An overview of FAIR aspects in biomedical standardisation efforts, with focuson COMBINE / biomedical simulation.

1. Prof. Dr. Dagmar Waltemath
Medical Informatics Laboratory
University Medicine Greifswald
dagmarwaltemath
FAIR data management
in biomedicine
QPTDat Workshop Plasma Medicine | Oct 28 2020 | slideshare

2. Systems Biology is …
the science that studies how biological function
emerges from the interactions
between the components of living systems.
… and how these emergent properties
enable/constrain the behavior
of these components.
2
Systems Medicine is the implementation of
Systems Biology approaches in medical
concepts, research and practice.
(https://www.casym.eu/)

3. Systems Biology is …
3
Biological scales DE Systems Further approaches
Images: https://doi.org/10.1002/wsbm.33, https://doi.org/10.1371/journal.pcbi.1002815, https://doi.org/10.1371/journal.pcbi.1004591

4. 4
Scharm & Waltemath (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in
Drosophila embryos. F1000Research 5
Biosimulation studies
comprise of many
heterogenous data items.
Original
publication
Visualisation Model encoding Simulation encoding
COMBINE
Archive

5. Systems Biology (Medicine)
research transformed from
purely paper-based reporting…
…to reproducible
and standardized
experiments.
How long
did this
take?
5

6. Dräger & Waltemath (2020) Overview: Standards for Modeling in Systems Medicine.
Systems Medicine https://doi.org/10.1016/B978-0-12-816077-0.00001-7
A glimpse at the
COMBINE standardisation
movement.
And why did
it work?
Invention of FAIR
6

7. The standardization movement was
driven by the community.
7
(2005) https://sbmlteam.smugmug.com/Other-
meetings/Model-database-curation/i-qtwsCH3/A
(2009) https://sbmlteam.smugmug.com/BioModels-
meetings/Second-BioModelsnet-Training/i-pqmnk7n/A
(2019) https://doi.org/10.1515/jib-2020-0005

8. 8
An umbrella organization coordinates
the standards developments.
Data formatsGuidelines Semantic layer
http://co.mbine.org/
Editorial Boards
Specifications
Software tool support
Mailing lists
Annual meetings

9. Journals and funders support
RDM efforts.
9
12/11/14
We will [..] offer expert technical peer
review specifically checking that
submitted systems biology or
physiology-based models run according
to the results presented in the
manuscript submitted to the journal.
Every article published in Physiome
is connected to a curated and
permanent version of the model
code with a persistent identifier.
Through the Physiome paper, the
code necessary to run the model is
easily accessible.

10. Modelers follow the FAIR guiding
principles when providing reusable
simulation models.
10
• Identifiable
data items
• Persistent
• Searchable
• Identifiers
following standard
protocols
• Authentification
• Access to meta
data, even if data
not accessible
• Formal,
accesssible
representation
of data
• Qualified
references
• Licensing
• Provenance
• Standards
compliance
https://fairsharing.org/ | https://github.com/FAIRMetrics

11. 11
Open, collaborative developments
involve both researchers and users.
Reproduce a simulation Detect differences
http://sed-ml.org/ https://github.com/SemsProject/BiVeS https://most.bio.informatik.uni-rostock.de/
https://yomost.bio.informatik.uni-rostock.de/
Frank
Bergmann
David
Nickerson
Martin
Scharm
Tom
Gebhardt
Vasundra
Touré
Understand model evolution
R1.2. (Meta)data
are associated with
detailed provenance
I1. (Meta)data use a
formal, accessible,
shared, and broadly
applicable language
for knowledge
representation.
F2. Data are
described with
rich metadata
(defined by R1
below)

12. 12
Open, collaborative developments
involve both researchers and users.
Bundle all files in one archive Develop management strategies Link models and clinical data
https://fairdomhub.org/
https://github.com/MaSyMoS
https://combinearchive.org/ https://github.com/matthiaskoenig/exsimo
Wolfgang
Müller
Ron
Henkel
Mariam
Nassar
Martin
Peters
Matthias
König
Henkel et al (2015) Combining computational models, semantic annotations and simulation experiments in
a graph database. Oxford DATABASE
2 experiments,
3 model versions,
changes, meta-data

13. Data is available online, using standard
formats, open protocols & PIDs.
13
12/11/14 © 2009 UNIVERSITÄT ROSTOCK | Fakultät für Informatik und Elektrotechnik
https://www.ebi.ac.uk/biomodels/
https://models.cellml.org/cellml
http://bigg.ucsd.edu/ http://www.opensourcebrain.org/

14. Automated tool chains for data and model
reuse support interoperable standards.
14
Scharm & Waltemath (2015) Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit.
BTW http://www.btw-2015.de/res/proceedings/Workshops/DMS/Scharm-Extracting_reproducible_sim.pdf

15. Guidelines help to perform the
necessary standardization tasks.
10 tips for building useful SBGN maps Building fully featured COMBINE archives
15

16. A community of FAIR-aware repositories,
tools, projects and work groups
contributes to better scientific practise.
16
12/11/14
FAIRDOMHub GMDS FAIR data infrastructures
GO FAIR FAIR4Health VODAN

17. 17
12/11/14 © 2009 UNIVERSITÄT ROSTOCK | Fakultät für Informatik und Elektrotechnik
https://www.ebi.ac.uk/biomodels/covid-19 (through EOSC OVID-19 fast track funding)
The COMBINE approach to FAIR RDM
and reproducible science connects to
the medical domain.

18. Harmonised and semantically enriched
COVID-19 studies contribute to fighting
the current pandemic.
18
Clinical platform
M-KIS
KAS+ TP-F
Kairos CentraXX
Medical Device
Integration
Klinic
systems
myMedis,
swisslab, …
Patient
information
system SAP
Biobanking
BIMS
Kairos CentraXX
metadata
management
Extraktion,
Transformation,
Load
transfer
trusted third party
Data transfer
federated
data
platform
Patient care Research data platform
NFN
Links: https://images.app.goo.gl/uxka5cMEMxJD1jVF8
project specific
solutions
data integration
center (DIC)

19. Bottom-up, community-driven approach to
standardising biomedical simulation studies.
What does it take to do FAIR
biomedical science?
Top-down, coordinated approach to research
data management.
Short-term funding
to drive research Sustainable
research software
Active and open
community
Enthusiastic and
visionary drivers
19

20. Thank you for your attention
Dagmar Waltemath
Medical Informatics Lab &
Core Unit Research Data Management
University Medicine Greifswald
0000-0002-5886-5563
Image source: Wikimedia Commons, Creative Commons
Attribution-Share Alike 4.0 International