Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurre...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Judith Somekh, Mordechai Choder, Dov Dori
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/12333863996b45aba38fa768b554ba44
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:12333863996b45aba38fa768b554ba44
record_format	dspace
spelling	oai:doaj.org-article:12333863996b45aba38fa768b554ba442021-11-18T08:04:00ZConceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.1932-620310.1371/journal.pone.0051430https://doaj.org/article/12333863996b45aba38fa768b554ba442012-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23308089/?tool=EBIhttps://doaj.org/toc/1932-6203We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.Judith SomekhMordechai ChoderDov DoriPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51430 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Judith Somekh Mordechai Choder Dov Dori Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
description	We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure-the objects that comprise the system, and behavior-how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point-the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model.
format	article
author	Judith Somekh Mordechai Choder Dov Dori
author_facet	Judith Somekh Mordechai Choder Dov Dori
author_sort	Judith Somekh
title	Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
title_short	Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
title_full	Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
title_fullStr	Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
title_full_unstemmed	Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.
title_sort	conceptual model-based systems biology: mapping knowledge and discovering gaps in the mrna transcription cycle.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/12333863996b45aba38fa768b554ba44
work_keys_str_mv	AT judithsomekh conceptualmodelbasedsystemsbiologymappingknowledgeanddiscoveringgapsinthemrnatranscriptioncycle AT mordechaichoder conceptualmodelbasedsystemsbiologymappingknowledgeanddiscoveringgapsinthemrnatranscriptioncycle AT dovdori conceptualmodelbasedsystemsbiologymappingknowledgeanddiscoveringgapsinthemrnatranscriptioncycle
_version_	1718422273281490944

Conceptual Model-based Systems Biology: mapping knowledge and discovering gaps in the mRNA transcription cycle.

Ejemplares similares