diff --git a/content/03.02.data-management.md b/content/03.02.data-management.md index 6fbc64e..fd7b15a 100644 --- a/content/03.02.data-management.md +++ b/content/03.02.data-management.md @@ -59,6 +59,20 @@ BIMS (Breeding Information Management System) [@doi:10.1093/database/baab054] is Germinate integrates and connects with other BrAPI-enabled tools such as GridScore for phenotypic data collection, Flapjack for genotypic data visualization and Helium for pedigree visualization, but, due to the nature of BrAPI, Germinate can act as a data repository for any BrAPI-compatible tool. Thanks to the interoperability provided by BrAPI the need for manual data handling becomes a rarity with the direct benefit of faster data processing, fewer to no human errors, data security and integrity. +#### PIPPA + +[PIPPA](https://pippa.psb.ugent.be) is a data management system used for collecting data from the [WIWAM](https://www.wiwam.be/) range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe in a variety of configurations with different types of equipment such as weighing scales, cameras and environment sensors. Examples are: + ++ [Umea Plant Science Centre](https://www.upsc.se/plant-growth-facilities-at-upsc-and-slu-umea/325-upsc-tree-phenotyping-platform.html) ++ [Fondazione Edmund Mach](https://cri.fmach.it/en/Facilities/Technological-Facilities/Plant-Phenotyping#application_fields) ++ [Phenovision](https://www.psb.ugent.be/phenotyping/phenovision) + +Developed from 2016 onwards, the software features a web interface with functionality for setting up new experiments for the platform(s), planning imaging and irrigation treatments, linking metadata to pots (genotype, growth media, manual treatments), exporting data, importing data and visualizing data as charts. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission. + +To share the phenotype data of the experiments linked to publications, an implementation of BrAPI 1.3 was developed on a separate public PIPPA server open to the public, which allowed read only access to the data in a standardized format. This endpoint was registered on [FAIDARE](https://urgi.versailles.inra.fr/faidare/) and allows the data to be found alongside data from other BrAPI endpoints. + +As the BrAPI ecosystem has matured, it created a clear path for the development of PIPPA as to how to share data in a manner according to the FAIR principles which are becoming standard in plant research data management best practices. In combination with the support for [MIAPPE](https://www.miappe.org/), these have served as guidelines in the current development, which is focussed on delivering a public BraPI 2.1 endpoint and making more high throughput datasets publicly available via BrAPI. + #### MGIS diff --git a/content/metadata.yaml b/content/metadata.yaml index f0793d2..7e4a22b 100644 --- a/content/metadata.yaml +++ b/content/metadata.yaml @@ -323,6 +323,14 @@ authors: affiliations: - Jülich research center, Institute of Bio- and Geosciences (IBG), Bioinformatics (IBG-4) and Bingen Technical University of Applied Sciences, Germany corresponding: false + - name: Rafael Abbeloos + initials: RA + github: raabb + orcid: 0000-0002-0177-3887 + email: rafael.abbeloos@vib.be + affiliations: + - VIB AgroIncubator + corresponding: false - name: Laszlo Lang initials: LL github: LzLang