H-Maps:  An Efficient Approach for Graphical Visualization and Navigation  of Topic Maps and Data Representation in Comput...
Topic Maps by Hölle & Hüttner AG <ul><li>Why Topic Maps ? </li></ul><ul><li>Merge new and exisiting data </li></ul><ul><li...
Applications in Computional Biology R&D projects EndoPlas  (supported by BMBF) PASSAGE  (supported by the Ministery of Sci...
Overview – Partial  Projects <ul><li>PyroMAP </li></ul><ul><li>Presentation of all information in one single knowledge man...
PyroMAP –  Information System Pyrogene <ul><li>Goals of the  project : </li></ul><ul><li>Ontology and data collection  </l...
PyroMAP –  Tool „Zotero“ <ul><li>Zotero is an open source Firefox extension for the collection, administration and serach ...
PyroMAP –  Conception and Ontology <ul><li>Research strategy – topics and questions must be determined </li></ul><ul><li>C...
PyroMAP –  Research <ul><li>Basics </li></ul><ul><li>Usage of the basic structure of Zotero </li></ul><ul><li>Ontology wit...
PyroMAP –  Mapping Properties Realisation as  Type Role1 Role1 Titel Name huh:title Autor Association huh:author Written b...
PyroMAP –  Overview Data Streaming Research Internet Browser Internet Browser Browser PlugIn Zotero SQL-Datenbank Topic Ma...
Outlook PyroMAP –  next steps <ul><li>Online version on the endoplas website </li></ul><ul><li>Usage for different project...
PASSAGE - The Problem <ul><ul><ul><li>30.000 genes (Human) </li></ul></ul></ul><ul><ul><ul><li>250.000 – 1.000.000 protein...
<ul><ul><li>PASSAGE </li></ul></ul>PASSAGE  Next Generation Sequencing for Expression analysis Goal:  Global gene expressi...
<ul><ul><li>Next Generation Sequencing (FLX Tech.) </li></ul></ul>
Understanding Requirements <ul><li>Possibilities </li></ul><ul><ul><li>Parallel sequencing technologies </li></ul></ul><ul...
Find the right way: Map of Knowlegde  Combination : Semantic technology and molecular biology Ontology Knowlegde PASSAGE M...
Hit the Mark: H-Maps Topic Maps Solution Data PASSAGE Map Experimental results H-Maps Bioinformatic Application Semantic S...
<ul><ul><li>PASSAGE – Topic Maps </li></ul></ul>Topic maps permit the networking of data from different experiments. Topic...
H-Maps Technology The Realisation
Architecture <ul><li>Agenda: </li></ul><ul><li>PASSAGE – Topic Maps </li></ul><ul><li>Endoplas </li></ul><ul><li>Current E...
Topic Maps by Hölle & Hüttner AG <ul><li>Engine </li></ul><ul><li>Self-development, covers the ISO standard and pass vario...
Topic Maps – Mapping-Framework <ul><li>Import of data/ Merge function  </li></ul><ul><li>Graphic providing of the Ontologi...
Topic Maps – Navigator  <ul><li>Idea:  Walk through the knowlegde matrix, step by step </li></ul><ul><li>Realization: </li...
Current projects with
Current projects with
Current projects with
Current projects with
Current projects with
Current projects with
Current projects with
Current projects with
Topic Maps – Outlook <ul><li>Data reduction and data compression as key feature </li></ul><ul><li>Improved features to fil...
Acknowledgements <ul><li>We thank… </li></ul><ul><li>Hölle & Hüttner Team: </li></ul><ul><li>Thilo Klöpfer </li></ul><ul><...
Thank you for your attention! <ul><ul><li>We meet your demands ! </li></ul></ul><ul><ul><li>Take Benefits by our Experienc...
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H-Maps: An Efficient Approach for Graphical Visualization and Navigation of Topic Maps and Data Representation in Computational Biology

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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.

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

  1. 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 AG Derendinger Str. 40 72072 Tübingen Email: lifescience@h-net.com
  2. 2. Topic Maps by Hölle & Hüttner AG <ul><li>Why Topic Maps ? </li></ul><ul><li>Merge new and exisiting data </li></ul><ul><li>Using a generic Interface </li></ul><ul><li>ISO Standard </li></ul>Topic Map Web services DB Documents (PDF, DOC,…) Various Exchange formats (Xml, RDF, CSV...)
