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Plazas, MariolaAuthorProhens, JaimeAuthor

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October 9, 2024
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From bits to bites: Advancement of the Germinate platform to support genetic resources collections and prebreeding informatics for crop wild relatives

Publicated to: CROP SCIENCE. 61 (3): 1538-1566 - 2021-01-01 61(3), DOI: 10.1002/csc2.20248

Authors:

Raubach, Sebastian; Kilian, Benjamin; Dreher, Kate; Amri, Ahmed; Bassi, Filippo M.; Cook, Douglas; Cruikshank, Alan; Fatokun, Christian; El Haddad, Noureddine; Humphries, Alan; Jordan, David; Kehel, Zakaria; Kumar, Shiv; Labarosa, Sandy Jan; Nguyen, Loi Huu; Plazas Ávila, María de la O; Prohens Tomás, Jaime
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Affiliations

Can Tho Univ, Mekong Delta Dev Res Inst, Can Tho, Vietnam - Author
Cornell Univ, Plant Breeding & Genet, Ithaca, NY 14850 USA - Author
Dept Agr & Fisheries, Warwick, Qld 4370, Australia - Author
Global Crop Div Trust, Pl Vereinten Nationen 7, D-53113 Bonn, Germany - Author
Int Agr Ctr Res Dry Areas ICARDA, Rabat, Morocco - Author
Int Crops Res Inst Semi Arid Trop ICRISAT Eastern, POB 39063-00623, Nairobi, Kenya - Author
Int Crops Res Inst Semi Arid Trop, Patancheru 502324, Andhra Pradesh, India - Author
Int Inst Trop Agr IITA, HQ, Ibadan, Nigeria - Author
Int Inst Trop Agr IITA, Kano, Nigeria - Author
Int Maize & Wheat Improvement Ctr CIMMYT, Edo De Mexico 56237, Texcoco, Mexico - Author
Int Rice Res Inst IRRI, Pili Dr, Los Banos 4031, Laguna, Philippines - Author
James Hutton Inst, Dept Informat & Computat Sci, Errol Rd, Dundee DD2 5DA, Scotland - Author
South Australian Res & Dev Inst SARDI, Waite Inst, Urrbrae 5064, Australia - Author
SRUC, Peter Wilson Bldg,West Mains Rd, Edinburgh EH9 3JG, Midlothian, Scotland - Author
Univ Bonn Crop Trust, Bonn, Germany - Author
Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada - Author
Univ Calif Davis, Dept Plant Pathol, Coll Agr & Environm Sci, One Shields Ave, Davis, CA 95616 USA - Author
Univ Politecn Valencia, Valencia 46022, Spain - Author
Univ Queensland, Warwick, Qld 4370, Australia - Author
World Vegetable Ctr, Shanhua, Taiwan - Author
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Abstract

Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs. Being able to access and share this data in standard formats is essential. The adoption of a common informatics platform for crops that may have limited resources brings economies of scale, allowing common informatics components to be used across multiple species. The close integration of such a platform with commonly used breeding software, visualization, and analysis tools reduces the barrier for entry to researchers and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing prebreeding data for 14 crops as part of the project 'Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives' (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on these species compliments data already publicly available in Germinate. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop Trust Crop Wild Relatives project demonstrates the usefulness of the system and the benefits a shared informatics platform provides. These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harness new data as it becomes available, and benefit collectively from future developments of the Germinate platform.
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Keywords

CollectionDesigEggplantGenotypeHybridsPhenolicsPopulationProjectRufipogonVisualization

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal CROP SCIENCE due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Agronomy and Crop Science.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 2.96. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 2.96 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-03, the following number of citations:

  • WoS: 33
  • Scopus: 37
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-03:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 70.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 70 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 37.
  • The number of mentions on the social network Facebook: 2 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 33 (Altmetric).
  • The number of mentions in news outlets: 1 (Altmetric).
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Australia; Canada; Germany; India; Kenya; Lebanon; Mexico; Morocco; Niger; Nigeria; Philippines; Syria; Taiwan; United Kingdom; United States of America; Vietnam.

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Awards linked to the item

This work was undertaken as part of the initiative 'Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives,' which is supported by the Government of Norway. The project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew, and implemented in partnership with national and international genebanks and plant breeding institutes around the world. For further information, see the project website: http://www.cwrdiversity.org.The authors also gratefully acknowledge funding from the Scottish Government's Rural and Environmental Science and Analytical Services (RESAS) division, Scottish Environment Food and Agriculture Research Institutes (SEFARI), the International Barley Hub (IBH) and the Templeton World Charity Foundation, Inc. Grant ID TWCF0400 ' Safeguarding crop diversity for food security: Prebreeding complemented with Innovative Finance.' Additional funding for Germinate components was provided by Seeds of Discovery (SeeD) Initiative component MasAgro Biodiversidad, funded through the Sustainable Modernization of Traditional Agriculture (MasAgro) Project by the Secretaria de Agricultura y Desarrollo Rural (SADER) of the government of Mexico as well as the MAIZE and WHEAT CGIAR Research Programs and the International Wheat Yield Partnership (IWYP). We would also like to thank colleagues at the James Hutton Institute, in particular, members of the Information and Computational Sciences and Cell and Molecular Sciences Departments in Invergowrie for their help and support throughout this work. Additionally, we would like to thank all of those who have been generous enough with their time, enthusiasm, and feedback over the development of Germinate and their help in carrying out user testing on the platform without whom projects such as these would not succeed.
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