Towards standardization of plant phenotypic data_Krajewski

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 [email protected]

mailto:[email protected]


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.











WP 3: Community standards for the interoperability of plant phenotypic data resources


• 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


Plant phenotypic data


• 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?


„Minimum Information About ...” approach Biosharing website

Minimum Information about Plant Phenotypic Experiment (MIAPPE)

http://www.biosharing.org/




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 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.org/Workgroups/MIAME/miame_2.0.html

Core Information for Metabolomics Reporting (Metabolomics Standards Initiative), Fiehn et al. (2007a) http://msi-workgroups.sourceforge.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


http://www.mged.org/Workgroups/MIAME/miame_2.0.html



http://msi-workgroups.sourceforge.net/




http://www.psidev.info/groups/miape

http://www.psidev.info/groups/miape

http://gensc.org/gc_wiki/index.php/MIxS

http://gensc.org/gc_wiki/index.php/MIxS


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)




http://www.biosharing.org/bsg-000543





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


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


http://www.isa-tools.org/






study file

bio

sou

rce

attribute

assay 2 file

sam

ple

attribute

Phenotyping assay (ISA-TAB phenotyping configuration)

metabolite profiling assay, transcription profiling assay, histone modification profiling, ...

Other assays (configurations provided with ISA Tools)


assay file

sou

rce

/sam

ple

attribute

raw data file

derived data file

trait def file


cropnet.pl/phenotypes



INRA, Versailles: data export from Ephesis database

Implementations

https://urgi.versailles.inra.fr/ephesis/ephesis/viewer.do




Implementations

• IPK, Gatersleben, Germany: data export from Laboratory Information Management System (LIMS)


Implementations

Gregor Mendel Institute, Vienna: data import and export in the GWAS web application

http://gwas.gmi.oeaw.ac.at/




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

http://www.isa-tools.org/tools.html

http://www.isa-tools.org/tools.html







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

Date post:	12-Apr-2017
Category:	Science
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