The gene regulation knowledge commons: the action area of GREEKC

Martin Kuiper; Joseph Bonello; Jesualdo T Fernández-Breis; Philipp Bucher; Matthias E Futschik; Pascale Gaudet; Ivan V Kulakovskiy; Luana Licata; Colin Logie; Ruth C Lovering; Vsevolod J Makeev; Sandra Orchard; Simona Panni; Livia Perfetto; David Sant; Stefan Schulz; Steven Vercruysse; Daniel R Zerbino; Astrid Lægreid; GRECO Consortium

doi:10.1016/j.bbagrm.2021.194768

The gene regulation knowledge commons: the action area of GREEKC

Biochim Biophys Acta Gene Regul Mech. 2022 Jan;1865(1):194768. doi: 10.1016/j.bbagrm.2021.194768. Epub 2021 Oct 30.

Authors

Martin Kuiper¹, Joseph Bonello², Jesualdo T Fernández-Breis³, Philipp Bucher⁴, Matthias E Futschik⁵, Pascale Gaudet⁶, Ivan V Kulakovskiy⁷, Luana Licata⁸, Colin Logie⁹, Ruth C Lovering¹⁰, Vsevolod J Makeev¹¹, Sandra Orchard¹², Simona Panni¹³, Livia Perfetto¹⁴, David Sant¹⁵, Stefan Schulz¹⁶, Steven Vercruysse¹⁷, Daniel R Zerbino¹⁸, Astrid Lægreid¹⁹; GRECO Consortium

Affiliations

¹ Systems Biology Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway. Electronic address: martin.kuiper@ntnu.no.
² Faculty of Information & Communication Technology, University of Malta, Msida, Malta.
³ Departamento de Informática y Sistemas, Universidad de Murcia, IMIB-Arrixaca, CP 30100, Murcia, Spain.
⁴ Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, 1015 Lausanne, Switzerland.
⁵ Systems Biology and Bioinformatics Laboratory (SysBioLab), Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.
⁶ SIB Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1204 Geneva, Switzerland.
⁷ Institute of Protein Research, Russian Academy of Sciences, 142290, Institutskaya 4, Pushchino, Russia.
⁸ Department of Biology, University of Rome Tor Vergata, Rome, Italy.
⁹ Department of Molecular Biology, Faculty of Science, Radboud University, PO box 9101, Nijmegen 6500HG, the Netherlands.
¹⁰ Functional Gene Annotation, Pre-clinical and Fundamental Science, Institute of Cardiovascular Science, University College London, 5 University Street, London WC1E 6JF, UK.
¹¹ Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Gubkina 3, Moscow, Russia.
¹² European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
¹³ Department DIBEST, University of Calabria, Rende, Italy.
¹⁴ Fondazione Human Technopole, Department of Biology, Via Cristina Belgioioso, 171, 20157 Milan, Italy.
¹⁵ Department of Biomedical Informatics, University of Utah, 421 Wakara Way #140, Salt Lake City, UT 84108, United States.
¹⁶ Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerpl. 2, Graz, Austria.
¹⁷ Systems Biology Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
¹⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
¹⁹ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway.

PMID: 34757206
DOI: 10.1016/j.bbagrm.2021.194768

Abstract

As computational modeling becomes more essential to analyze and understand biological regulatory mechanisms, governance of the many databases and knowledge bases that support this domain is crucial to guarantee reliability and interoperability of resources. To address this, the COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC, CA15205, www.greekc.org) organized nine workshops in a four-year period, starting September 2016. The workshops brought together a wide range of experts from all over the world working on various steps in the knowledge management process that focuses on understanding gene regulatory mechanisms. The discussions between ontologists, curators, text miners, biologists, bioinformaticians, philosophers and computational scientists spawned a host of activities aimed to standardize and update existing knowledge management workflows and involve end-users in the process of designing the Gene Regulation Knowledge Commons (GRKC). Here the GREEKC consortium describes its main achievements in improving this GRKC.

Keywords: Biocuration; Computational biology; Knowledge Commons; Ontologies; Text mining; Web services.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Regulation*
Reproducibility of Results