CellFinder

090f9e164337989b54dabd7fedfd39b4?s=47 Fritz Lekschas
September 20, 2013

 CellFinder

A web-based data repositories of cell types

Authors: Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz

Website: http://cellfinder.org

090f9e164337989b54dabd7fedfd39b4?s=128

Fritz Lekschas

September 20, 2013
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  1. CELLFINDER A web-based data repository of cell types 20.09.13 Fritz

    Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 1
  2. CONTENTS 1.  Introduction 2.  Data 3.  Web Application 4.  Outlook

    5.  Questions 20.09.13 Fritz Lekschas 2
  3. INTRODUCTION 1.  The problem 2.  CellFinder 20.09.13 Fritz Lekschas, Harald

    Stachelscheid, Stefanie Seltmann, Andreas Kurtz 3
  4. INTRODUCTION: PROBLEM (2) •  Many cell types but no consistent

    classification system •  No resource for sensible phenotype-based cell type differentiation •  Data spread across multitude resources à loss of valuable information 20.09.13 Fritz Lekschas 4
  5. INTRODUCTION: CELLFINDER •  One stop cell-centered data repository •  New

    infrastructure to combine and extend existing data à Comprehensive phenotype description •  Easy accessibility / high usability •  Focus bio-medical scientists 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 5
  6. DATA 1.  Ontology: CELDA 2.  Expression Data 3.  Text Mining

    4.  Imaging 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 6
  7. DATA: CELDA ONTOLOGY •  Comprehensive description of cell types • 

    Connect different domain specific ontologies •  Extend missing information 20.09.13 Fritz Lekschas 7
  8. DATA: EXPRESSION DATA •  Gene Expression: RNA Seq Atlas • 

    Protein Expression: Human Protein Atlas 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 8
  9. DATA: TEXT MINING •  Manual annotation (of 10 papers) – 

    Human embryonic stem cells –  Kidney cells •  Text mining pipeline with manual curation –  Event recognition is based on manual annotation à 4700 derived gene expression 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 9
  10. DATA: IMAGING •  Omero image server •  Manages wide range

    of microscopic image formats •  Open source 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 10
  11. WEB APPLICATION 1.  Architecture 2.  Search 3.  Exploration / Browsing

    4.  Protein Expression Comparison 5.  Live Demo 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 11
  12. WEB APPLICATION: ARCHITECTURE 20.09.13 Fritz Lekschas 12

  13. WEB APPLICATION: SEARCH •  Omnipresent •  Search first, then filter

    à Quick access •  Loose search •  Sorted by relevance 20.09.13 Fritz Lekschas 13
  14. WEB APPLICATION: EXPLORE (1) •  Semantic Body Browser •  Dynamic

    annotated vector graphics •  Little to no prior knowledge required 20.09.13 Fritz Lekschas 14
  15. WEB APPLICATION: EXPLORE (2) •  Developmental tree of cells and

    organs •  Interactive 20.09.13 Fritz Lekschas 15
  16. WEB APPLICATION: EXPRESSION •  Cell-Cell expression comparison •  Precalculated • 

    StemBase, Human Protein Atlas 20.09.13 Fritz Lekschas 16
  17. LIVE DEMO 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas

    Kurtz 17
  18. OUTLOOK •  More data •  Semantic Body Browser: Search +

    (Marker) Expression Heatmaps •  Developmental Tree: Ground-up new, forward- backword exploring, search •  Online curation tool 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 18
  19. QUESTION & IDEAS? 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann,

    Andreas Kurtz 19
  20. THANK YOU! Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Jean-Fred Fontain,

    Nancy Mah, Mariana Neves, Miguel A. Andrade-Navarro, Ulf Leser, Andreas Kurtz 20.09.13 Fritz Lekschas, Harald Stachelscheid, Stefanie Seltmann, Andreas Kurtz 20