Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon

Rutger Aldo Vos; Kessy Abarenkov; Jireh Agda; Josh Agda; Ruud Altenburg; Sarah J. Bourlat; Tom Brown; Eli Chadwick; Pierre-Etienne Cholley; Fabian Deister; Dick Groenenberg; Sharif Islam; Nick Juty; Vishnukumar Balavenkataraman Kadhirvelu; Maria Kamouyiaros; Douglas Lowe; Hana Merchant; Joana Pauperio; Benjamin Wills Price; Sujeevan Ratnasingham; Stian Soiland-Reyes; Giorgia Staffoni; Catherine Wei; Oliver White; Dimitris Koureas

doi:10.37044/osf.io/xb4ut_v1

Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon

Rutger Aldo Vos, Kessy Abarenkov, Jireh Agda, Josh Agda, Ruud Altenburg, Sarah J. Bourlat, Tom Brown, Eli Chadwick, Pierre-Etienne Cholley, Fabian Deister, Dick Groenenberg, Sharif Islam, Nick Juty, Vishnukumar Balavenkataraman Kadhirvelu, Maria Kamouyiaros, Douglas Lowe, Hana Merchant, Joana Pauperio, Benjamin Wills Price, Sujeevan RatnasinghamStian Soiland-Reyes, Giorgia Staffoni, Catherine Wei, Oliver White, Dimitris Koureas

Research output: Preprint/Working paper › Preprint

Abstract

The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought together 24 participants from various consortium member institutes to enhance workflows in DNA barcoding, which complements genome sequencing efforts within BGE. The hackathon was structured around four thematic pillars: Data Generation and Processing, BOLD Release Candidate, Wider Data Integration, and Reference Data Curation. Participants worked on optimizing barcode generation pipelines, developing a new version of the Barcode of Life Data Systems (BOLD) data publishing platform, harmonizing data standards for better integration with databases like ENA and UNITE, and automating curation processes for DNA barcoding records. The outcomes include improved workflows, enhanced data interoperability, and refined curation standards, which collectively support BGE's goals of achieving a step change in molecular biodiversity monitoring and research.

Original language	English
Publisher	BioHackrXiv
DOIs	https://doi.org/10.37044/osf.io/xb4ut_v1
Publication status	Submitted - 30 Jun 2025

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10.37044/osf.io/xb4ut_v1Licence: CC0

BGE: Biodiversity Genomics Europe
Goble, C. (PI), Soiland-Reyes, S. (CoI) & Juty, N. (Researcher)
1/09/22 → 28/02/26
Project: Research

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Vos, R. A., Abarenkov, K., Agda, J., Agda, J., Altenburg, R., Bourlat, S. J., Brown, T., Chadwick, E., Cholley, P.-E., Deister, F., Groenenberg, D., Islam, S., Juty, N., Kadhirvelu, V. B., Kamouyiaros, M., Lowe, D., Merchant, H., Pauperio, J., Price, B. W., ... Koureas, D. (2025). Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon. BioHackrXiv. https://doi.org/10.37044/osf.io/xb4ut_v1

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title = "Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon",

abstract = " The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought together 24 participants from various consortium member institutes to enhance workflows in DNA barcoding, which complements genome sequencing efforts within BGE. The hackathon was structured around four thematic pillars: Data Generation and Processing, BOLD Release Candidate, Wider Data Integration, and Reference Data Curation. Participants worked on optimizing barcode generation pipelines, developing a new version of the Barcode of Life Data Systems (BOLD) data publishing platform, harmonizing data standards for better integration with databases like ENA and UNITE, and automating curation processes for DNA barcoding records. The outcomes include improved workflows, enhanced data interoperability, and refined curation standards, which collectively support BGE's goals of achieving a step change in molecular biodiversity monitoring and research.",

