“Open Research Data: Implications for Science and Society”, Warsaw, Poland, May 28–29, 2015, conference organized by the Open Science Platform — an initiative of the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw. pon.edu.pl @OpenSciPlatform #ORD2015

1. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Towards standardization of plant phenotypic
data
Paweł Krajewski
Hanna Ćwiek
Wojciech Frohmberg
Institute of Plant Genetics,
Polish Academy of Sciences,
Poznań, Poland
pkra@igr.poznan.pl

2. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project
• A 4-year (2011-2015) EU FP7-funded project (DG CONNECT)
coordinated by EMBL-European Bioinformatic Institute,
Hinxton, UK, with elements of coordination, service and R&D
(I3).
• Aim: design, implement, deploy and operate the software
infrastructure important for the future needs of plant
scientists.

3. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project

4. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project

5. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project

6. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project

7. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
The transPLANT project
WP 3: Community standards for the interoperability of plant phenotypic data
resources

8. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
• Phenotypic data: observations of morphological, resistance, physiological,
yield-related, biochemical, ... traits.
• Characteristic features:
• dependence on genotype and environment,
• large spectrum of characteristics, sampling protocols, measurement
procedures, units.
• Main deliverables of WP3:
• recommended ontology set for use in phenotype description,
• content and format specifications for data exchange.
Plant phenotypic data

9. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Plant phenotypic data

10. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
• To be able to make the phenotypic data „open” preserving
their structure
• To improve (= make cheaper) storage, publication, exchange
between databases, ...
• Searching for experiments (metadata or data)
• Comparison of experiments
• Data integration
• Statistical analysis steered by metadata/annotation
Why to standardize?

11. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
„Minimum Information About ...” approach
Biosharing website
Minimum Information about Plant Phenotypic Experiment (MIAPPE)

12. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
s_ad_1 3 Dro1 Maresi ... ... 1.34 2.14 red ...Samples
(units)
Attributes
Checklist: the list of attributes which should
be given here
Experiment
Minimum Information about Plant Phenotypic Experiment (MIAPPE)

13. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Minimum
information
document
(initiative)
Microarrays
MIAME (MGED)
Metabolomics
CIMR (MSI)
Proteomics
MIAPE (PSI)
Sequence
MIxS (GSC)
Full name
(initiative),
publication,
document
Minimum
Information about a
Microarray
Experiment
(Microarray Gene
Expression Database
Group),
Brazma et al. (2001)
http://www.mged.o
rg/Workgroups/MIA
ME/miame_2.0.html
Core Information
for Metabolomics
Reporting
(Metabolomics
Standards
Initiative),
Fiehn et al. (2007a)
http://msi-
workgroups.source
forge.net/
Minimum
Information about
a Proteomics
Experiment
(Proteomics
Standards
Initiative)
Taylor et al. (2007)
http://www.psidev.
info/groups/miape
Minimum
Information about
any sequence
specifications
(Genomic Standards
Initiative)
Yilmaz et al. (2011)
http://gensc.org/gc_
wiki/index.php/MIxS
Minimum Information about Plant Phenotypic Experiment (MIAPPE)

14. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
List part Proposition
Study Accept existing list(s)
Assay Accept existing list(s) + additional
attributes
Biosource Accept existing list(s)
Environment New
Treatments Accept existing list(s)
Experimental design New (gap)
Sample: collection, processing,
management
Accept existing list(s) + additional
attributes (gap)
Phenotypic traits
Environmental variables
New (gap)
Minimum Information about Plant Phenotypic Experiment (MIAPPE)

15. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Minimum Information about Plant Phenotypic Experiment (MIAPPE)
http://www.biosharing.org/bsg-000543

16. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Requirements for the format to hold the metadata and data:
- human readable (with simple tools),
- compatible with all operating systems,
- easily made (with simple tools),
- possibility of having reusable templates,
- if possible – already accepted in some applications,
- appropriate for metadata, data and their semantic annotation.
RDF, XML ?
Proposition of data exchange format specification

17. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Investigation
Study
Assay
Data files
ISA-TAB format: Investigation/Study/Assay (after MAGE-TAB, http://www.isa-tools.org/ )c
Sansone & Rocca-Serra
(2012)
Text format files
Structures/terms:
- source/sample
- factor
- characteristics
- protocol
- parameter
- unit
- extract
- comment
Supports annotation
Tools:
ISA Software Suite
To-RDF converter
Proposition of data exchange format specification

18. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Proposition of data exchange format specification

19. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
study file
biosource
attribute
assay 2 file
sample
attribute
Phenotyping assay (ISA-TAB phenotyping configuration)
metabolite profiling assay,
transcription profiling assay,
histone modification profiling, ...
Other assays (configurations provided with ISA Tools)
Proposition of data exchange format specification
assay file
source/sample
attribute
raw
data
file
derived
data file
trait def
file

20. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
cropnet.pl/phenotypes
Proposition of data exchange format specification

21. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
INRA, Versailles: data export from Ephesis database
Implementations

22. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Implementations
• IPK, Gatersleben,
Germany: data export
from Laboratory
Information
Management System
(LIMS)

23. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Implementations
Gregor Mendel Institute, Vienna: data import and export in the
GWAS web application

24. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Implementations
IPG PAS: instance of BII Data
Manager
http://cropnet.pl/transplant-bii/
Migration to PSNC
man.poznan.pl
Submission in ISA-TAB format,
metadata search
Data analysis tools

25. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.

26. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.

27. www.transplantdb.eu
The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”. Contract number 283496.
Hanna Ćwiek
Wojtek Frohmberg
Augustyn Markiewicz
Paul Kersey
(Ensembl, Elixir)
Hadi Quesneville
Cyril Pommier
(RDA Wheat Data WG)
Magnus Nordborg
Ümit Seren
Jan van Oeveren
Marco van Shriek Matthias Lange
Astrid Junker
Uwe Scholz
Daniel Arendt
Stephan Weise
Christian Klukas
Dijun Chen
Aalt-Jan van Dijk
Jan Peter Nap
Björn Usadel
Fabio Fiorani
(EPPN, DPPN)
Philippe Rocca-Serra
Cezary Mazurek
Raul Palma
Fryderyk Raczyk