Data Management and Standardisation in Distributed Systems Biology Research

Transcription

1 Data Management and Standardisation in Distributed Systems Biology Research Martin Golebiewski Heidelberg Institute for Theoretical Studies (HITS) Heidelberg, Germany BioMedBridges workshop "Data strategies for Research Infrastructures Munich, 18 February 2015

2 Experimental Data ) ] ([ ] [ * * )* ( ]' [ K k K PLC PLC k cyt cyt cyt cyt ER ER = ) ] ([ ] [ )* ( ) ] ([ ] [ ]' [ K k K k cyt cyt cyt mit n n cyt n cyt Mito + + = Simulation Model DB collect & integrate simulate hypothesize & verify Systems Biology Workflows

3 The Virtual Liver Mission To create Dynamic mathematical models that represent the human liver physiology, morphology and function Models that integrate quantitative data from all scales, from (sub-)cellular levels to the whole organ and the whole body à True multi-scale models of the liver (modular, flexible and modifiable) Models that have a specific focus on applications in medicine

4 Virtual Liver Network German Systems Biology Flagship Programme (largest in Europe) 5 years (started in 2010) Almost 50 Mio 69 Groups >200 Scientists 36 Institutions 44 Projects Experimentalists, Modelers, Clinicians and Industry Different scales: The Liver Cell - Metabolism - Signalling - Functions Beyond the Cell: - Intercellular - Liver lobule - Whole organ Integration and Translation: - Model integration - Data management - Clinical translation

5 Our Data Management Mission Feels like buddy to buddy Attached systems as needed

6 Data management 6

7 The Data Management Challenges Technical: Standardisation & Integration Protocols (SOPs) Data formats Model formats Metadata for data and models Interfaces Tools for integration -> multi-scale modelling Social: Communication Complex project organisation structure Geographically dispersed Diverse scientific background Managing expectations Benefits for the users? Internal communication Outreach: Informing the public

8 Data Management Advocats&Multipliers PALs (Project Area Liasons): - Experts working within the project - Collect requirements from partners - Help to communicate the features

9 Challenges: Constructing Interfaces - Interfaces between data, workflows and models - Interfaces between modules of a model - Interfaces between different models - Interfaces between biological scales What information should transmitted? (entities, parameters, metadata,...) Which format is suitable for the transmission? How should the information be integrated?

10 Challenges: Metadata Standards Metadata: Data describing data or models - Context & Environment - Entities & Elements! SEMANTICS Helps to connect the dots (data, models...)

11 SEEK Metadata: Studies & Assays Data Files Models SOPs Publications

12 SEEK: Data

13 SEEK: Data

14 Just Enough Results Model JERM: Data model for metadata and results vs Just enough Just in case - Consensus minimal description of data and metadata - Shared minimum formatting standards (e.g. spread sheets) à Extractors could be build to extract the data and context information

15 Specimen and Sample Management Automated population of SEEK with specimen and sample descriptions from spreadsheets Parsing Spreadsheet in the lab Specimen and Sample Descriptions

16 SEEK: Systems Biology Data Hub Yellow Pages: - People - Institutions - Projects - Events Asset talogue: - Investigations, Studies, Assays - Data - Models - Standardized workflows (SOPs) - Publications & Presentations - Biological samples

17 From Grassroots Initiatives to Approved Standards

18 Grassroots Standards in Biology & Biotechnology Source: Susanna-Assunta Sansone (University of Oxford, UK)

19 Manifold Exchange Formats for Biological Models

20 So many standards...

21 So many standards...

22 Building a Bridge Research Communities Develop and apply de facto community standards in grass-roots initiatives Industries Need standards to integrate data Help to distribute and promote standards

23 Standardisation Organisations: How do they work? Mirrorcommittee Delegate Expert Working group Technical Committee National International

24 Biotechnology Committees at DIN and ISO

25 NormSys Standards for Systems Biology Transfer from grassroots to approved standards Identification and classification of existing initiatives Bring together all stakeholders - Standard developers providing the standards - Research initiatives and industries using and applying the standards - Publishers and Journals distributing (standardized) data and models - Funders having interest in sustainability and reuse of scientific results - Standardization bodies providing support for the standardization process How to publish and distribute the standards? How to convince the communities to apply standards? How to certify implementation of standards?