The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Briefings in Bioinformatics Année : 2020

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

Résumé

Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. Logical regulatory networks can be used to predict biological and cellular behaviors by system perturbations and in silico simulations. Today, broad sets of causal interactions are available in a variety of biological knowledge resources. However, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. It can therefore be challenging to efficiently explore various resources of causal interaction and maintain an overview of recorded contextual information that ensures valid use of the data. This review lists the different types of public resources with causal interactions, the different views on biological processes that they represent, the various data formats they use for data representation and storage, and the data exchange and conversion procedures that are available to extract and download these interactions. This may further raise awareness among the targeted audience, i.e. logical modelers and other scientists interested in molecular causal interactions, but also database managers and curators, about the abundance and variety of causal molecular interaction data, and the variety of tools and approaches to convert them into one interoperable resource.
Fichier principal
Vignette du fichier
bbaa390.pdf (951.89 Ko) Télécharger le fichier

Dates et versions

hal-03105365 , version 1 (26-01-2021)

Identifiants

Citer

Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper. The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics, 2020, pp.bbaa390. ⟨10.1093/bib/bbaa390⟩. ⟨hal-03105365⟩
116 Consultations
130 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More