h-maps: an efficient approach for graphical visualization and navigation of topic maps and data...
DESCRIPTION
Nowadays semantic networks become more important in industry and modern science. For this reason there is a need for an efficient tool allowing preparation and navigation through complex data spaces. We present the novel Topic Map tool H-Maps, which offers a web based navigator providing an enhanced utilization and graphical visualization of semantic networks. Present applications transform existing content to subject-centric Topic Map representations in a one-way fashion. Preserving the advantage of transferring diverse back ends into a unified topic map in existing applications the H-Maps approach goes one step further. The resulting topic map structure can be examined and extended with an iterative procedure. Especially in science this procedure is leading to a considerable improvement of flexibility and performance as can be shown within projects of computational biology.TRANSCRIPT
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]
TMRA 2009 © Hölle & Hüttner AG 2009 Folie 2
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...)
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Applications in Computional Biology
R&D projects
EndoPlas
(supported by BMBF)
PASSAGE
(supported by the Ministery of Sciences Baden-Württemberg)
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Overview – Partial Projects
PyroMAP
• Presentation of all information in one single knowledge
management system
PyroTEST
• Automated instrument for pyrogen examination
• Applications for pyrogen examination
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PyroMAP – Information System Pyrogene
Goals of the project:•Ontology and data collection •Topic Map technology (ISO/IEC 13250)•Presentation useable also for non experts
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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
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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
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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
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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)
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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
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Outlook PyroMAP – next steps
• Online version on the endoplas website
• Usage for different project partners
• Ongoing addition of content during this project
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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
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PASSAGE
PASSAGE
Next Generation Sequencing for
Expression analysis
Goal:
Global gene expression analysis
Generation of a digital profile based
only on sequence data
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Next Generation Sequencing (FLX Tech.)
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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…
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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
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Hit the Mark: H-Maps Topic Maps Solution
Data PASSAGE MapExperimental results
H-Maps
Bioinformatic Application Semantic Solution Suite
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PASSAGE – Topic Maps
Topic maps permit the networking of data from different experiments.
Topic = SubjectOccurence = Chracteristic of the TopicAssociation = relationship between Topics
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H-Maps Technology
The Realisation
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Architecture
Agenda:
•PASSAGE – Topic Maps
•Endoplas
•Current Examples with H-Maps
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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
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• 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
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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
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Current projects with
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Current projects with
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Current projects with
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Current projects with
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Current projects with
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Current projects with
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Current projects with
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Current projects with
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• 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
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Acknowledgements
We thank…
Hölle & Hüttner Team:
• Thilo Klöpfer
• Dr. Markus Leber
• Peter Kuhn
• Joachim Zühlke
• Claudia Gerlach-Reck
Collaborators…
• Partners in R&D projects
TMRA 2009 © Hölle & Hüttner AG 2009 Folie 34
• 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