Nature Communications (Oct 2021)
A proteomics sample metadata representation for multiomics integration and big data analysis
- Chengxin Dai,
- Anja Füllgrabe,
- Julianus Pfeuffer,
- Elizaveta M. Solovyeva,
- Jingwen Deng,
- Pablo Moreno,
- Selvakumar Kamatchinathan,
- Deepti Jaiswal Kundu,
- Nancy George,
- Silvie Fexova,
- Björn Grüning,
- Melanie Christine Föll,
- Johannes Griss,
- Marc Vaudel,
- Enrique Audain,
- Marie Locard-Paulet,
- Michael Turewicz,
- Martin Eisenacher,
- Julian Uszkoreit,
- Tim Van Den Bossche,
- Veit Schwämmle,
- Henry Webel,
- Stefan Schulze,
- David Bouyssié,
- Savita Jayaram,
- Vinay Kumar Duggineni,
- Patroklos Samaras,
- Mathias Wilhelm,
- Meena Choi,
- Mingxun Wang,
- Oliver Kohlbacher,
- Alvis Brazma,
- Irene Papatheodorou,
- Nuno Bandeira,
- Eric W. Deutsch,
- Juan Antonio Vizcaíno,
- Mingze Bai,
- Timo Sachsenberg,
- Lev I. Levitsky,
- Yasset Perez-Riverol
Affiliations
- Chengxin Dai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications
- Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Julianus Pfeuffer
- Algorithmic Bioinformatics, Freie Universität Berlin
- Elizaveta M. Solovyeva
- Moscow Institute of Physics and Technology
- Jingwen Deng
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications
- Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Selvakumar Kamatchinathan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Deepti Jaiswal Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Björn Grüning
- Bioinformatics Group Department of Computer Science, Albert-Ludwigs-University Freiburg
- Melanie Christine Föll
- Institute for Surgical Pathology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg
- Johannes Griss
- Department of Dermatology, Medical University of Vienna
- Marc Vaudel
- Department of Clinical Sciences, University of Bergen
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel
- Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
- Michael Turewicz
- Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
- Martin Eisenacher
- Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
- Julian Uszkoreit
- Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
- Tim Van Den Bossche
- VIB – UGent Center for Medical Biotechnology, VIB
- Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55
- Henry Webel
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
- Stefan Schulze
- University of Pennsylvania, Department of Biology
- David Bouyssié
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, UPS
- Savita Jayaram
- nference Labs
- Vinay Kumar Duggineni
- nference Labs
- Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich
- Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich
- Meena Choi
- Department of Microchemistry, Proteomics and Lipidomics, Genentech
- Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
- Oliver Kohlbacher
- Department of Computer Science, Applied Bioinformatics, University of Tübingen
- Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
- Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Ave N
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Mingze Bai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications
- Timo Sachsenberg
- Department of Computer Science, Applied Bioinformatics, University of Tübingen
- Lev I. Levitsky
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences
- Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- DOI
- https://doi.org/10.1038/s41467-021-26111-3
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 8
Abstract
The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.
