The gene regulation knowledge commons: the action area of GREEKC.

Kuiper, M.; Bonello, J.; Fernández-Breis, J.T.; Bucher, P.; Futschik, M.E.; Gaudet, P.; Kulakovskiy, I.V.; Licata, L.; Logie, C.; Lovering, R.C.; Makeev, V.J.; Orchard, S.; Panni, S.; Perfetto, L.; Sant, D.; Schulz, S.; Vercruysse, S.; Zerbino, D.R.; Lægreid, A.

doi:10.1016/j.bbagrm.2021.194768

The gene regulation knowledge commons: the action area of GREEKC.

Details

Download: The gene regulation knowledge commons.pdf (868.70 [Ko])
State: Public
Version: Final published version
License: CC BY 4.0

Serval ID

serval:BIB_72A2178C27DE

Type

Article: article from journal or magazin.

Publication sub-type

Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.

Collection

Publications

Institution

UNIL/CHUV

Title

The gene regulation knowledge commons: the action area of GREEKC.

Journal

Biochimica et biophysica acta. Gene regulatory mechanisms

Author(s)

Kuiper M., Bonello J., Fernández-Breis J.T., Bucher P., Futschik M.E., Gaudet P., Kulakovskiy I.V., Licata L., Logie C., Lovering R.C., Makeev V.J., Orchard S., Panni S., Perfetto L., Sant D., Schulz S., Vercruysse S., Zerbino D.R., Lægreid A.

Working group(s)

GRECO Consortium

Contributor(s)

Schulz S., Bock C., Aerts S., Vandepoele K., Kapur-Pojskic L., Lojo-Kadrić N., Lemke N., Baev V., Wasserman W., van Helden J., Ballester B., Vaquerizas J., Gazouli M., Kardassis D., Fazekas D., Higgins D., Perfetto L., Panni S., Licata L., Carninci P., Viksna J., Acencio M., Hartmann A., Kreis S., Cachia E., Bonello J., Pace N., Vides J.C., Moodley K., Dumontier M., Logie C., Schmeier S., Lægreid A., Kuiper M., Vercruysse S., Mathelier A., Futschik M., Sobral D., Castro F., Monteiro P.T., Costache M., Pistol G.C., Gras M.A., Dinescu S., Kulakovskiy I.V., Medvedeva Y., Makeev V., Pruner I., Gemovic B., Djordjevic V., Rozman D., Krallinger M., Valencia A., Vazquez M., Navas-Delgado I., Aldana J.F., García-Nieto J.M., Del Mar Roldán M., Breis JTF, Bucher P., Rinaldi F., Oktay Y., Tokdemir S.S., Popov A., Orchard S., Lovering R., Mungall C., Thomas P., Eibeck K.

ISSN

1876-4320 (Electronic)

ISSN-L

1874-9399

Publication state

Published

Issued date

01/2022

Peer-reviewed

Oui

Volume

1865

Number

Pages

194768

Language

english

Notes

Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish

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

Gene Expression Regulation, Reproducibility of Results, Biocuration, Computational biology, Knowledge Commons, Ontologies, Text mining, Web services

URN

urn:nbn:ch:serval-BIB_72A2178C27DE9

OAI-PMH

oai:serval.unil.ch:BIB_72A2178C27DE

DOI

10.1016/j.bbagrm.2021.194768

Pubmed

34757206

Web of science

000727751500001