From 91e5febd8e2bf13e73fac6e390ab8495ef991573 Mon Sep 17 00:00:00 2001 From: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:28:36 +0000 Subject: [PATCH] Merge pull request #11 from plantbreeding/cpommier-patch-2 [ci skip] This build is based on https://github.com/plantbreeding/BrAPI-Manuscript2/commit/bbbe0c0843123d36f9b7701e83725d4f9c401dc7. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8103455032 --- manuscript.html | 20 ++++++----- manuscript.md | 22 +++++++----- manuscript.pdf | Bin 626603 -> 629310 bytes spelling-error-locations.txt | 66 ++++++++++++++++++++++++++--------- spelling-errors.txt | 30 +++++++++++----- variables.json | 18 +++++----- 6 files changed, 104 insertions(+), 52 deletions(-) diff --git a/manuscript.html b/manuscript.html index 77ad652..eddc0f5 100644 --- a/manuscript.html +++ b/manuscript.html @@ -65,8 +65,8 @@ - - + + @@ -117,9 +117,9 @@ - - - + + + @@ -136,9 +136,9 @@

BrAPI Success Stories

This manuscript -(permalink) +(permalink) was automatically generated -from plantbreeding/BrAPI-Manuscript2@33af47f +from plantbreeding/BrAPI-Manuscript2@bbbe0c0 on February 29, 2024.

Authors

@@ -467,8 +467,10 @@

Data Portal

* Alternate solutions/ why is it better with BrAPI * future related use cases, areas to improve -->

FAIDARE

- -

FAIDARE is an indexing and search portal for the wider breeding community. While it can extract data from various sources via a flat file, the preferred method uses the BrAPI standard APIs. As data is added or updated in data repositories around the world, FAIDARE keeps its index up to date automatically through BrAPI.

+ +

FAIDARE (https://urgi.versailles.inrae.fr/faidare/) is a data discovery portal providing a biologist friendly search system over a global federation of 33 plant research databases. It allows to identify data resources using a full text approach completed with domain specific filters and to link back to the original database for visualisaiton, analysis and download. For instance, it is possible to search for “wheat drought” then to refine the search to the “Triticum aestivum” taxon and yield compononent traits such as “Thousand Grain Wheight”. The indexed data types are very broad and include genomic features, such as genes or transposable elements, selected bibliography, QTL, markers, genetic variation studies, phenomic studies and plant genetic resources ie germplasms. This inclusiveness is achieved thanks to a two stage indexation data model. The most generic one provides basic search functionalities and relies on five fields : name, link back URL, data type, species and exhaustive description. The filtering is directly tied to some of those fields. Therefore, to provide more advanced filtering, FAIDARE is also providing a second stage indexation mechanism by taking advantage of BrAPi endpoints to get more detailled metadata on genotyping and phenotyping studies as well as germplasms. In parralel, FAIDARE provides a previsualisaiton of germplasm and studies using dedicated cards. +The indexation mechanism relies on a dedicated public software (https://github.com/elixir-europe/plant-brapi-etl-faidare) that allows data resources manager to request the indexation of there database using pull requests. It is able to extract data from any BrAPI 1.3 and 1.2 endpoint and development of BrAPI 2.x indexation will be intitated in 2025. Since not all databases are willing to implement BrAPI endpoints, we also provide the possibility to generate metadata as BrAPI json files, hence using the standard as a file exchange format. +FAIDARE has been adopted by several communities and in particular in the ELIXIR and EMPHASIS european infrastructures. It is also used by the WheatIS of the Wheatinitiative. Several databases are added each year to the FAIDARE global federation, allowing to increase both the portal and the BrAPI adoption.

Phenospex - HortControl

HortControl, developed by Phenospex, is a data repository. HortControl has a BrAPI implementation to be used to automate workflows and analytics software.