author = "Vos, \{Rutger Aldo\} and Kessy Abarenkov and Jireh Agda and Josh Agda and Ruud Altenburg and Bourlat, \{Sarah J.\} and Tom Brown and Eli Chadwick and Pierre-Etienne Cholley and Fabian Deister and Dick Groenenberg and Sharif Islam and Nick Juty and Kadhirvelu, \{Vishnukumar Balavenkataraman\} and Maria Kamouyiaros and Douglas Lowe and Hana Merchant and Joana Pauperio and Price, \{Benjamin Wills\} and Sujeevan Ratnasingham and Stian Soiland-Reyes and Giorgia Staffoni and Catherine Wei and Oliver White and Dimitris Koureas",

year = "2025",

month = jun,

day = "30",

doi = "10.37044/osf.io/xb4ut\_v1",

language = "English",

publisher = "BioHackrXiv",

address = "United States",

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Vos, RA, Abarenkov, K, Agda, J, Agda, J, Altenburg, R, Bourlat, SJ, Brown, T, Chadwick, E, Cholley, P-E, Deister, F, Groenenberg, D, Islam, S, Juty, N, Kadhirvelu, VB, Kamouyiaros, M, Lowe, D, Merchant, H, Pauperio, J, Price, BW, Ratnasingham, S, Soiland-Reyes, S, Staffoni, G, Wei, C, White, O & Koureas, D 2025 'Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon' BioHackrXiv. https://doi.org/10.37044/osf.io/xb4ut_v1

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AU - Vos, Rutger Aldo

AU - Abarenkov, Kessy

AU - Agda, Jireh

AU - Agda, Josh

AU - Altenburg, Ruud

AU - Bourlat, Sarah J.

AU - Brown, Tom

AU - Chadwick, Eli

AU - Cholley, Pierre-Etienne

AU - Deister, Fabian

AU - Groenenberg, Dick

AU - Islam, Sharif

AU - Juty, Nick

AU - Kadhirvelu, Vishnukumar Balavenkataraman

AU - Kamouyiaros, Maria

AU - Lowe, Douglas

AU - Merchant, Hana

AU - Pauperio, Joana

AU - Price, Benjamin Wills

AU - Ratnasingham, Sujeevan

AU - Soiland-Reyes, Stian

AU - Staffoni, Giorgia

AU - Wei, Catherine

AU - White, Oliver

AU - Koureas, Dimitris

PY - 2025/6/30

Y1 - 2025/6/30

N2 - The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought together 24 participants from various consortium member institutes to enhance workflows in DNA barcoding, which complements genome sequencing efforts within BGE. The hackathon was structured around four thematic pillars: Data Generation and Processing, BOLD Release Candidate, Wider Data Integration, and Reference Data Curation. Participants worked on optimizing barcode generation pipelines, developing a new version of the Barcode of Life Data Systems (BOLD) data publishing platform, harmonizing data standards for better integration with databases like ENA and UNITE, and automating curation processes for DNA barcoding records. The outcomes include improved workflows, enhanced data interoperability, and refined curation standards, which collectively support BGE's goals of achieving a step change in molecular biodiversity monitoring and research.

AB - The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought together 24 participants from various consortium member institutes to enhance workflows in DNA barcoding, which complements genome sequencing efforts within BGE. The hackathon was structured around four thematic pillars: Data Generation and Processing, BOLD Release Candidate, Wider Data Integration, and Reference Data Curation. Participants worked on optimizing barcode generation pipelines, developing a new version of the Barcode of Life Data Systems (BOLD) data publishing platform, harmonizing data standards for better integration with databases like ENA and UNITE, and automating curation processes for DNA barcoding records. The outcomes include improved workflows, enhanced data interoperability, and refined curation standards, which collectively support BGE's goals of achieving a step change in molecular biodiversity monitoring and research.

U2 - 10.37044/osf.io/xb4ut_v1

DO - 10.37044/osf.io/xb4ut_v1

M3 - Preprint

BT - Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding

PB - BioHackrXiv

ER -

Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding: the 2024 BGE Barcoding Hackathon

Abstract

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Projects

BGE: Biodiversity Genomics Europe

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