A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio Vizcaíno; Mathias Walzer; Rafael C Jiménez; Wout Bittremieux; David Bouyssié; Christine Carapito; Fernando Corrales; Myriam Ferro; Albert J R Heck; Peter Horvatovich; Martin Hubalek; Lydie Lane; Kris Laukens; Fredrik Levander; Frederique Lisacek; Petr Novak; Magnus Palmblad; Damiano Piovesan; Alfred Pühler; Veit Schwämmle; Dirk Valkenborg; Merlijn van Rijswijk; Jiri Vondrasek; Martin Eisenacher; Lennart Martens; Oliver Kohlbacher

doi:10.12688/f1000research.11751.1

A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio Vizcaíno, Mathias Walzer, Rafael C Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J R Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit SchwämmleDirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

Original language	English
Journal	F1000Research
Volume	6
DOIs	https://doi.org/10.12688/f1000research.11751.1
Publication status	Published - 2017

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Vizcaíno, J. A., Walzer, M., Jiménez, R. C., Bittremieux, W., Bouyssié, D., Carapito, C., Corrales, F., Ferro, M., Heck, A. J. R., Horvatovich, P., Hubalek, M., Lane, L., Laukens, K., Levander, F., Lisacek, F., Novak, P., Palmblad, M., Piovesan, D., Pühler, A., ... Kohlbacher, O. (2017). A community proposal to integrate proteomics activities in ELIXIR. F1000Research, 6. https://doi.org/10.12688/f1000research.11751.1

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title = "A community proposal to integrate proteomics activities in ELIXIR",

abstract = "Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in T{\"u}bingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.",

author = "Vizca{\'i}no, {Juan Antonio} and Mathias Walzer and Jim{\'e}nez, {Rafael C} and Wout Bittremieux and David Bouyssi{\'e} and Christine Carapito and Fernando Corrales and Myriam Ferro and Heck, {Albert J R} and Peter Horvatovich and Martin Hubalek and Lydie Lane and Kris Laukens and Fredrik Levander and Frederique Lisacek and Petr Novak and Magnus Palmblad and Damiano Piovesan and Alfred P{\"u}hler and Veit Schw{\"a}mmle and Dirk Valkenborg and {van Rijswijk}, Merlijn and Jiri Vondrasek and Martin Eisenacher and Lennart Martens and Oliver Kohlbacher",

year = "2017",

doi = "10.12688/f1000research.11751.1",

language = "English",

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Vizcaíno, JA, Walzer, M, Jiménez, RC, Bittremieux, W, Bouyssié, D, Carapito, C, Corrales, F, Ferro, M, Heck, AJR, Horvatovich, P, Hubalek, M, Lane, L, Laukens, K, Levander, F, Lisacek, F, Novak, P, Palmblad, M, Piovesan, D, Pühler, A, Schwämmle, V, Valkenborg, D, van Rijswijk, M, Vondrasek, J, Eisenacher, M, Martens, L & Kohlbacher, O 2017, 'A community proposal to integrate proteomics activities in ELIXIR', F1000Research, vol. 6. https://doi.org/10.12688/f1000research.11751.1

TY - JOUR

T1 - A community proposal to integrate proteomics activities in ELIXIR

AU - Vizcaíno, Juan Antonio

AU - Walzer, Mathias

AU - Jiménez, Rafael C

AU - Bittremieux, Wout

AU - Bouyssié, David

AU - Carapito, Christine

AU - Corrales, Fernando

AU - Ferro, Myriam

AU - Heck, Albert J R

AU - Horvatovich, Peter

AU - Hubalek, Martin

AU - Lane, Lydie

AU - Laukens, Kris

AU - Levander, Fredrik

AU - Lisacek, Frederique

AU - Novak, Petr

AU - Palmblad, Magnus

AU - Piovesan, Damiano

AU - Pühler, Alfred

AU - Schwämmle, Veit

AU - Valkenborg, Dirk

AU - van Rijswijk, Merlijn

AU - Vondrasek, Jiri

AU - Eisenacher, Martin

AU - Martens, Lennart

AU - Kohlbacher, Oliver

PY - 2017

Y1 - 2017

N2 - Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

AB - Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

U2 - 10.12688/f1000research.11751.1

DO - 10.12688/f1000research.11751.1

M3 - Article

C2 - 28713550

SN - 2046-1402

VL - 6

JO - F1000Research

JF - F1000Research

ER -

A community proposal to integrate proteomics activities in ELIXIR

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