diff --git a/manuscript.md b/manuscript.md index 55c3f3a..09a581a 100644 --- a/manuscript.md +++ b/manuscript.md @@ -36,8 +36,8 @@ header-includes: | - - + + @@ -88,9 +88,9 @@ header-includes: | - - - + + + @@ -112,9 +112,9 @@ manubot-clear-requests-cache: false This manuscript -([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/)) +([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/)) was automatically generated -from [plantbreeding/BrAPI-Manuscript2@33af47f](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/33af47f71b3fba2a27bd70b3a00e45cf68190776) +from [plantbreeding/BrAPI-Manuscript2@bbbe0c0](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/bbbe0c0843123d36f9b7701e83725d4f9c401dc7) on February 29, 2024. @@ -564,8 +564,12 @@ Users access the crop databases either with direct calls to the PHG embedded ser #### FAIDARE - -FAIDARE is an indexing and search portal for the wider breeding community. While it can extract data from various sources via a flat file, the preferred method uses the BrAPI standard APIs. As data is added or updated in data repositories around the world, FAIDARE keeps its index up to date automatically through BrAPI. + +FAIDARE (https://urgi.versailles.inrae.fr/faidare/) is a data discovery portal providing a biologist friendly search system over a global federation of 33 plant research databases. It allows to identify data resources using a full text approach completed with domain specific filters and to link back to the original database for visualisaiton, analysis and download. For instance, it is possible to search for "wheat drought" then to refine the search to the "Triticum aestivum" taxon and yield compononent traits such as "Thousand Grain Wheight". The indexed data types are very broad and include genomic features, such as genes or transposable elements, selected bibliography, QTL, markers, genetic variation studies, phenomic studies and plant genetic resources ie germplasms. This inclusiveness is achieved thanks to a two stage indexation data model. The most generic one provides basic search functionalities and relies on five fields : name, link back URL, data type, species and exhaustive description. The filtering is directly tied to some of those fields. Therefore, to provide more advanced filtering, FAIDARE is also providing a second stage indexation mechanism by taking advantage of BrAPi endpoints to get more detailled metadata on genotyping and phenotyping studies as well as germplasms. In parralel, FAIDARE provides a previsualisaiton of germplasm and studies using dedicated cards. +The indexation mechanism relies on a dedicated public software (https://github.com/elixir-europe/plant-brapi-etl-faidare) that allows data resources manager to request the indexation of there database using pull requests. It is able to extract data from any BrAPI 1.3 and 1.2 endpoint and development of BrAPI 2.x indexation will be intitated in 2025. Since not all databases are willing to implement BrAPI endpoints, we also provide the possibility to generate metadata as BrAPI json files, hence using the standard as a file exchange format. +FAIDARE has been adopted by several communities and in particular in the ELIXIR and EMPHASIS european infrastructures. It is also used by the WheatIS of the Wheatinitiative. Several databases are added each year to the FAIDARE global federation, allowing to increase both the portal and the BrAPI adoption. + + #### Phenospex - HortControl diff --git a/manuscript.pdf b/manuscript.pdf index 2a9fe1200097f4e0681f7b7718218b48862d68bf..44d1c581e48b0d050b3f431f8dccf73a4bd26693 100644 GIT binary patch delta 18620 zcmV)uK$gF&pC-PvCXitSGB`0Zk!2qQGB`0Zk%&A2Gm*t41;9Xlz$B6GEr08`m;ZjT z;RgSDV{b9!C55Ei?Qj3_@^Ale`!BefB*XD+nwZZe|`DW zpVjTJ|MQ}58oq}dZyM|W%Zn;?LXq_Y{POd!FMs+)-ArDrz5V)^7u~w6vt7IkDc!8P z{rc_YpOiBGpKrhZ=ZnruRDUj62S5Dv-*0fi*9&&BI%XH?igD$NQH!xIWZy4XyB0}{ z(}8~erAV=XY&7(!T~O=K;}Udow#-efC#>~^MSE+LrXoJI-kRu*p$o1S@r#Pt27Tf} zttu|o#NZ9JQA@bR$E2OIC$3x>N?fm)C0dnqrZV2NY1BTMQ%mC3Ie$(|_OPPC3Zt~~ zek?!#x@rsPhFOeJIFzO`i}9#55oRuF_#9l-8M}5pEYalT6YIw3It?ycZ`u6R{@Fz( z=QS%)yWy8)OwQ?kLhYiXQ(CjtQR{#-%z;iRlb$)(dX=&_eA%?ntEx>07ldB9F83yx ze7`Vm$)I96=@a8_3V-7wESHY=YT*{^z16`yo)PuAt>nMJpJIrT^3?);t9I%2#rsSj z=m)Rc-@m^626O8ctw8eO6n~#fc2D4AoJM8uOemvSOv7t#juA|9-o73im#vJCo*JetWS1ON>hR 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content/03.07.data-portals.md:11:FAIDARE -content/03.07.data-portals.md:13:HortControl -content/03.07.data-portals.md:13:Phenospex -content/03.07.data-portals.md:16:analytics -content/03.07.data-portals.md:16:BrAPI -content/03.07.data-portals.md:16:HortControl -content/03.07.data-portals.md:16:HortControl -content/03.07.data-portals.md:16:Phenospex -content/03.07.data-portals.md:18:GLIS -content/03.07.data-portals.md:21:BrAPI -content/03.07.data-portals.md:21:DOIs -content/03.07.data-portals.md:21:germplasm -content/03.07.data-portals.md:21:GLIS -content/03.07.data-portals.md:21:GLIS -content/03.07.data-portals.md:21:GLIS +content/03.07.data-portals.md:11:FAIDARE +content/03.07.data-portals.md:11:genomic +content/03.07.data-portals.md:11:genotyping +content/03.07.data-portals.md:11:germplasm +content/03.07.data-portals.md:11:germplasms +content/03.07.data-portals.md:11:germplasms +content/03.07.data-portals.md:11:inrae +content/03.07.data-portals.md:11:parralel +content/03.07.data-portals.md:11:phenomic +content/03.07.data-portals.md:11:phenotyping +content/03.07.data-portals.md:11:previsualisaiton +content/03.07.data-portals.md:11:QTL +content/03.07.data-portals.md:11:transposable +content/03.07.data-portals.md:11:Triticum +content/03.07.data-portals.md:11:urgi +content/03.07.data-portals.md:11:visualisaiton +content/03.07.data-portals.md:11:Wheight +content/03.07.data-portals.md:12:brapi +content/03.07.data-portals.md:12:BrAPI +content/03.07.data-portals.md:12:BrAPI +content/03.07.data-portals.md:12:BrAPI +content/03.07.data-portals.md:12:BrAPI +content/03.07.data-portals.md:12:faidare +content/03.07.data-portals.md:12:intitated +content/03.07.data-portals.md:12:json +content/03.07.data-portals.md:13:BrAPI +content/03.07.data-portals.md:13:FAIDARE +content/03.07.data-portals.md:13:FAIDARE +content/03.07.data-portals.md:13:Wheatinitiative +content/03.07.data-portals.md:13:WheatIS +content/03.07.data-portals.md:17:HortControl +content/03.07.data-portals.md:17:Phenospex +content/03.07.data-portals.md:20:analytics +content/03.07.data-portals.md:20:BrAPI +content/03.07.data-portals.md:20:HortControl +content/03.07.data-portals.md:20:HortControl +content/03.07.data-portals.md:20:Phenospex +content/03.07.data-portals.md:22:GLIS +content/03.07.data-portals.md:25:BrAPI +content/03.07.data-portals.md:25:DOIs +content/03.07.data-portals.md:25:germplasm +content/03.07.data-portals.md:25:GLIS +content/03.07.data-portals.md:25:GLIS +content/03.07.data-portals.md:25:GLIS content/04.discussion.md:3:BrAPI content/04.discussion.md:5:Analytics content/04.discussion.md:11:BrAPI diff --git a/spelling-errors.txt b/spelling-errors.txt index 4bea329..29715e2 100644 --- a/spelling-errors.txt +++ b/spelling-errors.txt @@ -1,10 +1,10 @@ +aestivum Agrosystem agrosystems Alic alshamaa -Analytics +analytics ANR -APIs arial ARS aspirational @@ -27,6 +27,7 @@ Casstevens chaneylc CLI ClimMob +compononent CottonGEN COVID cpommier @@ -34,6 +35,7 @@ CRAN DArTView datasets DeltaBreed +detailled digitalization DivBrowse DOIs @@ -48,12 +50,13 @@ genomic genotype Genotypes genotypic -genotyping +Genotyping Germplasm +germplasms GIGWA GLIS hackathon -Hackathons +hackathons haplotype haplotypes HortControl @@ -63,12 +66,13 @@ ImageBreed imbedded imilne INBS -INRAE +inrae interoperable +intitated IPK ISA JSON -Khaled +khaled leetaei LIDAR metabolomics @@ -82,17 +86,21 @@ NIFA ontologies OpenSILEX pangenome +parralel PHENOME +phenomic Phenospex phenotypes Phenotypic -Phenotyping +phenotyping PHG PHIS’s Pommier +previsualisaiton programmatically QBMS -raubach +QTL +Raubach Rosaceae rPHG Saclay @@ -105,7 +113,9 @@ Taein tcasstevens TCP transcriptomics +transposable trife +Triticum UAVs UGVs Université @@ -113,4 +123,8 @@ URGI Vaccinium variantsets VCF +visualisaiton +Wheatinitiative +WheatIS +Wheight zrm diff --git a/variables.json b/variables.json index 2eb100f..6d143af 100644 --- a/variables.json +++ b/variables.json @@ -25,7 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