ibu mad 29 nov 2004, frans verster 1 generic tools and methods for data handling generic vs....

1IBU MAD 29 nov 2004, Frans Verster

Generic Tools and Methodsfor Data Handling

Generic vs. SpecificGeneric vs. Specific

2IBU MAD 29 nov 2004, Frans Verster

Generic

Models for “-omics” experimentsModels for “-omics” experiments Generate database scheme from modelGenerate database scheme from model Generate XML schema from modelGenerate XML schema from model Generate access code from modelGenerate access code from model Special Interest Group Generic Tools and Methods Special Interest Group Generic Tools and Methods

Data HandlingData Handling Using ontologiesUsing ontologies ‘‘Investment for the future’Investment for the future’

3IBU MAD 29 nov 2004, Frans Verster

Specific

Micro Array Gene Expression (MAGE) Micro Array Gene Expression (MAGE) datadata

MAGE-stk toolkit:MAGE-stk toolkit: MAGE-ML import/exportMAGE-ML import/export MAGE-OM api accessMAGE-OM api access

‘‘Quick and dirty’Quick and dirty’

4IBU MAD 29 nov 2004, Frans Verster

SIG Generic Tools and Methods Data Handling

5IBU MAD 29 nov 2004, Frans Verster

Status ‘generic’ Get the best from 3 worlds: doc+DB+codeGet the best from 3 worlds: doc+DB+code Unified tools not yet foundUnified tools not yet found Evaluate part-to-part connections:Evaluate part-to-part connections:

Databases

DocumentsXML

Programming

CastorJDOHibernate

Codegeneration

X / R / OO

Data / Doccentric Castor

JDOHibernate

Codegeneration

Mt, XTables

6IBU MAD 29 nov 2004, Frans Verster

Framework so far

UML

XMI ODL

DDL OODBMSMatisse)

models

VL OOprograms

XQueryBridge ?

Xqueryad hoc queries

GraphViz

Graphicaloutput

Tabularoutput

converterMAGE-VLfile

code

Mt.exe

XML Schema

XformsXGUI

MAGE-MLfile

7IBU MAD 29 nov 2004, Frans Verster

Visualization using Xquery,dotty and Graphviz

8IBU MAD 29 nov 2004, Frans Verster

Matisse+J2EE+SVG data viewer Objects are NodesObjects are Nodes Relations are EdgesRelations are Edges Looks like graph visualization with few Looks like graph visualization with few

algorithms and parameters:algorithms and parameters: Too many neighbors: pruningToo many neighbors: pruning Hubs and authorities; clusters; networksHubs and authorities; clusters; networks Multiple views: IsA, HasA, etc.Multiple views: IsA, HasA, etc.

9IBU MAD 29 nov 2004, Frans Verster

Example ‘select * from Person’

10IBU MAD 29 nov 2004, Frans Verster

Summary, The End

Nice ideasNice ideas Model independentModel independent Re-use of tools in VLERe-use of tools in VLE

Progress (too ?) slow on my ownProgress (too ?) slow on my own Crappy toolsCrappy tools More resourcesMore resources Or skip partsOr skip parts

11IBU MAD 29 nov 2004, Frans Verster

Normalization project VLE

(too much?) Focus on ‘generic’(too much?) Focus on ‘generic’ Build VLE like ‘-omics’ framework.Build VLE like ‘-omics’ framework. Using Matisse OO-DBMSUsing Matisse OO-DBMS With web-access data viewerWith web-access data viewer Java and R accessJava and R access (specific) MAGE-ML I/O(specific) MAGE-ML I/O Web-servicesWeb-services

12IBU MAD 29 nov 2004, Frans Verster

Status Matisse OO-DBMS

MAGE-OM model to Matisse OO DBMSMAGE-OM model to Matisse OO DBMS Lose some information (packages export Lose some information (packages export

MAGE-ML)MAGE-ML) Matisse is ‘cripple-ware’Matisse is ‘cripple-ware’ Almost no supportAlmost no support

MAGE-ML data converter for importMAGE-ML data converter for import But Matisse gives no error messageBut Matisse gives no error message

13IBU MAD 29 nov 2004, Frans Verster

Status web-access data viewer

Access with J2EE+HTML in tablesAccess with J2EE+HTML in tables Data is too complex for tablesData is too complex for tables

J2EE+Form based editor for mage-mlJ2EE+Form based editor for mage-ml Have DTD but need XSDHave DTD but need XSD

J2EE+SVG data viewerJ2EE+SVG data viewer Nice, wait for 2Nice, wait for 2ndnd presentation presentation Need tighter integrationNeed tighter integration Tools (dot) are crashyTools (dot) are crashy

14IBU MAD 29 nov 2004, Frans Verster

Status Java and R access

R coupling of data files via J2EE+XMLR coupling of data files via J2EE+XML Too slowToo slow

Java code generationJava code generation Matisse works wellMatisse works well Reflection also (everything is just a Reflection also (everything is just a

generic object)generic object)

15IBU MAD 29 nov 2004, Frans Verster

Status MAGE-ML I/O

ImportImport Matisse gives no error messageMatisse gives no error message

ExportExport Lose some information (packages export Lose some information (packages export

MAGE-ML)MAGE-ML)

16IBU MAD 29 nov 2004, Frans Verster

Status Web-services and Ontologies Kept in mind but no work doneKept in mind but no work done

Connection with Taverna should be Connection with Taverna should be possiblepossible

What the heck are ontologies?What the heck are ontologies?