About PHIS

PHIS is an ontology-driven Information System designed for Plant Phenomics.

PLANT PHENOMICS DATA

PHIS is designed to store, organise and manage highly heterogeneous (e.g. images, spectra, growth curves) and multi-spatial and temporal scale data (leaf to canopy level) originating from multiple sources (field, greenhouse).

ONTOLOGY ARCHITECTURE

Its ontology-driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms including field and greenhouse.

FAIR DATA

PHIS allows to enrich datasets with knowledge and metadata enabling the reuse of data and meta-analyses. It interoperates and integrates data into external resources (e.g. modelling platforms or external databases) and provides FAIR data.

How it works?

PHIS main features.

Web user Interface

A Web user interface allows exploration of phenomics data through interactive and user-friendly menus and tools.

Data Integration

PHIS allows to store, organise and manage heterogenous multi-deminsional phenomics data originating from multiple sources.

Object indentification

The use of URIs allows standardized, unique and unambiguous identification of objects involved in experiments.

Ontologies

Two application ontologies (OEPO and OEEV) describe objects and events involved in phenotyping experiments.

Events and Annotations

Datasets are enriched with knowledge and metadata enabling the reuse of data and meta-analyses.

Object tracking

Tracking features based on oject identifcation and events allows following the different objects involved in experiment in time and space.

Advanced data querying

An inference engine based on the semantics and rules represented in the ontologies enables advanced queries, thereby linking the knowledge stored in the Triple Store to the information distributed among the different storage systems.

Graphic Visualisation

Advanced visualization features allow displaying images, dynamic graphs of static or time courses of phenotypic and environmental variables.

Analysis and Workflows

Different tools allow advanced data querying and computing features including data analysis tools and integration of workflows.

Hybrid storage system

PHIS is a hybrid system based on different storage databases (PostgreSQL, MongoDB, iRODS, RDF4J).

Web Service API

The Web Service API allows integration of data from external databases and resources, export to computing and modelling platforms and integration of phenomic data into other systems.

Open Source

PHIS is available as an open source software under a GNU Affero General Public License version 2. Source code, user and developer documentation are available at github.com/OpenSILEX.

Availability & Requirements

The source code, user and developer documentation of latest version of PHIS are available at https://github.com/OpenSILEX under a GNU Affero General Public License version 2. PHIS requires Java JRE or JDK version 1.7, PHP 5.6, PostgreSQL 10.1, RDF4j 2.2.1, MongoDB 3.4.4 and R 3.3.1 and runs on Linux, Mac, and Microsoft Windows platforms.

PHIS Stats

PHIS is currently being used in several platforms in the field and controlled conditions. In the case of M3P in Montpellier, these installations have generated

20,000,000

Images

250,000,000

Phenotypic measurements

154,000,000

Environmental data points

PHIS Portfolio

See some images of sensors, plant images and installations using PHIS

  • All
  • PLANT IMAGES
  • Sensors
  • Installations

hemispheric image

PLANT IMAGES

m3p greenhouses

Installations

hemispheric segmented

PLANT IMAGES

phenoarch

Installations

harvesting

PLANT IMAGES

wheat plots

PLANT IMAGES

diaphen

Installations

phenopsis

Installations

arabidopsis

PLANT IMAGES

soils sensors

Sensors

watering system

Sensors

phenodyn

Installations

PEOPLE

PHIS is the result of collaboration between two research teams of INRA (the French National Institute for Agricultural Research) of Montpellier:
the LEPSE (Laboratory of Plant Ecophysiological responses to Environmental Stresses) and MISTEA (Mathematics, Informatics and Statistics for Environment and Agronomy).

Contact Us

Contact us or just say hello!

Address

2 Place Pierre Viala, 34060, Montpellier, FRANCE

Phone Number

+33 499 612 956

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