data and model management in systems biology

Data and model management in Systems Biology

Dagmar WaltemathUniversity of Rostock, Germany

Kinetics on the move – Happy 10th anniversary to SABIO-RK!Heidelberg, 31st May, 2016

http://www.slideshare.net/dagwa/data-and-model-management-in-systems-biology

http://www.slideshare.net/dagwa/data-and-model-management-in-systems-biology

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Junior research group: Management of simulation studies in systems biology

Tool development: SBGN-ED for the graphical representation of networks

Infrastructure: Data management for systems biology in Germany

Standards and tools for model management

www.sems.uni-rostock.de

https://sems.uni-rostock.de/

© 2009 UNIVERSITÄT ROSTOCK 3

NBI-SysBio: Data management for systems biology in Germany

3● Sustainable infrastructure for data management

● Access to documented and reproducible results

● Systems Biology Standards

● Tool Development

● Education

www.denbi.de (training – services – jobs)

http://www.denbi.de/


Photo: NY - http://nyphotographic.com (CC BY-SA 3.0) Photo: janneke staaks on flickr

Fig. courtesy 10.1371/journal.pbio.1001779

TM

http://nyphotographic.com/

https://www.flickr.com/photos/jannekestaaks/14391226325/in/photostream/

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001779


Data management is …

● Data management describes procedures and actions that help to store, preserve, organize and control the data generated during a (research) project.

● Aspects of data management include: – Data Ownership;– Metadata Compilation;– Data Lifecycle Control;– Data Quality; – Data Access and Dissemination Photo: NY - http://nyphotographic.com (CC BY-SA 3.0)

http://nyphotographic.com/

5/31/16 © 2009 UNIVERSITÄT ROSTOCK 6

● Data about data● Improved understanding of encoded data items● Descriptive details● Discovery and search for existing data, online browsing of data● Standardized and structured information

– Purpose, origin, time references, geographic location, creator, access conditions, and terms of use of your data collection

● Often encoded in ontologieshttps://www.libraries.psu.edu/psul/pubcur/what_is_dm.html#data-management

Metadata

https://www.libraries.psu.edu/psul/pubcur/what_is_dm.html#data-management


● Well-structured, controlled vocabularies

● Capture and convey commonly agreed definitions and concepts in a domain

● Communication across people and software tools

● Enable reuse of domain knowledge

● Make implicit domain knowledge explicit and queryable

● Bio-ontologies

– Gene Ontology, ChEBI, UniProt

– Systems Biology Ontology (concepts and terminology for modeling)

Ontologies

http://geneontology.org/

https://www.ebi.ac.uk/chebi/

http://www.uniprot.org/

http://www.ebi.ac.uk/sbo/main/

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Example: Definition of „cell growth“ in the Gene Ontology

5/31/16

id: GO:0016049name: cell growthnamespace: biological_processdef: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present."synonym: "cell expansion" RELATED []synonym: "cellular growth" EXACT []synonym: "growth of cell" EXACT []is_a: GO:0009987 ! cellular processis_a: GO:0040007 ! Growthrelationship: part_of GO:0008361 ! regulation of cell size

© 2009 UNIVERSITÄT ROSTOCK

http://www.ebi.ac.uk/QuickGO/


● Increased confidence and trust in the data● Better understanding of how to use the data, and of the data itself● Better data quality ● Coherent data when standards are used● Improved business processes (saving time, guaranteeing high quality)● Improved access to data and improved reproducibility● Better exploitation of data through easier data exchange and

integration

Advantages of careful & planned data management


● Reusable

● Exchangeable

● Interoperable

● Long-term available (in open repositories)

● Curateable

● Shareable

Advantages of standardised data


Photo: janneke staaks on flickr

https://www.flickr.com/photos/jannekestaaks/14391226325/in/photostream/


Research data in the modeling life cycle

Modelsequations, parameters,data tables

Ideastext,

drawings

Experimental results

text, data tables

Publicationstext,

figures

Analysesconfiguration files,

data tables

Fig. courtesy Martin Scharm (adapted)

https://www.sbi.uni-rostock.de/team/single/martin-scharm/



● Mathematical formulae

● Networks, diagrams

● Image data

● Publications

● Experiment descriptions

● Experimental results (both lab and simulation)

● Definitions of things (e.g., gene functions, chemical structures...)

