Web of venom: exploration of big data resources in animal toxin research

Giulia Zancolli; Björn Marcus Von Reumont; Gregor Anderluh; Figen Caliskan; Maria Luisa Chiusano; Jacob Fröhlich; Evroula Hapeshi; Benjamin Florian Hempel; Maria P. Ikonomopoulou; Florence Jungo; Pascale Marchot; Tarcisio Mendes De Farias; Maria Vittoria Modica; Yehu Moran; Ayse Nalbantsoy; Jan Procházka; Andrea Tarallo; Fiorella Tonello; Rui Vitorino; Mark Lawrence Zammit; Agostinho Antunes

doi:10.1093/gigascience/giae054

Web of venom: exploration of big data resources in animal toxin research

Giulia Zancolli^*, Björn Marcus Von Reumont, Gregor Anderluh, Figen Caliskan, Maria Luisa Chiusano, Jacob Fröhlich, Evroula Hapeshi, Benjamin Florian Hempel, Maria P. Ikonomopoulou, Florence Jungo, Pascale Marchot, Tarcisio Mendes De Farias, Maria Vittoria Modica, Yehu Moran, Ayse Nalbantsoy, Jan Procházka, Andrea Tarallo, Fiorella Tonello, Rui Vitorino, Mark Lawrence ZammitAgostinho Antunes^*

^*Corresponding author for this work

Department of Ecology, Evolution & Behavior (EEB)

Research output: Contribution to journal › Review article › peer-review

Abstract

Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.

Original language	English
Article number	giae054
Journal	GigaScience
Volume	13
DOIs	https://doi.org/10.1093/gigascience/giae054
State	Published - 2024

Bibliographical note

Publisher Copyright:
© 2024 The Author(s). Published by Oxford University Press on behalf of Giga Science.

Keywords

antivenom
drug discovery
genomics
machine learning
peptidomics
proteomics
toxin databases
transcriptomics
venom resources

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10.1093/gigascience/giae054

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Zancolli, G., Von Reumont, B. M., Anderluh, G., Caliskan, F., Chiusano, M. L., Fröhlich, J., Hapeshi, E., Hempel, B. F., Ikonomopoulou, M. P., Jungo, F., Marchot, P., De Farias, T. M., Modica, M. V., Moran, Y., Nalbantsoy, A., Procházka, J., Tarallo, A., Tonello, F., Vitorino, R., ... Antunes, A. (2024). Web of venom: exploration of big data resources in animal toxin research. GigaScience, 13, Article giae054. https://doi.org/10.1093/gigascience/giae054

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title = "Web of venom: exploration of big data resources in animal toxin research",

abstract = "Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.",

keywords = "antivenom, drug discovery, genomics, machine learning, peptidomics, proteomics, toxin databases, transcriptomics, venom resources",

author = "Giulia Zancolli and {Von Reumont}, {Bj{\"o}rn Marcus} and Gregor Anderluh and Figen Caliskan and Chiusano, {Maria Luisa} and Jacob Fr{\"o}hlich and Evroula Hapeshi and Hempel, {Benjamin Florian} and Ikonomopoulou, {Maria P.} and Florence Jungo and Pascale Marchot and {De Farias}, {Tarcisio Mendes} and Modica, {Maria Vittoria} and Yehu Moran and Ayse Nalbantsoy and Jan Proch{\'a}zka and Andrea Tarallo and Fiorella Tonello and Rui Vitorino and Zammit, {Mark Lawrence} and Agostinho Antunes",

note = "Publisher Copyright: {\textcopyright} 2024 The Author(s). Published by Oxford University Press on behalf of Giga Science.",

year = "2024",

doi = "10.1093/gigascience/giae054",

language = "אנגלית",

volume = "13",

journal = "GigaScience",

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Zancolli, G, Von Reumont, BM, Anderluh, G, Caliskan, F, Chiusano, ML, Fröhlich, J, Hapeshi, E, Hempel, BF, Ikonomopoulou, MP, Jungo, F, Marchot, P, De Farias, TM, Modica, MV, Moran, Y, Nalbantsoy, A, Procházka, J, Tarallo, A, Tonello, F, Vitorino, R, Zammit, ML & Antunes, A 2024, 'Web of venom: exploration of big data resources in animal toxin research', GigaScience, vol. 13, giae054. https://doi.org/10.1093/gigascience/giae054

TY - JOUR

T1 - Web of venom

T2 - exploration of big data resources in animal toxin research

AU - Zancolli, Giulia

AU - Von Reumont, Björn Marcus

AU - Anderluh, Gregor

AU - Caliskan, Figen

AU - Chiusano, Maria Luisa

AU - Fröhlich, Jacob

AU - Hapeshi, Evroula

AU - Hempel, Benjamin Florian

AU - Ikonomopoulou, Maria P.

AU - Jungo, Florence

AU - Marchot, Pascale

AU - De Farias, Tarcisio Mendes

AU - Modica, Maria Vittoria

AU - Moran, Yehu

AU - Nalbantsoy, Ayse

AU - Procházka, Jan

AU - Tarallo, Andrea

AU - Tonello, Fiorella

AU - Vitorino, Rui

AU - Zammit, Mark Lawrence

AU - Antunes, Agostinho

PY - 2024

Y1 - 2024

N2 - Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.

AB - Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.

KW - antivenom

KW - drug discovery

KW - genomics

KW - machine learning

KW - peptidomics

KW - proteomics

KW - toxin databases

KW - transcriptomics

KW - venom resources

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U2 - 10.1093/gigascience/giae054

DO - 10.1093/gigascience/giae054

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C2 - 39250076

AN - SCOPUS:85203781290

SN - 2047-217X

VL - 13

JO - GigaScience

JF - GigaScience

M1 - giae054

ER -

Web of venom: exploration of big data resources in animal toxin research

Abstract

Bibliographical note

Keywords

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