  3. 3. Applications in Computional Biology R&D projects EndoPlas (supported by BMBF) PASSAGE (supported by the Ministery of Sciences Baden-Württemberg)
  4. 4. Overview – Partial Projects <ul><li>PyroMAP </li></ul><ul><li>Presentation of all information in one single knowledge management system </li></ul><ul><li>PyroTEST </li></ul><ul><li>Automated instrument for pyrogen examination </li></ul><ul><li>Applications for pyrogen examination </li></ul>
  5. 5. PyroMAP – Information System Pyrogene <ul><li>Goals of the project : </li></ul><ul><li>Ontology and data collection </li></ul><ul><li>Topic Map technology (ISO/IEC 13250) </li></ul><ul><li>Presentation useable also for non experts </li></ul>
  6. 6. PyroMAP – Tool „Zotero“ <ul><li>Zotero is an open source Firefox extension for the collection, administration and serach of different online and offline sources </li></ul><ul><li>Zotero provides tools for handling of bibliographic data especially in scientific publications </li></ul><ul><li>The software application was developed by the Center for History and New Media of George Mason University </li></ul>
  7. 7. PyroMAP – Conception and Ontology <ul><li>Research strategy – topics and questions must be determined </li></ul><ul><li>Chemistry, medecine, examination and materials </li></ul><ul><li>Questions for example in chemsitry: Which substance groups do exist? </li></ul><ul><li>Setup an ontology (fitting to Zotero) </li></ul><ul><li>Collections – hierarchical structure of topics </li></ul><ul><li>Tags – tags for article/document </li></ul>
  8. 8. PyroMAP – Research <ul><li>Basics </li></ul><ul><li>Usage of the basic structure of Zotero </li></ul><ul><li>Ontology with Collections and Tags </li></ul><ul><li>Associations are created by placement of tags or allocating of Collections </li></ul><ul><li>Research </li></ul><ul><li>Ongoing adjustment of ontology </li></ul><ul><li>Important content will be recorded as a memo </li></ul><ul><li>Link to online literature per URL </li></ul>
  9. 9. PyroMAP – Mapping Properties Realisation as Type Role1 Role1 Titel Name huh:title Autor Association huh:author Written by Author Zusammenfassung Occurrence huh:abstract Datum Occurrence huh:Date Kurztitel Variant Name huh:shortTitle URL Occurrence huh:url Verlag Association huh:publishinghouse Published by Publishing House ISBN Occurrence huh:isbn ISSN Occurrence huh:issn Erfinder Association huh:inventor Invented from Inventor Patent-Nummer Occurrence huh:patentnr Vortragender Association Huh:lecturer Lectured by Lecturer Erscheinungsort 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)
  10. 10. PyroMAP – Overview Data Streaming Research Internet Browser Internet Browser Browser PlugIn Zotero SQL-Datenbank Topic Map Mapper Topic Map Engine User in Research PyroMAP Ontologie RDF File Topic Map Navigator Topic Map File
  11. 11. Outlook PyroMAP – next steps <ul><li>Online version on the endoplas website </li></ul><ul><li>Usage for different project partners </li></ul><ul><li>Ongoing addition of content during this project </li></ul>
  12. 12. PASSAGE - The Problem <ul><ul><ul><li>30.000 genes (Human) </li></ul></ul></ul><ul><ul><ul><li>250.000 – 1.000.000 proteins (Human) </li></ul></ul></ul><ul><ul><ul><li>Identify the function of gene and protein </li></ul></ul></ul><ul><ul><ul><li>Understand the regulation process </li></ul></ul></ul><ul><li>New Method for Proteomics Research </li></ul>
  13. 13. <ul><ul><li>PASSAGE </li></ul></ul>PASSAGE Next Generation Sequencing for Expression analysis Goal: Global gene expression analysis Generation of a digital profile based only on sequence data
  14. 14. <ul><ul><li>Next Generation Sequencing (FLX Tech.) </li></ul></ul>
  15. 15. Understanding Requirements <ul><li>Possibilities </li></ul><ul><ul><li>Parallel sequencing technologies </li></ul></ul><ul><ul><li>Expression profiling is required to identify the function of a gene </li></ul></ul><ul><ul><li>Faster & cheaper new technique for expression analysis </li></ul></ul><ul><ul><li>Problems </li></ul></ul><ul><ul><li>New Bioinformatic algorithm required </li></ul></ul><ul><ul><li>Correlation of results to existing databases </li></ul></ul><ul><ul><li>Include Comparisions and statistics </li></ul></ul><ul><ul><li>Include annotations </li></ul></ul><ul><ul><li>Include other experimental data </li></ul></ul><ul><ul><li>Free workflow for research people </li></ul></ul>Application specific… more standard IT…
