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
TY - JOUR
AU - Kuiper, Martin
AU - Bonello, Joseph
AU - Fernández-Breis, Jesualdo T.
AU - Bucher, Philipp
AU - Futschik, Matthias E.
AU - Gaudet, Pascale
AU - Kulakovskiy, Ivan V.
AU - Licata, Luana
AU - Logie, Colin
AU - Lovering, Ruth C.
AU - Makeev, Vsevolod J.
AU - Orchard, Sandra
AU - Panni, Simona
AU - Perfetto, Livia
AU - Sant, David
AU - Schulz, Stefan
AU - Vercruysse, Steven
AU - Zerbino, Daniel R.
AU - Lægreid, Astrid
PY - 2022
UR - https://vinar.vin.bg.ac.rs/handle/123456789/10768
AB - 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.
T2 - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
T1 - The gene regulation knowledge commons: the action area of GREEKC
VL - 1865
IS - 1
SP - 194768
DO - 10.1016/j.bbagrm.2021.194768
ER -
@article{
author = "Kuiper, Martin and Bonello, Joseph and Fernández-Breis, Jesualdo T. and Bucher, Philipp and Futschik, Matthias E. and Gaudet, Pascale and Kulakovskiy, Ivan V. and Licata, Luana and Logie, Colin and Lovering, Ruth C. and Makeev, Vsevolod J. and Orchard, Sandra and Panni, Simona and Perfetto, Livia and Sant, David and Schulz, Stefan and Vercruysse, Steven and Zerbino, Daniel R. and Lægreid, Astrid",
year = "2022",
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.",
journal = "Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms",
title = "The gene regulation knowledge commons: the action area of GREEKC",
volume = "1865",
number = "1",
pages = "194768",
doi = "10.1016/j.bbagrm.2021.194768"
}
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.. (2022). The gene regulation knowledge commons: the action area of GREEKC. in Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1865(1), 194768.
https://doi.org/10.1016/j.bbagrm.2021.194768
Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Vercruysse S, Zerbino DR, Lægreid A. The gene regulation knowledge commons: the action area of GREEKC. in Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 2022;1865(1):194768.
doi:10.1016/j.bbagrm.2021.194768 .
Kuiper, Martin, Bonello, Joseph, Fernández-Breis, Jesualdo T., Bucher, Philipp, Futschik, Matthias E., Gaudet, Pascale, Kulakovskiy, Ivan V., Licata, Luana, Logie, Colin, Lovering, Ruth C., Makeev, Vsevolod J., Orchard, Sandra, Panni, Simona, Perfetto, Livia, Sant, David, Schulz, Stefan, Vercruysse, Steven, Zerbino, Daniel R., Lægreid, Astrid, "The gene regulation knowledge commons: the action area of GREEKC" in Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1865, no. 1 (2022):194768,
https://doi.org/10.1016/j.bbagrm.2021.194768 . .
