From c8fdcd8ba39982ec0085804d606c9244af0bf9e7 Mon Sep 17 00:00:00 2001 From: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com> Date: Fri, 5 Jul 2024 16:59:36 +0000 Subject: [PATCH] Merge pull request #59 from plantbreeding/Isabelle-inrae-patch-2-1 [ci skip] This build is based on https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01f97e786525879db23a1d72a3716051fe743bd3. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01f97e786525879db23a1d72a3716051fe743bd3/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9811436575 --- manuscript.html | 18 +++++++++--------- manuscript.md | 18 +++++++++--------- manuscript.pdf | Bin 1422646 -> 1423059 bytes spelling-errors.txt | 4 ++-- variables.json | 18 +++++++++--------- 5 files changed, 29 insertions(+), 29 deletions(-) diff --git a/manuscript.html b/manuscript.html index 770cbf1..1970071 100644 --- a/manuscript.html +++ b/manuscript.html @@ -123,8 +123,8 @@ - - + + @@ -340,9 +340,9 @@ - - - + + + @@ -359,9 +359,9 @@
This manuscript -(permalink) +(permalink) was automatically generated -from plantbreeding/BrAPI-Manuscript2@f87c419 +from plantbreeding/BrAPI-Manuscript2@01f97e7 on July 5, 2024.
The Hybrid Phenotyping Information System (PHIS6), based on the OpenSILEX framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the French national PHENOME and European EMPHASIS infrastructures. It manages and collects data from basic phenotyping and high throughput phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.
-PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment (MIAPPE7). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in FAIDARE8 very easy to implement.
-Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.
+PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms, such as OLGA, a genebank accessions management system, to retrieve accession information. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment (MIAPPE7). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services enables indexing of PHIS in FAIDARE8.
+Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adhesion to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.
PIPPA9 is a data management system used for collecting data from the WIWAM10 range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe. They can be setup in a variety of configurations with different types of equipment including weighing scales, cameras, and environment sensors. The software features a web interface with functionality for setting up new experiments, planning imaging and irrigation treatments, linking metadata to pots (genotype, growth media, manual treatments), importing data, exporting data, and visualizing data. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission.
diff --git a/manuscript.md b/manuscript.md index ceb75be..16ba1d5 100644 --- a/manuscript.md +++ b/manuscript.md @@ -94,8 +94,8 @@ header-includes: | - - + + @@ -311,9 +311,9 @@ header-includes: | - - - + + + @@ -335,9 +335,9 @@ manubot-clear-requests-cache: false This manuscript -([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/f87c4197b7cb26dfecb51960773f70097e1bdfd5/)) +([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/)) was automatically generated -from [plantbreeding/BrAPI-Manuscript2@f87c419](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f87c4197b7cb26dfecb51960773f70097e1bdfd5) +from [plantbreeding/BrAPI-Manuscript2@01f97e7](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/01f97e786525879db23a1d72a3716051fe743bd3) on July 5, 2024. @@ -1140,9 +1140,9 @@ When the raw images have been processed through the standardization pipelines in The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/) [@doi:10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the French national [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) infrastructures. It manages and collects data from basic phenotyping and high throughput phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics. -PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/) [@doi:10.1111/nph.16544]). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in [FAIDARE](https://urgi.versailles.inrae.fr/faidare/) [@https://urgi.versailles.inrae.fr/faidare] very easy to implement. +PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms, such as OLGA, a genebank accessions management system, to retrieve accession information. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/) [@doi:10.1111/nph.16544]). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services enables indexing of PHIS in [FAIDARE](https://urgi.versailles.inrae.fr/faidare/) [@https://urgi.versailles.inrae.fr/faidare]. -Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community. +Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adhesion to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community. #### PIPPA diff --git a/manuscript.pdf b/manuscript.pdf index 90f27fdd9f35c4f0fa539724b7c28c5683bc1930..8c05eda6cfb6ab26f5faaab8a7a537e585b8500a 100644 GIT binary patch delta 29017 zcmY(JV{j)yx5i`JwryiK-Z&fEww(z#HvX}VjW@Q>jj-e4&U*zozr+LY{k#iYC?mVCoZFvvC_SH72Mb3a
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