diff --git a/content/03.01.04.Image_Breed.md b/content/03.01.04.Image_Breed.md index 479b4a4..bacdd09 100644 --- a/content/03.01.04.Image_Breed.md +++ b/content/03.01.04.Image_Breed.md @@ -1,5 +1,5 @@ #### ImageBreed -[ImageBreed](https://imagebreed.org/) [@doi:10.1002/ppj2.20004] is an image collection pipeline tool to support regular use of UAVs and UGVs. High-throughput phenotyping has been gaining significant traction lately as a way to collect lots of data very quickly. Image collection from unmanned aerial and ground vehicles (UAVs and UGVs) are a great way to collect a lot of raw data all at once, then analyze it later. +[ImageBreed](https://imagebreed.org/) [@doi:10.1002/ppj2.20004] is an image collection pipeline tool to support regular use of UAVs and UGVs. High-throughput phenotyping has been gaining significant traction lately as a way to collect large amounts of data very quickly. Image collection from unmanned aerial and ground vehicles (UAVs and UGVs) are a great way to collect a lot of raw data all at once, then analyze it later. When the raw images have been processed through the standardization pipelines in ImageBreed, useful phenotypes can be extracted from the images. The BrAPI standard is used to push these phenotypes back to a central breeding database where they can be analyzed with other data. In addition to this, ImageBreed has the ability to use BrAPI to upload the raw images to the central breeding database, or any other BrAPI compatible long term storage service. In the current version of the standard (V2.1), the BrAPI data models for images are rudimentary, but effective. The ImageBreed team has put in some work into enhancing the BrAPI image data standards, collaborating with others in the community. diff --git a/content/03.05.01.G-Crunch.md b/content/03.05.01.G-Crunch.md index d867146..83c3e64 100644 --- a/content/03.05.01.G-Crunch.md +++ b/content/03.05.01.G-Crunch.md @@ -1,6 +1,6 @@ #### G-Crunch -G-Crunch is an upcoming user-facing analysis tool that attempts to fill the space of simple, user driven analytics requests, with a generic user interface and the ability to swap out data sources and analysis tools. G-Crunch hopes to streamline repeatable, debuggable, simple analytic requests and results. +G-Crunch is an upcoming user-facing analysis tool that integrates genomic and phenotypic data to fulfill the need for simple, user driven analytics requests. It includes a generic user interface and the ability to swap out data sources and analysis tools. The G-Crunch team hopes to streamline repeatable, debuggable, simple analytic requests and results. G-Crunch, as a tool, couldn't feasibly exist without BrAPI. The support of BrAPI interfaces allows G-Crunch to use one unified request method, and adapt to the user's (BrAPI-compliant) existing network of tools. This lowers the barrier to entry for adoption, and makes analysis pipelines easily repeatable. diff --git a/content/04.discussion.md b/content/04.discussion.md index d29cec8..f6e534d 100644 --- a/content/04.discussion.md +++ b/content/04.discussion.md @@ -16,7 +16,7 @@ The BrAPI technical specification document is meant to be read and used by softw ### Looking Ahead -The BrAPI specification will continue a controlled and necessary growth. It will enable more use cases and new types of data that might include newer scientific techniques and technologies. There will be careful evaluation the relevance of using REST web service approaches, and in particular BrAPI, for things like drone imaging data, spectroscopy, LIDAR, metabolomics, transcriptomics, high-throughput phenotyping, pan genomes, and machine learning analysis. All of these technologies can open new avenues for research and development of new crop varieties. All of these technologies also generate more data, and require data sharing between different software applications and data repositories. The BrAPI project leadership and community is committed to building the standards to support these new use cases as they arrive and become accepted by the scientific community. In fact, small groups within the BrAPI community have already start building generic data models and proposed communication standards for many of the technologies listed above. These community efforts will eventually become part of the BrAPI standard in a future version of the specification