# Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii

Cyril Pommier, Pawel Krajewski, Thomas Letellier, Hanna Cwiek, Célia Michotey, Pierre Roumet, Raphaël-Gauthier Flores, Guillaume Merceron, Erik Kimmel, Michael Alaux, et al.

► To cite this version:

Cyril Pommier, Pawel Krajewski, Thomas Letellier, Hanna Cwiek, Célia Michotey, et al. Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii. 23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States. hal-02739236

HAL Id: hal-02739236

https://hal.inrae.fr/hal-02739236v1

Submitted on 2 Jun 2020

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Phenotypic data exchange and processing
using ISA-Tab standard

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INRA
SCIENCE & IMPACT

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TransPlant project use case with GnplS.Ephesis and Bii.

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Cyril Planmer/ Phenotypic data exchange and processing using ISA-Tab standard, transPlant project use case with GnplS.Ephesis and Bii

10 Jan 2015

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TRANSPLANT, ISATAB FOR PHENOTYPING

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TransPLANT

* 4 year EU FP7-funded project (DG CONNECT) coordinated by EMBL-EBI,

* Until septembre 2015

* An I3 project with elements of coordination, service and RTD

* http://www.transplantdb.eu/

* Aims

- ...

- Provide of an integrating point of interactive access to diverse data sets

- Develop common standards for use within transPLANT and a wider community

- Engage with other related communities to share experiences, tools and roadmaps

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Transplant Standardization

* Work Package 3

- Community standards for the interoperability of data resources

- Aim: To develop recommendations concerning annotation and formatting methods of data sets containing phenotypic observations

* Main deliverables

- Recommended ontology set for use in phenotype description and epigenetic variability

- Format specifications for data exchange by flat file and web services

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Recommended ontology set

* Ontologies

- References

* Plant Ontology, cROP

- Application Ontologies

* Species/domain specific

* Crop Ontology : www.cropontology.org

- Vitis : Grape Ontology

- Wheat : Wheat Ontology

* INRA Ontologies

- EO, to be developed

- Chebi, Brenda Enzyme, Golm Metabolome

- User specific ontology

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Recommended ontology set

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ISA-TAB format: Investigation/Study/Assay

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http://www.isa-tools.org

Sansone & Rocca-Serra (2012)

* text files

* structures/terms:

* source/sample

* factor

* characteristics

* protocol

* parameter

* unit

* extract

* comment

* supports annotation

Tools:

ISA Software Suite

To-RDF converter

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BII USE CASE

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BII

* ISA TAB Archive system

* Index capabilities

* Polapgen/Transplant instance

- http://cropnet.pl/transplant-bii/

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Bii manager

* Administrator credentials form

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Bii Manager

* Data management

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Bii Manager

* Loading ISA-TAB into database

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## Bii Web interface

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## Bii Web interface
ISA File informations

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## GNPIS USE CASE

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## GnpIS

* Integrative information system

- Plant and bioagressors

- Multi thematic

* Genetic

* Genomic

* Phenotyping

- Public and private data : partners, international consortium

* INRA : French National Center for Agronomic Research

* URGI : INRA Research laboratory

- Production

- Data integration

- Development

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Cyril Planremier : Phenotypic, data exchange and processing using ISA-Tab standard, transPlant project use case with GraphEphesos and Bi

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## GnpIS: user web interfaces

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## GNPIS PHENOTYPING DATA

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## Phenotyping in GnpIS
Ephesis application scientific perimeter

* **Phenotype and environment Experimental data**

- Whole Trials

- Generic : Ontology driven

- Levels: Whole trial, plot, plant data in experimentation

- Observation variables : traits, environment, ...

- Multiple factors

- Genotype factor is mandatory

- 0 to n other factors : treatments, stress, etc...

- Punctual observation or temporal series/kinetic

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### EPHESIS WEB APPLICATION

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## Phenotyping in GnpIS
Ephesis application scientific perimeter

* **Raw or elaborated data**

- Alphanumeric or complex, no images

- Volume limitation

- archiving system : Phenome example.

* **Integration and interoperability based on Pivot scientific objects**

- Phenotype → GWAS, Genomic Selection, Genotyping, ...

- Germplasm/plant material

- Ontologies

- Project

* **Functionalities**

- Phenotyping trial archive

- Dataset builder

- Multi trial

- Multi annual

- For GxE or Genetic studies

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## Phenotyping Interface Overview
Ephesis

* https://urgi.versailles.inra.fr/ephesis

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## Search criterions overview

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## Genotype/Germplasm tab

* Taxon

* Genetic resource
accession

* Collections

* Panel (soon)

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## Variable tabs

* Ontology driven

* Reference Ontologies

* Specific ontologies

- Trait

- Environment

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## Trial details tabs

* Trial identificaiton

- ID

- Name

* Year, Date

* Experimental site

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## Multi Trial Dataset

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## Trial Details

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CyntPlanner

10 Jan 2015

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## GnpIS Ephesia ISA Tab export

* One search result

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→ one ISA archive / investigation

* Each Trial

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→ one study

* Investigation

- Ontologies declaration

- Ephesia query parameter, date, version

* Study

- Trial identification (Number, name, site, date, design, Contacts, ...)

- Trial Publications

- Experimental Factors: Cultural practice (itk), nitrogen, water

- Plant Material list: full Identification (taxon, variety, BRC, Accession Number, Lot Number)+ Isa Archive short ID

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## GnpIS Ephesia ISA Tab export

* Assays

- Type: phenotyping

- Factor Values: low nitrogen, high water...

- Assay Name: combination of factors: lownitrogen+accesion1, lownitrogen+accesion2, highnitrogen+accesion1, highnitrogen+accesion2

* Trait definition file

- Reference existing ontologies, including Scale, unit, protocol (Crop Ontology, INRA Ontologies, ...)

* Raw data file

- Not mandatory

- Not used (volume) can be a pointer/URI to an archive in the future

* Derived Data File

- Use ID declared in ISA and Trait files

- Germplasm + Factor = Assay Name

- Traits

- As many datafile by assay as needed

- Trace the transformation protocol (analysis tool, data transformation procedure, etc...)

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CyntPlanner: Phenotypic data exchange and processing using ISA-Tab standard. InTransPlant project use case with GraphEphesia and ISI

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## STANDARDS AND DISTRIBUTED INFORMATIONS SYSTEMS

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Transplant
Phenome

## GnpIS.Ephesia: Phenome Integrative portal

* **French Plant Phenotyping Platform**

- High throughput Phenotyping

- Field

- Controlled environment

- 9 Nodes across France

* **Distributed information system**

* **Open API Web Service**

- Need of a common Phenotyping OpenAPI

- Need to build a metadata standard

- PODD

- Crop research Ontology

- Distributed index system, document based (SolR, Elastic Search)

## Perspectives

* Isa Tab standard dissemination

* Dataset building for analysis

* Phenotype API building

- Phenome

- France

- Europe

- International

- Triticeae Toolbox?, IBP?, PODD?, ...

Contact: cpommier_at_versailles.inra.fr

## Acknowledgements

Pommier C., Krajewski P., Letelier T., Cwiek H., Michotey C., Markiewicz A., Roumet P., Flores R., Merceron G., Kimmel E., Alaux M., Steinbach D., Quesneville H.

Thank you

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