H-Maps: An Efficient Approach for Graphical Visualization and Navigation of Topic Maps and Data Representation in Computational Biology

TMRA 2009 © Hölle & Hüttner AG 2009 Folie 1

H-Maps: An Efficient Approach for Graphical Visualization and Navigation of Topic Maps and Data Representation in Computational Biology

Dr. Steffen Hüttner

Hölle & Hüttner AGDerendinger Str. 4072072 TübingenEmail: [email protected]


Topic Maps by Hölle & Hüttner AG

Why Topic Maps ?

• Merge new and exisiting data

• Using a generic Interface

• ISO Standard

TopicMap

Web services

DB

Documents(PDF, DOC,…)

VariousExchange formats(Xml, RDF, CSV...)


Applications in Computional Biology

R&D projects

EndoPlas

(supported by BMBF)

PASSAGE

(supported by the Ministery of Sciences Baden-Württemberg)


Overview – Partial Projects

PyroMAP

• Presentation of all information in one single knowledge

management system

PyroTEST

• Automated instrument for pyrogen examination

• Applications for pyrogen examination


PyroMAP – Information System Pyrogene

Goals of the project:•Ontology and data collection •Topic Map technology (ISO/IEC 13250)•Presentation useable also for non experts


PyroMAP – Tool „Zotero“

• Zotero is an open source Firefox extension for the collection,

administration and serach of different online and offline sources

• Zotero provides tools for handling of bibliographic data especially in

scientific publications

• The software application was developed by the Center for History and

New Media of George Mason University


PyroMAP – Conception and Ontology

Research strategy – topics and questions must be determined

• Chemistry, medecine, examination and materials

• Questions for example in chemsitry: Which substance groups do exist?

Setup an ontology (fitting to Zotero)

• Collections – hierarchical structure of topics

• Tags – tags for article/document


PyroMAP – Research

Basics

• Usage of the basic structure of Zotero

• Ontology with Collections and Tags

• Associations are created by placement of tags or allocating of

Collections

Research

• Ongoing adjustment of ontology

• Important content will be recorded as a memo

• Link to online literature per URL


PyroMAP – Mapping

Properties Realisation as Type Role1 Role1Titel Name huh:titleAutor Association huh:author Written by AuthorZusammenfassung Occurrence huh:abstractDatum Occurrence huh:DateKurztitel Variant Name huh:shortTitleURL Occurrence huh:urlVerlag Association huh:publishinghouse Published by Publishing HouseISBN Occurrence huh:isbnISSN Occurrence huh:issnErfinder Association huh:inventor Invented from InventorPatent-Nummer Occurrence huh:patentnrVortragender Association Huh:lecturer Lectured by LecturerErscheinungsort Association huh:place place of publication Place

Verweise Umsetzung als Typ Role1 Role1

Notizen Association huh:note Note Note

Schlagwörter Association huh:tag Tag Tag

Verweise Association Huh:related (*1) Name of Parent Collection (*1)

Name of Parent Collection (*1)


PyroMAP – Overview Data Streaming

InternetBrowserInternetBrowser

InternetBrowserInternetBrowser

Browser PlugInZotero

SQL-Datenbank

Topic MapMapper

Topic MapMapper

Topic Map Engine

Topic Map Engine

User in Research

PyroMAPOntologiePyroMAPOntologie

RDFFile

RDFFile

Topic Map NavigatorTopic Map Navigator

Topic MapFile

Topic MapFile

Research


Outlook PyroMAP – next steps

• Online version on the endoplas website

• Usage for different project partners

• Ongoing addition of content during this project


PASSAGE - The Problem

30.000 genes (Human)? 250.000 – 1.000.000 proteins (Human)

? Identify the function of gene and protein? Understand the regulation process

New Method for Proteomics Research


PASSAGE

PASSAGE

Next Generation Sequencing for

Expression analysis

Goal:

Global gene expression analysis

Generation of a digital profile based

only on sequence data


Next Generation Sequencing (FLX Tech.)


Understanding Requirements

Possibilities• Parallel sequencing technologies

• Expression profiling is required to identify the function of a gene

• Faster & cheaper new technique for expression analysis

Problems • New Bioinformatic algorithm required

• Correlation of results to existing databases

• Include Comparisions and statistics

• Include annotations

• Include other experimental data

• Free workflow for research people Application specific…

more standard IT…


Find the right way: Map of Knowlegde

Combination: Semantic technology and molecular biology

PASSAGE ModuleBioinformatics

H-MapsTopic Maps

Sugar metabolism

10%

Expression level

Influence sugar metabolism

Function

Glucose

Parameter

GAPDH Gene

Assay 1 – Stress factor A

Experiment

Project

Hans Müller

Person

Experimentsdatabase

Enzymedatanbase

Publi-cation

Glucose

DatabaseSingle reads

hasressources

Cluster OntologyKnowlegde


Hit the Mark: H-Maps Topic Maps Solution

Data PASSAGE MapExperimental results

H-Maps

Bioinformatic Application Semantic Solution Suite


PASSAGE – Topic Maps

Topic maps permit the networking of data from different experiments.

Topic = SubjectOccurence = Chracteristic of the TopicAssociation = relationship between Topics


H-Maps Technology

The Realisation


Architecture

Agenda:

•PASSAGE – Topic Maps

•Endoplas

•Current Examples with H-Maps


Engine•Self-development, covers the ISO standard and pass various standard tests•Support of other standardised exchange formats (XTM) •Implementation of quasi-standards such as TMAPI 2,0 as standardized programming interface

Mapping-Framework•API and GUI as interface to heterogeneous data sources •Batch-Modus

Topic-Map-Server•Access on Topic Map with Web services •Adds application logic (Authentification, validation etc.)

Silverlight-Client•Rich-Client as a Browser Application•Supports different browsers and operating systems•Permits Branding and simply adaptation of the surface

Topic Maps by Hölle & Hüttner AG


• Import of data/ Merge function • Graphic providing of the Ontologie and rule set

• Flexible architecture with Plug in mechanism for the simple integration of new sources

• Plug in for the purposeful processing of specific data

Topic Maps – Mapping-Framework


Idea: Walk through the knowlegde matrix, step by step

Realization:Version 1.0 available

Features:

• Navigation through Topic Maps

• Graphical Presentation

• Bookmarks with note function (saved in Topic Map)

• search for information

• Printing feature

• Upload-feature for any Topic Maps

• Possibility to process many Topic Maps

at the same time

Topic Maps – Navigator


Current projects with
















• Data reduction and data compression as key feature• Improved features to filter/to group/to sort data• Support more types of data (Occurrences)• Support of Scopes• Continual improvement through collaboration with other Topic

Map experts• New features supporting the extraction of results

Topic Maps – Outlook

Topic A Topic B Topic C

new information

Is related to Is related to


Acknowledgements

We thank…

Hölle & Hüttner Team:

• Thilo Klöpfer

• Dr. Markus Leber

• Peter Kuhn

• Joachim Zühlke

• Claudia Gerlach-Reck

Collaborators…

• Partners in R&D projects


• We meet your demands !

• Take Benefits by our Experiences!

• Tell us your Questions, Problems and Wishes!

Thank you for your attention!

Hölle & Hüttner AGDerendinger Strasse 4072072 Tübingen, GermanyTelefon +49-7071-9761-1Telefax + 49-7071-9761-90www.h-net.com