document. +The BrAPI specification will continue a controlled and necessary growth. It will enable more use cases and new types of data that might include newer scientific techniques and technologies. There will be careful evaluation of the relevance of using REST web service approaches, and in particular BrAPI, for things like drone imaging data, spectroscopy, LIDAR, metabolomics, transcriptomics, high-throughput phenotyping, pan genomes, and machine learning analysis. All of these technologies can open new avenues for research and development of new crop varieties. However, they will also generate more data, more types of data, and require data sharing between different software applications and data repositories. The BrAPI project leadership and community is committed to building the standards to support these new use cases as they arrive and become accepted by the scientific community. In fact, small groups within the BrAPI community have already start building generic data models and proposed communication standards for many of the technologies listed above. These community efforts will eventually become part of the BrAPI standard in a future version of the specification document. Expanding the BrAPI specification is important for the community, however it is just as important not to reinvent or compete with existing functional standards. Additions to the BrAPI specification are reviewed thoroughly by the community to make sure BrAPI is compliant with existing standards and data structures. For example, the community has requested compliance with the GFF3 standard for genomic data and the GeoTIFF standard for aerial image data. Pieces of these existing popular data structures might be integrated into the overall BrAPI standard documentation. In some cases, BrAPI will only reference other standards instead of including them in the specification. For example, there have been community discussions around developing connections with the NOAA CDO standard for weather data, or the Galaxy Analytics API for analytics pipeline controls and information. These standards are perfectly adequate on their own, recreating them in the BrAPI standard would be redundant and outside the main scope of the project. diff --git a/content/90.back-matter.md b/content/90.back-matter.md index 6eb1a06..3c5c4e8 100644 --- a/content/90.back-matter.md +++ b/content/90.back-matter.md @@ -15,7 +15,7 @@ The authors declare no competing interests. The authors would like to acknowledge the following funding sources: + The BrAPI Project is funded by the USDA grant NIFA-DSFAS 2022-67021-37024. -+ Innovation Lab for Crop Improvement Cornell, FFAR ++ Innovation Lab for Crop Improvement Cornell, ILCI: 7200AA19LE00005, FFAR: CA20-SS-0000000103 + The AGENT project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 862613. + USDA National Institute of Food and Agriculture National Research Support Project 10 + USDA NIFA: 2022-51181-38449 diff --git a/content/metadata.yaml b/content/metadata.yaml index fdd8602..5a74283 100644 --- a/content/metadata.yaml +++ b/content/metadata.yaml @@ -14,22 +14,24 @@ authors: github: BrapiCoordinatorSelby orcid: 0000-0001-7151-4445 email: ps664@cornell.edu + corresponding: true affiliations: - Cornell University funders: - The BrAPI Project is funded by the USDA grant NIFA-DSFAS 2022-67021-37024. - corresponding: true - name: Rafael Abbeloos initials: RA github: raabb orcid: 0000-0002-0177-3887 email: rafael.abbeloos@vib.be + corresponding: false affiliations: - VIB Agro-Incubator - name: Anne-Francoise Adam-Blondon initials: AFAB orcid: 0000-0002-3412-9086 email: anne-francoise.adam-blondon@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -38,6 +40,7 @@ authors: github: agostof orcid: 0000-0002-5059-253X email: fja32@cornell.edu + corresponding: false affiliations: - Cornell University funders: @@ -46,6 +49,7 @@ authors: initials: MA orcid: 0000-0001-9356-4072 email: michael.alaux@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -56,6 +60,7 @@ authors: github: Isabelle-inrae orcid: 0000-0002-8961-6068 email: isabelle.alic@inrae.fr + corresponding: false affiliations: - MISTEA, University of Montpellier, INRAE, Institut Agro, Montpellier, France - name: Khaled Al-Shamaa @@ -63,21 +68,25 @@ authors: github: khaled-alshamaa orcid: 0000-0002-7668-3798 email: k.el-shamaa@cgiar.org + corresponding: false