  16. 16. Find the right way: Map of Knowlegde Combination : Semantic technology and molecular biology Ontology Knowlegde PASSAGE Module Bioinformatics H-Maps Topic Maps Sugar metabolism 10% Expression level Influence sugar metabolism Function Glucose Parameter GAPDH Gene Assay 1 – Stress factor A Experiment Project Hans Müller Person Experiments database Enzyme datanbase Publi- cation Glucose Database Single reads has ressources Cluster
  17. 17. Hit the Mark: H-Maps Topic Maps Solution Data PASSAGE Map Experimental results H-Maps Bioinformatic Application Semantic Solution Suite
  18. 18. <ul><ul><li>PASSAGE – Topic Maps </li></ul></ul>Topic maps permit the networking of data from different experiments. Topic = Subject Occurence = Chracteristic of the Topic Association = relationship between Topics
  19. 19. H-Maps Technology The Realisation
  20. 20. Architecture <ul><li>Agenda: </li></ul><ul><li>PASSAGE – Topic Maps </li></ul><ul><li>Endoplas </li></ul><ul><li>Current Examples with H-Maps </li></ul>
  21. 21. Topic Maps by Hölle & Hüttner AG <ul><li>Engine </li></ul><ul><li>Self-development, covers the ISO standard and pass various standard tests </li></ul><ul><li>Support of other standardised exchange formats (XTM) </li></ul><ul><li>Implementation of quasi-standards such as TMAPI 2,0 as standardized programming interface </li></ul><ul><li>Mapping-Framework </li></ul><ul><li>API and GUI as interface to heterogeneous data sources </li></ul><ul><li>Batch-Modus </li></ul><ul><li>Topic-Map-Server </li></ul><ul><li>Access on Topic Map with Web services </li></ul><ul><li>Adds application logic (Authentification, validation etc.) </li></ul><ul><li>Silverlight-Client </li></ul><ul><li>Rich-Client as a Browser Application </li></ul><ul><li>Supports different browsers and operating systems </li></ul><ul><li>Permits Branding and simply adaptation of the surface </li></ul>
  22. 22. Topic Maps – Mapping-Framework <ul><li>Import of data/ Merge function </li></ul><ul><li>Graphic providing of the Ontologie and rule set </li></ul><ul><li>Flexible architecture with Plug in mechanism for the simple integration of new sources </li></ul><ul><li>Plug in for the purposeful processing of specific data </li></ul>
  23. 23. Topic Maps – Navigator <ul><li>Idea: Walk through the knowlegde matrix, step by step </li></ul><ul><li>Realization: </li></ul><ul><li>Version 1.0 available </li></ul><ul><li>Features: </li></ul><ul><li>Navigation through Topic Maps </li></ul><ul><li>Graphical Presentation </li></ul><ul><li>Bookmarks with note function (saved in Topic Map) </li></ul><ul><li>search for information </li></ul><ul><li>Printing feature </li></ul><ul><li>Upload-feature for any Topic Maps </li></ul><ul><li>Possibility to process many Topic Maps </li></ul><ul><li>at the same time </li></ul>
  24. 24. Current projects with
  25. 25. Current projects with
  26. 26. Current projects with
  27. 27. Current projects with
  28. 28. Current projects with
  29. 29. Current projects with
  30. 30. Current projects with
  31. 31. Current projects with
  32. 32. Topic Maps – Outlook <ul><li>Data reduction and data compression as key feature </li></ul><ul><li>Improved features to filter/to group/to sort data </li></ul><ul><li>Support more types of data (Occurrences) </li></ul><ul><li>Support of Scopes </li></ul><ul><li>Continual improvement through collaboration with other Topic Map experts </li></ul><ul><li>New features supporting the extraction of results </li></ul>Topic A Topic B Topic C new information Is related to Is related to
  33. 33. Acknowledgements <ul><li>We thank… </li></ul><ul><li>Hölle & Hüttner Team: </li></ul><ul><li>Thilo Klöpfer </li></ul><ul><li>Dr. Markus Leber </li></ul><ul><li>Peter Kuhn </li></ul><ul><li>Joachim Zühlke </li></ul><ul><li>Claudia Gerlach-Reck </li></ul><ul><li>Collaborators… </li></ul><ul><li>Partners in R&D projects </li></ul>
  34. 34. Thank you for your attention! <ul><ul><li>We meet your demands ! </li></ul></ul><ul><ul><li>Take Benefits by our Experiences! </li></ul></ul><ul><ul><li>Tell us your Questions, Problems and Wishes! </li></ul></ul>Hölle & Hüttner AG Derendinger Strasse 40 72072 Tübingen, Germany Telefon +49-7071-9761-1 Telefax + 49-7071-9761-90 www.h-net.com

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