diff --git a/citations.tsv b/citations.tsv index 4d13919..84716d9 100644 --- a/citations.tsv +++ b/citations.tsv @@ -24,6 +24,7 @@ doi:10.3390/plants10081557 doi:10.3390/plants10081557 doi:10.3390/plants10081557 doi:10.2135/cropsci2017.01.0014 doi:10.2135/cropsci2017.01.0014 doi:10.2135/cropsci2017.01.0014 USun3Z8l https://glis.fao.org/glis/ https://glis.fao.org/glis/ url:https://glis.fao.org/glis/ i0Aj9IwD doi:10.12688/f1000research.109080.2 doi:10.12688/f1000research.109080.2 doi:10.12688/f1000research.109080.2 31NWAHsO +doi:10.5281/zenodo.12625360 doi:10.5281/zenodo.12625360 doi:10.5281/zenodo.12625360 QRzg4OSs doi:10.22004/AG.ECON.266624 doi:10.22004/AG.ECON.266624 doi:10.22004/ag.econ.266624 6VGwG9za doi:10.1186/1471-2105-15-259 doi:10.1186/1471-2105-15-259 doi:10.1186/1471-2105-15-259 X22hwO1v doi:10.1111/j.1365-2052.2011.02183.x doi:10.1111/j.1365-2052.2011.02183.x doi:10.1111/j.1365-2052.2011.02183.x 1CKLIIaug diff --git a/manuscript.html b/manuscript.html index 1970071..08e5a00 100644 --- a/manuscript.html +++ b/manuscript.html @@ -65,6 +65,7 @@ + @@ -123,8 +124,8 @@ - - + + @@ -182,12 +183,14 @@ + + @@ -228,6 +231,7 @@ + @@ -305,6 +309,8 @@ + + @@ -340,9 +346,9 @@ - - - + + + @@ -359,9 +365,9 @@

BrAPI Success Stories

This manuscript -(permalink) +(permalink) was automatically generated -from plantbreeding/BrAPI-Manuscript2@01f97e7 +from plantbreeding/BrAPI-Manuscript2@7d2efae on July 5, 2024.

Authors

@@ -512,6 +518,8 @@

Authors

  • Keo Corak
    +ORCID icon +0000-0002-4129-3319 · GitHub icon keocorak
    @@ -533,8 +541,14 @@

    Authors

  • Gouripriya Davuluri
    +ORCID icon +0009-0005-2308-0773 +· GitHub icon +Gouripriya5 +
    Leibniz Institute of Plant Genetics and Crop Plant Research +· Funded by {‘Short version’: ‘This work was supported by the project AGENT project under EU H2020 grant agreement No 862613.’}; {‘Long Version’: ‘The AGENT project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862613.’}

  • Jeremy Destin
    @@ -650,6 +664,11 @@

    Authors

  • Suman Kumar
    +ORCID icon +0009-0005-5832-7190 +· GitHub icon +sumankumar1 +
    Leibniz Institute of Plant Genetics and Crop Plant Research

    • @@ -882,6 +901,14 @@

    Authors

    CIRAD (french agricultural research and international cooperation organization); South Green Platform

    +

  • Romil Mayank Shah +
    +· GitHub icon +romil2807 +
    + +North Carolina State University +

  • Paul Shaw
    ORCID icon @@ -1102,7 +1129,7 @@

    MGIS

    AGENT Portal

    In the global system for ex situ conservation of plant genetic resources (PGR)22, a total of ~5.8 million accessions are conserved in 1750 ex situ genebanks23. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions24. Each DOI is linked to some basic descriptive data that facilitates the use of these resources. Many DOIs are also linked to additional data from different domains or will be in the future. However, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. This space will help answer questions on the global biological diversity of a plant species, on duplicate detection, on provenance tracking for the identification of genetic integrity, on the selection of the most suitable material for various purposes, and to support further applications in data mining or AI. In this context, the aim of the AGENT project, funded by the European Commission, is to develop a concept for the digital exploitation and activation of this PGR data space,11 and to test it in practice using two important crops, barley and wheat. Thirteen European genebanks and five bioinformatics centers are cooperating and have agreed on standards and protocols for the data flow and data formats25 for central archiving of genotypic and phenotypic data.

    -

    The BrAPI specification is one of the agreed standards. The implemented BrAPI interface enables AGENT to mine current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data about wheat and barley accessions from the 18 project partners. This data is integrated via BrAPI endpoints and explorable in a web portal. Genotyping data uses the DivBrowse15 storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA26.

    +

    The BrAPI specification is one of the agreed standards, that are detailed in the AGENT guidelines for dataflowdoi:10.5281/zenodo.12625360?. The implemented BrAPI interface enables AGENT to mine current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data about wheat and barley accessions from the 18 project partners. This data is integrated via BrAPI endpoints and explorable in a web portal. Genotyping data uses the DivBrowse15 storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA26.