Figures top to bottom: (1) By Noah A. Rosenberget al. Slightly modified by User:Wobble. - Public Library of Science, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=2839383; (2) By http://rsb.info.nih.gov/ij/images/, Public Domain, https://commons.wikimedia.org/w/index.php?curid=655748; (3) BIOM005, generated using CellDesigner 4, (4,5) PMID:18669651

https://commons.wikimedia.org/w/index.php?curid=2839383


http://europepmc.org/articles/PMC2504824


● Heterogenuous

● Highly connected

● Context-dependent

● Distributed

● Big


Figures top to bottom: (1) By Noah A. Rosenberget al. Slightly modified by User:Wobble. - Public Library of Science, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=2839383; (2) By http://rsb.info.nih.gov/ij/images/, Public Domain, https://commons.wikimedia.org/w/index.php?curid=655748; (3) BIOM005, generated using CellDesigner 4, (4,5) PMID:18669651



http://europepmc.org/articles/PMC2504824


The model

● Mathematical equations

● Biological entities

● Kinetic information

● Encoding: & semantic annotationsTM

<bqmodel:isDescribedBy><rdf:Bag>

<rdf:li rdf:resource="http://identifiers.org/pubmed/18669651"/></rdf:Bag>

</bqmodel:isDescribedBy>

<parameter id="parameter_49" name="L" metaid="metaid_0000078" value="20670"/>

http://identifiers.org/pubmed/18669651


SBML – Standard for model encoding

● Systems Biology Markup Language

● Community-driven de-facto Standard

● Free & open source: www.sbml.org

● Supported by many organizations and tools

● Encodes computational models of biological processes (compartments – species – reactions - parameters)

http://www.sbml.org/


SBGN – Standard for visual representation

● Systems Biology Graphical Notation● Standardised glyphs for biological entities

● Three levels

– SBGN-AF | SBGN-ER | SBGN-PD

● Free & open source: www.sbgn.org

● Tool support

● Interpretable Format: SBGN-ML

Fig.: http:sbgn.org

http://www.sbgn.org/

http://sbgn.org/


Fig.: SBGN map for BIOM183, CellDesigner

SBGN – Standard for visual representation

Fig.: SBGN map for BIOM005, CellDesigner


● Reproduce behaviour of the model

● Publish and share virtualexperiments– Simulation setup / conditions– Pre- and post-processing– Observations

● Encoding: & & result data in Excel, CSV files <listOfSimulations> <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="100" numberOfPoints="100"> <algorithm kisaoID="KISAO:0000019"/> </uniformTimeCourse> </listOfSimulations>

The analysis

Fig. M. Stefan et al, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596252/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596252/


SED-ML – Standard for model analysis

● Links to models used in an analysis

● Pre- and Post-processing of models

● Type of simulation

● Definition of output

● Free an open source: www.sed-ml.org

● Tool support

→Showcase your tool support online ←

http://www.sed-ml.org/

http://sed-ml.org/


SED-ML – Standard for model analysis

Fig. M. Stefan et al, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596252/

Simulation of BIOM183 in SED-ML Web Tools without simulation description

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596252/


m nCoordinate annual meetings

SimulationGuidelinesOntologies

- Next HARMONY: Auckland, June 7-11, 2016

- Next COMBINE:Newcastle, Sep 19-23, 2016

Coordinate standards development

- Common procedures- Interoperable software tools- Discussion forums, mailing lists...

Represent community

- Funders- Other communities

Provide standards resources

- Single entry point- Resolvable URI- Web infrastructure

Standard-compliant software tools for modeling


The path2models project integrated data from different databases into more than 140.000 SBML models.

Fig.: Büchel et al BMC Sys Biol (2013)http://www.ebi.ac.uk/biomodels-main/path2models

http://www.ebi.ac.uk/biomodels-main/path2models


The Systems Biology Workbench is a software framework to help heterogeneous application components communicate with each other.

Modeling

Editing

Simulating

Analysinghttp://sbw.sourceforge.net

Standard-compliant software tools for modeling

http://sbw.sourceforge.net/


The decision whether and how to share data often rests with researchers. Roche DG, Lanfear R, Binning SA, Haff TM, Schwanz LE, et al. (2014) Troubleshooting Public Data Archiving: Suggestions to Increase Participation. PLoS Biol 12(1): e1001779. doi:10.1371/journal.pbio.1001779


● Bundling files● Shipping results● Exchanging data● Keeping provenance

● Encoding: zip-like file with a manifest (meta-data)● Generate, modify & share through WebCAT

COMBINE Archive

http://webcat.sems.uni-rostock.de/


COMBINE Archive

Original publication

SBGN map

SBML model versions

SED-ML files

Open in Webcat

Open in SEEK

https://www.fairdomhub.org/publications/253


Model curation & publication

http://www.ebi.ac.uk/biomodels-main/


Model curation & publication

http://models.cellml.org/cellml


Model curation, simulation & publication

http://jjj.biochem.sun.ac.za/models/experiments/bachmann-user/


Introduction to SEEK & FAIRDOM by Olga Krebs.

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Thank you for your attention.

http://www.denbi.de/ @SemsProject

m nhttp://co.mbine.org

http://www.denbi.de/

http://co.mbine.org/