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


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’


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’


SIG Generic Tools and Methods Data Handling


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


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


Visualization using Xquery,dotty and Graphviz


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.


Example ‘select * from Person’


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


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


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


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


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)


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)


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?

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

Documents

frans verster

ibu mad

status mage

import mage

data handling generic

tables data

access code

data converter