CellFinder

A web-based data repositories of cell types

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

Website: http://cellfinder.org

Transcript

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