    Helium

    diff --git a/manuscript.md b/manuscript.md index 16ba1d5..c2b8e14 100644 --- a/manuscript.md +++ b/manuscript.md @@ -70,6 +70,7 @@ author-meta: - Mathieu Rouard - Joseph Ruff - Guilhem Sempéré +- Romil Mayank Shah - Paul Shaw - Becky Smith - Nahuel Soldevilla @@ -94,8 +95,8 @@ header-includes: | - - + + @@ -153,12 +154,14 @@ header-includes: | + + @@ -199,6 +202,7 @@ header-includes: | + @@ -276,6 +280,8 @@ header-includes: | + + @@ -311,9 +317,9 @@ header-includes: | - - - + + + @@ -335,9 +341,9 @@ manubot-clear-requests-cache: false This manuscript -([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/)) +([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/7d2efaea4b473861f4000c80c42a17eade5dcdb8/)) was automatically generated -from [plantbreeding/BrAPI-Manuscript2@01f97e7](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/01f97e786525879db23a1d72a3716051fe743bd3) +from [plantbreeding/BrAPI-Manuscript2@7d2efae](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7d2efaea4b473861f4000c80c42a17eade5dcdb8) on July 5, 2024. @@ -509,6 +515,8 @@ on July 5, 2024. + **Keo Corak**
    + ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16} + [0000-0002-4129-3319](https://orcid.org/0000-0002-4129-3319) · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16} [keocorak](https://github.com/keocorak)
    @@ -533,8 +541,14 @@ on July 5, 2024. + **Gouripriya Davuluri**
    + ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16} + [0009-0005-2308-0773](https://orcid.org/0009-0005-2308-0773) + · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16} + [Gouripriya5](https://github.com/Gouripriya5) +
    Leibniz Institute of Plant Genetics and Crop Plant Research + · Funded by {'Short version': 'This work was supported by the project AGENT project under EU H2020 grant agreement No 862613.'}; {'Long Version': 'The AGENT project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862613.'} + **Jeremy Destin** @@ -665,6 +679,11 @@ on July 5, 2024. + **Suman Kumar**
    + ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16} + [0009-0005-5832-7190](https://orcid.org/0009-0005-5832-7190) + · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16} + [sumankumar1](https://github.com/sumankumar1) +
    Leibniz Institute of Plant Genetics and Crop Plant Research @@ -924,6 +943,15 @@ on July 5, 2024. CIRAD (french agricultural research and international cooperation organization); South Green Platform ++ **Romil Mayank Shah** +
    + · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16} + [romil2807](https://github.com/romil2807) +
    + + North Carolina State University + + + **Paul Shaw**
    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16} @@ -1248,7 +1276,7 @@ Suggested Authors: Matthias Lange, Patrick König, Stephan Weise, Gouripriya Dav In the global system for ex situ conservation of plant genetic resources (PGR) [@doi:10.3390/plants10081557], a total of ~5.8 million accessions are conserved in 1750 ex situ genebanks [@doi:10.2135/cropsci2017.01.0014]. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions [@{https://glis.fao.org/glis/}]. Each DOI is linked to some basic descriptive data that facilitates the use of these resources. Many DOIs are also linked to additional data from different domains or will be in the future. However, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. This space will help answer questions on the global biological diversity of a plant species, on duplicate detection, on provenance tracking for the identification of genetic integrity, on the selection of the most suitable material for various purposes, and to support further applications in data mining or AI. In this context, the aim of the [AGENT project](https://www.agent-project.eu/), funded by the European Commission, is to develop a concept for the digital exploitation and activation of this PGR data space, [@doi:10.1038/sdata.2016.18] and to test it in practice using two important crops, barley and wheat. Thirteen European genebanks and five bioinformatics centers are cooperating and have agreed on standards and protocols for the data flow and data formats [@doi:10.12688/f1000research.109080.2] for central archiving of genotypic and phenotypic data. -The BrAPI specification is one of the agreed standards. The implemented BrAPI interface enables AGENT to mine current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data about wheat and barley accessions from the 18 project partners. This data is integrated via [BrAPI endpoints](https://github.com/AGENTproject/BrAPI) and explorable in a [web portal](https://agent.ipk-gatersleben.de). Genotyping data uses the DivBrowse [@doi:10.1093/gigascience/giad025] storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA [@doi:10.22004/AG.ECON.266624]. +The BrAPI specification is one of the agreed standards, that are detailed in the AGENT guidelines for dataflow [@doi:10.5281/zenodo.12625360]. The implemented BrAPI interface enables AGENT to mine current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data about wheat and barley accessions from the 18 project partners. This data is integrated via [BrAPI endpoints](https://github.com/AGENTproject/BrAPI) and explorable in a [web portal](https://agent.ipk-gatersleben.de). Genotyping data uses the DivBrowse [@doi:10.1093/gigascience/giad025] storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA [@doi:10.22004/AG.ECON.266624]. diff --git a/manuscript.pdf b/manuscript.pdf index 8c05eda..72a4424 100644 Binary files a/manuscript.pdf and b/manuscript.pdf differ diff --git a/spelling-error-locations.txt b/spelling-error-locations.txt index 9a4272b..d53f592 100644 --- a/spelling-error-locations.txt +++ b/spelling-error-locations.txt @@ -23,6 +23,7 @@ content/03.03.01.MGIS.md:4:Florilège content/03.03.02.AGENT_Portal.md:2:König content/03.03.02.AGENT_Portal.md:6:situ content/03.03.02.AGENT_Portal.md:6:situ +content/03.03.02.AGENT_Portal.md:8:dataflow content/03.03.05.FLORILEGE.md:1:Florilège content/03.03.05.FLORILEGE.md:4:Florilège content/03.03.05.FLORILEGE.md:4:Florilège diff --git a/spelling-errors.txt b/spelling-errors.txt index dfee4d3..19e4d68 100644 --- a/spelling-errors.txt +++ b/spelling-errors.txt @@ -28,6 +28,7 @@ curation customizable DArTdb DArTView’s +dataflow Dhungana DSBrAPP EE @@ -62,6 +63,7 @@ lukasmueller Madriz marieALaporte matthijsbrouwer +Mayank MISTEA MrBot Nderitu @@ -74,9 +76,10 @@ OpenAPI Palladino pascalneveu Pérez -Puthick +puthick Rami Rica +romil RShiny SCT SCYarnes @@ -89,6 +92,7 @@ SSRs STABrAPP StatGen Straße +sumankumar SwaggerHub timparsons Tireau diff --git a/variables.json b/variables.json index 6d7f5d9..f716e78 100644 --- a/variables.json +++ b/variables.json @@ -72,6 +72,7 @@ "Mathieu Rouard", "Joseph Ruff", "Guilhem Sempéré", + "Romil Mayank Shah", "Paul Shaw", "Becky Smith", "Nahuel Soldevilla", @@ -83,7 +84,7 @@ "Stephan Weise", "Shawn C Yarnes" ], - "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n", + "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n", "bibliography": [ "content/manual-references.json" ], @@ -95,7 +96,7 @@ "manubot": { "date": "2024-07-05", "date_long": "July 5, 2024", - "generated": "2024-07-05T16:57:53+00:00", + "generated": "2024-07-05T16:59:27+00:00", "generated_date_long": "July 5, 2024", "randomize_author_order": false, "authors": [ @@ -329,6 +330,7 @@ "github": "keocorak", "initials": "KC", "email": "keo.corak@usda.gov", + "orcid": "0000-0002-4129-3319", "affiliations": [ "USDA-ARS Genomics and Bioinformatics Research Unit" ], @@ -361,11 +363,21 @@ }, { "name": "Gouripriya Davuluri", - "email": "davuluri@ipk-gatersleben.de", + "email": "Gouripriya.Davuluri@leibniz-ipk.de", "initials": "GD", + "github": "Gouripriya5", + "orcid": "0009-0005-2308-0773", "affiliations": [ "Leibniz Institute of Plant Genetics and Crop Plant Research" ], + "funders": [ + { + "Short version": "This work was supported by the project AGENT project under EU H2020 grant agreement No 862613." + }, + { + "Long Version": "The AGENT project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862613." + } + ], "affiliation_numbers": [ 18 ] @@ -548,8 +560,10 @@ }, { "name": "Suman Kumar", - "email": "kumar@ipk-gatersleben.de", + "email": "Suman.Kumar@leibniz-ipk.de", "initials": "SK", + "github": "sumankumar1", + "orcid": "0009-0005-5832-7190", "affiliations": [ "Leibniz Institute of Plant Genetics and Crop Plant Research" ], @@ -903,6 +917,18 @@ 37 ] }, + { + "name": "Romil Mayank Shah", + "email": "rmshah3@ncsu.edu", + "initials": "RMS", + "github": "romil2807", + "affiliations": [ + "North Carolina State University" + ], + "affiliation_numbers": [ + 38 + ] + }, { "name": "Paul Shaw", "initials": "PDS", @@ -951,7 +977,7 @@ "Digital Inclusion, Bioversity International, Montpellier, France" ], "affiliation_numbers": [ - 38 + 39 ] }, { @@ -1187,8 +1213,12 @@ "affiliation_number": 37 }, { - "affiliation": "Digital Inclusion, Bioversity International, Montpellier, France", + "affiliation": "North Carolina State University", "affiliation_number": 38 + }, + { + "affiliation": "Digital Inclusion, Bioversity International, Montpellier, France", + "affiliation_number": 39 } ], "ci_source": { @@ -1196,19 +1226,19 @@ "repo_slug": "plantbreeding/BrAPI-Manuscript2", "repo_owner": "plantbreeding", "repo_name": "BrAPI-Manuscript2", - 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