H-Maps: An Efficient Approach for Graphical Visualization and Navigation of Topic Maps and Data Representation in Computational Biology
- 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. Topic Maps by Hölle & Hüttner AG Why Topic Maps ? Merge new and exisiting data Using a generic Interface ISO Standard Topic Map Web services DB Documents (PDF, DOC,…) Various Exchange formats (Xml, RDF, CSV...)
- 3. Applications in Computional Biology R&D projects EndoPlas (supported by BMBF) PASSAGE (supported by the Ministery of Sciences Baden-Württemberg)
- 4. Overview – Partial Projects PyroMAP Presentation of all information in one single knowledge management system PyroTEST Automated instrument for pyrogen examination Applications for pyrogen examination
- 5. PyroMAP – Information System Pyrogene Goals of the project : Ontology and data collection Topic Map technology (ISO/IEC 13250) Presentation useable also for non experts
- 6. 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
- 7. 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
- 8. 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
- 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. 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. Outlook PyroMAP – next steps Online version on the endoplas website Usage for different project partners Ongoing addition of content during this project
- 12. 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
- 13. PASSAGE PASSAGE Next Generation Sequencing for Expression analysis Goal: Global gene expression analysis Generation of a digital profile based only on sequence data
- 14. Next Generation Sequencing (FLX Tech.)
- 15. 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…
- 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. Hit the Mark: H-Maps Topic Maps Solution Data PASSAGE Map Experimental results H-Maps Bioinformatic Application Semantic Solution Suite
- 18. PASSAGE – Topic Maps Topic maps permit the networking of data from different experiments. Topic = Subject Occurence = Chracteristic of the Topic Association = relationship between Topics
- 19. H-Maps Technology The Realisation
- 20. Architecture Agenda: PASSAGE – Topic Maps Endoplas Current Examples with H-Maps
- 21. Topic Maps by Hölle & Hüttner AG 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
- 22. Topic Maps – Mapping-Framework 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
- 23. Topic Maps – Navigator 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
- 32. Topic Maps – Outlook 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 A Topic B Topic C new information Is related to Is related to
- 33. Acknowledgements We thank… Hölle & Hüttner Team: Thilo Klöpfer Dr. Markus Leber Peter Kuhn Joachim Zühlke Claudia Gerlach-Reck Collaborators… Partners in R&D projects
- 34. Thank you for your attention! We meet your demands ! Take Benefits by our Experiences! Tell us your Questions, Problems and Wishes! Hölle & Hüttner AG Derendinger Strasse 40 72072 Tübingen, Germany Telefon +49-7071-9761-1 Telefax + 49-7071-9761-90 www.h-net.com