From ea3c9b70887567669d667d644a5f774d93e9f393 Mon Sep 17 00:00:00 2001
From: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:59:37 +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
---
README.md | 4 +-
index.html | 18 +-
manuscript.pdf | Bin 1422646 -> 1423059 bytes
.../images/AGENT_Genotyping_Data_Flow.png | Bin 0 -> 177493 bytes
.../images/AGENT_WebFrontend.pptx | Bin 0 -> 1447179 bytes
.../images/AGENT_Web_Frontend.png | Bin 0 -> 268377 bytes
.../images/BrAPI_Application_Chart-1.png | Bin 0 -> 220527 bytes
.../images/BrAPI_Application_Chart.pdf | Bin 0 -> 54048 bytes
.../images/BrAPI_Application_Chart.xlsx | Bin 0 -> 12247 bytes
.../images/BrAPI_Domains_v2-1_vertical.png | Bin 0 -> 458430 bytes
.../images/BrAPI_Paper_Applications_Chart.png | Bin 0 -> 841692 bytes
.../images/BrAPI_org_structure.jpg | Bin 0 -> 41681 bytes
.../images/Schema_FAIDARE.png | Bin 0 -> 142775 bytes
.../images/Schema_Florilege.jpg | Bin 0 -> 72787 bytes
.../images/github.svg | 4 +
.../images/mastodon.svg | 4 +
.../images/orcid.svg | 4 +
.../images/twitter.svg | 4 +
.../index.html | 4645 +++++++++++++++++
.../index.html.ots | Bin 0 -> 503 bytes
.../manuscript.pdf | Bin 0 -> 1423059 bytes
.../manuscript.pdf.ots | Bin 0 -> 503 bytes
v/freeze/index.html | 6 +-
v/latest/index.html | 18 +-
v/latest/index.html.ots | Bin 503 -> 503 bytes
v/latest/manuscript.pdf | Bin 1422646 -> 1423059 bytes
v/latest/manuscript.pdf.ots | Bin 573 -> 503 bytes
27 files changed, 4684 insertions(+), 23 deletions(-)
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/AGENT_Genotyping_Data_Flow.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/AGENT_WebFrontend.pptx
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/AGENT_Web_Frontend.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_Application_Chart-1.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_Application_Chart.pdf
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_Application_Chart.xlsx
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_Domains_v2-1_vertical.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_Paper_Applications_Chart.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/BrAPI_org_structure.jpg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/Schema_FAIDARE.png
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/Schema_Florilege.jpg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/github.svg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/mastodon.svg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/orcid.svg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/images/twitter.svg
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/index.html
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/index.html.ots
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/manuscript.pdf
create mode 100644 v/01f97e786525879db23a1d72a3716051fe743bd3/manuscript.pdf.ots
diff --git a/README.md b/README.md
index 8943813..a3d9993 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# Output directory containing the formatted manuscript
The [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) branch hosts the contents of this directory at
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.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
zM}PzNES_EdrPl5FeImMx+a?F`^7^F(BucoyVTh9V_aiB;tq(6|CSLUKT>|NI-Zbh4
z`yuIdx7SXsqt;cakt1qwmq_~e+m~=h)Zx1jCn6X}agvqy-d0<}u^1kOg %$(d?-@vSpb`6K2%Cb492%OpeRo~v}8E?<=L7XpZG8MleUb%*5UP6;xvy~zz&
zltc$NQDCp=@jxgQShJu{1T8+5uK#Yx$Pw|&NPT*|0EMfC=oqNE|F3lISL& i~SK?562;}%?}0$y;Y{QSiVDRD=jiGVP`+2
zEsl796V~OSxk>o>49zpyNAg-h$rVVMpa-i<1HI03iWbb+{c9!dK0fkkBOf+Bj!!K-huJ&(E~9ujjH2U~pqtyTJB_+R#^H;RkRxjO%Ir
z_4XvVb43MwZA|8U(%AuTJD841Qd>F?oDnZyk7C7q#N)4Ez3
9RAJ&Sy|J>4uY}pA*03J
zF1K9Gjg`uGxHvdn(JA^T9>>^)XXJqkSO!|P@sT)f0mtU0Q?SjJWZ3O~*L>eNda7A&
zSuZXNe~O+gvaKEaAw)_pm8>3+RDAaOgJ{?=0QK5L%ETuEBTn53i=9zNO?qTS{uXaO
zgwL0DcVtxT0?E4Fa_5V0;u%Fyd}9>UT<>S-wfrRyzkQQh`T0Y4FS#k@#p?C;Qh7tS
zLkA|}Z^VNw%vwBe1mUCp2!`^L8Z`oYrn_S`f-HijbL`7gZ4a3hi&(-RUz_CjD$b*f
zKt|b$IPK$9wQeuiMu2S$(LiiUgUueFm%tREd9P;5e(JWv`dV%Mtn-Ufc*%*0FCGSqG>Pc%?AER8=emKUYvbGyPeFh
z!=ac4;G{Oj@On~QHE&r%h~Bckx9@TPhc}gffy`*it}oFzg_qG2dJN?GVi7e<5UT*g
z_SC&KOU`e7BUYcT>1QUtrse4R(Hj0;#^pI3(=|*w@6BNz8`g-pmk_WQZ
Ik||DW!Mh1s(pnRzD#)Z#h&8RP#Dr
zlHFfA!)QlnyH39NuCnth{?A5KkXaHd78Sr1)L0TvyFqGKB7ZN)vTu9eE+m