Literature DB >> 28606610

Data management and data enrichment for systems biology projects.

Ulrike Wittig1, Maja Rey1, Andreas Weidemann1, Wolfgang Müller2.   

Abstract

Collecting, curating, interlinking, and sharing high quality data are central to de.NBI-SysBio, the systems biology data management service center within the de.NBI network (German Network for Bioinformatics Infrastructure). The work of the center is guided by the FAIR principles for scientific data management and stewardship. FAIR stands for the four foundational principles Findability, Accessibility, Interoperability, and Reusability which were established to enhance the ability of machines to automatically find, access, exchange and use data. Within this overview paper we describe three tools (SABIO-RK, Excemplify, SEEK) that exemplify the contribution of de.NBI-SysBio services to FAIR data, models, and experimental methods storage and exchange. The interconnectivity of the tools and the data workflow within systems biology projects will be explained. For many years we are the German partner in the FAIRDOM initiative (http://fair-dom.org) to establish a European data and model management service facility for systems biology.
Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Keywords:  Data management; FAIR; Reaction kinetics; SABIO-RK; SEEK; Systems biology

Mesh:

Year:  2017        PMID: 28606610     DOI: 10.1016/j.jbiotec.2017.06.007

Source DB:  PubMed          Journal:  J Biotechnol        ISSN: 0168-1656            Impact factor:   3.307


  5 in total

1.  The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

Authors:  Aurélien Naldi; Céline Hernandez; Nicolas Levy; Gautier Stoll; Pedro T Monteiro; Claudine Chaouiya; Tomáš Helikar; Andrei Zinovyev; Laurence Calzone; Sarah Cohen-Boulakia; Denis Thieffry; Loïc Paulevé
Journal:  Front Physiol       Date:  2018-06-19       Impact factor: 4.566

2.  Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.

Authors:  Olivia Eriksson; Upinder Singh Bhalla; Kim T Blackwell; Sharon M Crook; Daniel Keller; Andrei Kramer; Marja-Leena Linne; Ausra Saudargienė; Rebecca C Wade; Jeanette Hellgren Kotaleski
Journal:  Elife       Date:  2022-07-06       Impact factor: 8.713

3.  The grant is dead, long live the data - migration as a pragmatic exit strategy for research data preservation.

Authors:  Tomasz Zielinski; Johnny Hay; Andrew J Millar
Journal:  Wellcome Open Res       Date:  2019-09-23

4.  The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR.

Authors:  Daniel Wibberg; Bérénice Batut; Peter Belmann; Jochen Blom; Frank Oliver Glöckner; Björn Grüning; Nils Hoffmann; Nils Kleinbölting; René Rahn; Maja Rey; Uwe Scholz; Malvika Sharan; Andreas Tauch; Ulrike Trojahn; Björn Usadel; Oliver Kohlbacher
Journal:  F1000Res       Date:  2019-11-07

Review 5.  Deep Learning in Mining Biological Data.

Authors:  Mufti Mahmud; M Shamim Kaiser; T Martin McGinnity; Amir Hussain
Journal:  Cognit Comput       Date:  2021-01-05       Impact factor: 5.418

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.