizing
- presentation,
- validation,
- storage and
- filtering
Java User
Datamodel
Lupus key features
• Written in java / jsp
• Integrating the powerful Jakarta Lucene search engine
• Data miners for selected public databases like OMIM, Swissprot, Ensembl, ...
• Advanced filtering when browsing data
• User manageable agents to allow notification when new data matches specified criteria
• Reference source of information on all data and parsing of these sources to produce
search results
• Internal crosslinkage
• Discussion forums on all data entities
• News bulletin
• Access control system on all data
• Detailed log of any changes of any data
• User submission of data
• User upload of images and files
• Flexible XML definition of the database
• XML import and export of all data
• Fully customizable data presentation and input forms
References (Centered)Acknowledgements:
A European Union funded research project under the thematic programme “Quality of Life and Management of Living Resources” within the
5th RTD Framework Programme (1998 - 2002). Wilhelm Johannsen Centre for Functional Genome Research is established by The Danish National Research Foundation
This poster can be obtained as a PDF-file at
www.wjc.ku.dk