# Sharing phenotyping data: Deploying the open-source Phenotyping Hybrid Information System PHIS on the EGI Infrastructure

Isabelle Alic, Vincent Nègre, Andrea Manzi, Sylvain Poque, Jesper Cairo

Westergaard

► To cite this version:

Isabelle Alic, Vincent Nègre, Andrea Manzi, Sylvain Poque, Jesper Cairo Westergaard. Sharing phenotyping data: Deploying the open-source Phenotyping Hybrid Information System PHIS on the EGI Infrastructure. 24. International Semantic Web Conference (ISWC 2025), EOSC, Nov 2025, Nara, Japan. 10p. hal-04985950

HAL Id: hal-04985950

https://hal.inrae.fr/hal-04985950v1

Submitted on 11 Mar 2025

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# Sharing phenotyping data:
## Deploying the open-source Phenotyping Hybrid Information System
## PHIS on the EGI Infrastructure

Contact: Isabelle Alic - [isabelle.alic@inrae.fr](mailto:isabelle.alic@inrae.fr)

EOSC Symposium 2022 - Prague - 17th of November 2022
# Phenotyping communities

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EMPHASIS

Field Installation

Controlled Environment

Data and Computational Services

Modelling

Field Site

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Map data © OpenStreetMap contributors, CC-BY-SA, Imagery © Mapbox
# Phenomics Data Challenge

## Plant Phenomics Experiments

* Expensive, require a lot of resources and often very hard

* Cannot be reproduced

* Huge and complex datasets

* Strong needs of transparence: reproducibility for data analytics

## Save time, make data valuable!

But re-analyses, meta-analyses and new analyses

→ impossible without rich metadata

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# Make FAIR data, structure your data

## Identification

* Everything can be identified: plants, experiments, sensors, events, etc.

* Persistent, unambiguous, resolvable

## Semantics

* Naming Conventions

* Controlled vocabulary

* Formalized relationships between entities

* Data annotation and enrichment

## How?

**PHIS, an ontology driven**
**Information System**

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INRAO

Deploying PHIS on the EGI Cloud
2022-11-17 / EOSC Symposium 2022

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# PHIS: an Ontology driven Information System for Plant Phenomics

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# EGI-ACE: PHIS Deployment on EGI Infrastructure

## Our Strategy

* Rely on **EGI infrastructure and services** to build a **European e-infrastructure** for plant phenotyping

* Access to these services through the **EGI-ACE call for uses program**

* Setup a **Proof Of Concept**

https://phis.emphasis.fedcloud.eu/egi-demo/app/

* Tested by **Early Adopter users** (University of Helsinki, University of Copenhagen, INRAE)

* Disseminate services to a wider audience

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# PHIS and the EGI Infrastructure and Services

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Analyse

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RÉPUBLIQUE
FRANÇAISE

2022
Élèves
Pratiquants

recherche.data.gouv.fr

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Scripts

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Sensor

Interface Web

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EGI Check-In

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Java

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API, Web Services
REST / JSON

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NoSQL
(MongoDB)

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Triplestore
(RDF4J, GraphDB)

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Datafiles

Data

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Amazon S3

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EGI DataHub

eINfrastructure

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## EGI Services used

### Cloud Computing

- Host our information system (CESNET-MCC provider)

- Dynamic DNS service provides a unified, federation-wide Dynamic DNS support

### Authentication

- EGI Check-in service has been integrated as the authentication system

### Storage

- Connected with the online storage service provided by IN2P3-IRES and the FranceGrilles (FG-iRODS).

- Connected with S3 storage

- DataHub, based on OneData technology

### Data analysis

- Deep Hybrid DataCloud portal hosts our DL models
# EGI-ACE & PHIS: Perspectives

## Next Steps

* **Data integration:** Allow interconnection of these data thanks to PHIS Web Services and BrAPI layer

* Connecting **EGI DataHub File storage system**

* Export dataset to recherche.data.gouv.fr

- EOSC Pillar Project

- Constitution of the dataset in PHIS

- Deposit on recherche.data.gouv.fr :

- Declaration of the dataset with the associated metadata

- Recovery of the DOI in PHIS

* Link to DeepLearning models (hosted on the Deep Hybrid DataCloud portal)

* Disseminate
EGI-ACE & PHIS: Data integration

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# Acknowledgements & Links

## Acknowledgements

* Vincent Negre - INRAE LEPSE

* Andrea Manzi - EGI Foundation

* Sylvain Poque, Kristiina Himanen, Tatu Polvinen - University of Helsinki

* Jesper Cairo Westergaard - University of Copenhagen

* Cyril Pommier - URGI

* Pascal Neveu, Anne Tireau, Valentin Rigolle, Renaud Colin - INRAE MISTEA

## Useful Links

* OpenSILEX website: http://opensilex.org/

* PHIS demonstration: http://phis.inra.fr/

* How to contribute to OpenSILEX?
  Github repository: https://github.com/OpenSILEX/

* OpenSILEX Docker: https://github.com/OpenSILEX/opensilex-docker-compose

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UNIVERSITY OF HELSINKI

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University of Copenhagen

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