affiliations: - ICARDA - name: Johan Steven Aparicio initials: JSA email: J.Aparicio@cgiar.org + corresponding: false affiliations: - Alliance Bioversity-CIAT - name: Jan Erik Backlund initials: JEB email: j.backlund@integratedbreeding.net + corresponding: false affiliations: - Integrated Breeding Platform - name: Aldrin Batac initials: AB email: aldrin.batac@leafnode.io + corresponding: false affiliations: - Integrated Breeding Platform - Leafnode LLC @@ -86,6 +95,7 @@ authors: github: sebeier orcid: 0000-0002-2177-8781 email: s.beier@fz-juelich.de + corresponding: false affiliations: - 'Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, 52428 Jülich, Germany' - Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany @@ -94,6 +104,7 @@ authors: github: Gabriel-Besombes orcid: 0009-0004-1359-2145 email: gabriel.besombes@inrae.fr + corresponding: false affiliations: - MISTEA, University of Montpellier, INRAE, Institut Agro, Montpellier, France - name: Alice Boizet @@ -101,6 +112,7 @@ authors: github: aliceboizet orcid: 0000-0003-4096-6689 email: alice.boizet@cirad.fr + corresponding: false affiliations: - CIRAD, UMR AGAP Institut, Montpellier, France. - AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France. @@ -109,6 +121,7 @@ authors: github: matthijsbrouwer orcid: 0000-0001-8183-0484 email: matthijs.brouwer@wur.nl + corresponding: false affiliations: - Wageningen University and Research - name: Terry Casstevens @@ -116,6 +129,7 @@ authors: github: tcasstevens orcid: 0000-0001-7602-0487 email: tmc46@cornell.edu + corresponding: false affiliations: - Buckler Lab and Institute for Genomic Diversity, Cornell University - name: Arnaud Charleroy @@ -123,6 +137,7 @@ authors: github: niio972 orcid: 0009-0009-7575-3617 email: arnaud.charleroy@inrae.fr + corresponding: false affiliations: - MISTEA, University of Montpellier, INRAE, Institut Agro, Montpellier, France - name: Keo Corak @@ -130,17 +145,20 @@ authors: github: keocorak orcid: 0000-0002-4129-3319 email: kecorak@ncsu.edu + corresponding: false affiliations: - USDA-ARS Genomics and Bioinformatics Research Unit - name: Chaney Courtney initials: CC github: chaneylc email: ccourtn@clemson.edu + corresponding: false affiliations: - Clemson University - name: Mariano Crimi initials: MC email: m.crimi@integratedbreeding.net + corresponding: false affiliations: - Integrated Breeding Platform - name: Gouripriya Davuluri @@ -148,6 +166,7 @@ authors: github: Gouripriya5 orcid: 0009-0005-2308-0773 email: Gouripriya.Davuluri@leibniz-ipk.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research funders: @@ -157,11 +176,13 @@ authors: github: kauedesousa orcid: 0000-0002-7571-7845 email: k.desousa@cgiar.org + corresponding: false affiliations: - Digital Inclusion, Bioversity International, Montpellier, France - name: Jeremy Destin initials: JD email: jeremy.destin3@gmail.com + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -169,12 +190,14 @@ authors: initials: SD orcid: 0000-0003-4402-2191 email: stijn.dhondt@vib.be + corresponding: false affiliations: - VIB AgroIncubator - name: Ajay Dhungana initials: AD github: GenAjay email: adhung4@lsu.edu + corresponding: false affiliations: - Louisiana State University (LSU) - name: Bert Droesbeke @@ -182,6 +205,7 @@ authors: github: bedroesb orcid: 0000-0003-0522-5674 email: bert.droesbeke@vib.be + corresponding: false affiliations: - VIB Data Core - name: Manuel Feser @@ -189,6 +213,7 @@ authors: github: feserm orcid: 0000-0001-6546-1818 email: feser@ipk-gatersleben.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research - Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI) @@ -197,6 +222,7 @@ authors: github: mflores202 orcid: 0000-0002-7759-1617 email: mrf252@cornell.edu + corresponding: false affiliations: - Boyce Thompson Institute - name: Valentin Guignon @@ -204,11 +230,13 @@ authors: github: guignonv orcid: 0000-0003-0903-6811 email: v.guignon@cgiar.org + corresponding: false affiliations: - Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France - name: Corina Habito initials: CH email: c.habito@integratedbreeding.net + corresponding: false affiliations: - Integrated Breeding Platform - name: Asis Hallab @@ -216,24 +244,28 @@ authors: github: asishallab orcid: 0000-0002-2421-5431 email: a.hallab@fz-juelich.de + corresponding: false affiliations: - Jülich research center, Institute of Bio- and Geosciences (IBG), Bioinformatics (IBG-4) and Bingen Technical University of Applied Sciences, Germany - name: Puthick Hok initials: PH github: puthick email: puthick@diversityarrays.com + corresponding: false affiliations: - Diversity Arrays Technology (DArT) - name: Lynn Carol Johnson initials: LCJ orcid: 0000-0001-8103-2722 email: lcj34@cornell.edu + corresponding: false affiliations: - Buckler Lab and Institute for Genomic Diversity, Cornell University - name: Sook Jung initials: SJ orcid: 0000-0003-3968-2769 email: sook_jung@wsu.edu + corresponding: false affiliations: - Department of Horticulture, Washington State University funders: @@ -241,6 +273,7 @@ authors: - name: Paul Kersey initials: PK email: P.Kersey@kew.org + corresponding: false affiliations: - Royal Botanic Gardens, Kew funders: @@ -248,6 +281,7 @@ authors: - name: Andrzej Kilian initials: AK email: zej@diversityarrays.com + corresponding: false affiliations: - Diversity Arrays Technology (DArT) - name: Patrick König @@ -255,6 +289,7 @@ authors: github: patrick-koenig orcid: 0000-0002-8948-6793 email: koenig@ipk-gatersleben.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research funders: @@ -264,6 +299,7 @@ authors: github: sumankumar1 orcid: 0009-0005-5832-7190 email: Suman.Kumar@leibniz-ipk.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research funders: @@ -272,6 +308,7 @@ authors: initials: JDLS github: jlamossweeney email: jdl232@cornell.edu + corresponding: false affiliations: - Cornell University - name: Laszlo Lang @@ -279,6 +316,7 @@ authors: github: LzLang orcid: 0009-0009-8936-4532 email: laszlo.lang@stud.th-bingen.de + corresponding: false affiliations: - Bingen Technical University of Applied Sciences, Berlinstraße 109, 55411 Bingen am Rhein, Germany - name: Matthias Lange @@ -286,6 +324,7 @@ authors: github: langeipk orcid: 0000-0002-4316-078X email: lange@ipk-gatersleben.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research funders: @@ -295,6 +334,7 @@ authors: github: marieALaporte orcid: 0000-0002-8461-9745 email: m.a.laporte@cgiar.org + corresponding: false affiliations: - Digital Inclusion, Bioversity International, Montpellier, France. - name: Taein Lee @@ -302,6 +342,7 @@ authors: github: leetaei orcid: 0000-0002-2000-2586 email: taein_lee@hotmail.com + corresponding: false affiliations: - Department of Horticulture, Washington State University - name: Erwan Le-Floch @@ -309,23 +350,27 @@ authors: github: erlefloch orcid: 0000-0002-1010-6859 email: erwan.le-floch@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France - name: Francisco López initials: FL email: francisco.lopez@fao.org + corresponding: false affiliations: - International Treaty on Plant Genetic Resources for Food and Agriculture, FAO - name: Brandon Madriz initials: BM email: bmadriz@mrbotcr.com + corresponding: false affiliations: - MrBot Software Solutions, Cartago, Costa Rica - name: Dorrie Main initials: DM orcid: 0000-0002-1162-2724 email: dorrie@wsu.edu + corresponding: false affiliations: - Department of Horticulture, Washington State University funders: @@ -334,6 +379,7 @@ authors: initials: MM orcid: 0000-0003-0334-8785 email: marco.marsella@fao.org + corresponding: false affiliations: - International Treaty on Plant Genetic Resources for Food and Agriculture, FAO - name: Maud Marty @@ -341,6 +387,7 @@ authors: github: maudmarty orcid: 0009-0001-8764-6466 email: maud.marty@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -349,6 +396,7 @@ authors: github: cmichotey orcid: 0000-0003-1877-1703 email: celia.michotey@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -357,6 +405,7 @@ authors: github: zrm22 orcid: 0000-0002-5454-4527 email: zrm22@cornell.edu + corresponding: false affiliations: - Buckler Lab and Institute for Genomic Diversity, Cornell University - name: Iain Milne @@ -364,6 +413,7 @@ authors: github: imilne orcid: 0000-0002-4126-0859 email: iain.milne@hutton.ac.uk + corresponding: false affiliations: - The James Hutton Institute - name: Lukas A. Mueller @@ -371,12 +421,14 @@ authors: github: lukasmueller orcid: 0000-0001-8640-1750 email: lam87@cornell.edu + corresponding: false affiliations: - The Boyce Thompson Institute - name: Moses Nderitu initials: MN github: jndmose email: m.nderitu@seqart.net + corresponding: false affiliations: - SEQART AFRICA - name: Pascal Neveu @@ -384,6 +436,7 @@ authors: github: pascalneveu orcid: 0000-0003-4189-7793 email: pascal.neveu@inrae.fr + corresponding: false affiliations: - MISTEA, University of Montpellier, INRAE, Institut Agro, Montpellier, France funders: @@ -393,6 +446,7 @@ authors: github: nickpalladino orcid: 0009-0009-1645-297X email: np398@cornell.edu + corresponding: false affiliations: - Breeding Insight, Cornell University funders: @@ -402,6 +456,7 @@ authors: github: timparsons orcid: 0000-0001-6209-2455 email: tim@timparsons.io + corresponding: false affiliations: - Breeding Insight, Cornell University funders: @@ -411,6 +466,7 @@ authors: github: cpommier orcid: 0000-0002-9040-8733 email: cyril.pommier@inrae.fr + corresponding: false affiliations: - Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, 78026, Versailles, France - Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France @@ -419,6 +475,7 @@ authors: github: jframi orcid: 0000-0002-5679-3877 email: jean-francois.rami@cirad.fr + corresponding: false affiliations: - CIRAD, UMR AGAP Institut, Montpellier, France. - AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France. @@ -427,6 +484,7 @@ authors: github: sebastian-raubach orcid: 0000-0001-5659-247X email: sebastian.raubach@hutton.ac.uk + corresponding: false affiliations: - The James Hutton Institute - name: Trevor Rife @@ -434,26 +492,30 @@ authors: github: trife orcid: 0000-0002-5974-6523 email: twrife@clemson.edu + corresponding: false affiliations: - Clemson University - name: Kelly Robbins initials: KR orcid: 0000-0001-9522-9585 email: krr73@cornell.edu + corresponding: false affiliations: - Cornell University funders: - - The Bill and Malinda Gates Foundation in cooperation with the Excellence in Breeding Platform of the CGIAR + - The BrAPI Project is funded by the USDA grant NIFA-DSFAS 2022-67021-37024. - name: Mathieu Rouard initials: MR github: mrouard orcid: 0000-0003-0284-1885 email: m.rouard@cgiar.org + corresponding: false affiliations: - Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France - name: Joseph Ruff initials: JR email: J.Ruff@kew.org + corresponding: false affiliations: - Royal Botanic Gardens, Kew funders: @@ -463,6 +525,7 @@ authors: github: GuilhemSempere orcid: 0000-0001-7429-2091 email: guilhem.sempere@cirad.fr + corresponding: false affiliations: - CIRAD, UMR INTERTRYP, Montpellier, France INTERTRYP, Univ Montpellier, CIRAD, IRD, Montpellier, France French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France @@ -470,6 +533,7 @@ authors: initials: RMS github: romil2807 email: rmshah3@ncsu.edu + corresponding: false affiliations: - North Carolina State University - name: Paul Shaw @@ -477,6 +541,7 @@ authors: github: cardinalb orcid: 0000-0002-0202-1150 email: paul.shaw@hutton.ac.uk + corresponding: false affiliations: - The James Hutton Institute - name: Becky Smith @@ -484,11 +549,13 @@ authors: github: Batbaby91 orcid: 0000-0002-8968-3383 email: becky.smith@hutton.ac.uk + corresponding: false affiliations: - The James Hutton Institute - name: Nahuel Soldevilla initials: NS email: n.soldevilla@integratedbreeding.net + corresponding: false affiliations: - Integrated Breeding Platform - Leafnode LLC @@ -497,11 +564,13 @@ authors: github: annetireau orcid: 0000-0001-8501-6922 email: anne.tireau@inrae.fr + corresponding: false affiliations: - MISTEA, University of Montpellier, INRAE, Institut Agro, Montpellier, France - name: Clarysabel Tovar initials: CT email: clarysabel@leafnode.io + corresponding: false affiliations: - Integrated Breeding Platform - Leafnode LLC @@ -509,6 +578,7 @@ authors: initials: GU github: grzegorz69 email: grzegorz@diversityarrays.com + corresponding: false affiliations: - Diversity Arrays Technology (DArT) - name: Vivian Bass Vega @@ -516,12 +586,14 @@ authors: github: VivianBass orcid: 0009-0002-2476-9888 email: vivbass4@gmail.com + corresponding: false affiliations: - Bingen Technical University of Applied Sciences, Berlinstraße 109, 55411 Bingen am Rhein, Germany - name: Stephan Weise initials: SW orcid: 0000-0003-4031-9131 email: weise@ipk-gatersleben.de + corresponding: false affiliations: - Leibniz Institute of Plant Genetics and Crop Plant Research funders: @@ -531,6 +603,7 @@ authors: github: SCYarnes orcid: 0000-0002-1090-0403 email: scy32@cornell.edu + corresponding: false affiliations: - Breeding Insight, Cornell University funders: