Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.
Bottom Line: With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format.Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed.Moreover, networks may be downloaded for further visualization and evaluation.
Affiliation: Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA.Show MeSH
Related in: MedlinePlus
Mentions: The initial focus of the NVC revolved around mechanisms implicated in COPD disease pathophysiology. Therefore, before the start of the challenge, COPD-relevant mechanisms, including B-cell and T-cell activation, airway remodeling, extracellular matrix (ECM) degradation, efferocytosis, mucus hypersecretion and emphysema were added to the published ‘non-disease’ pulmonary networks. In addition, prior to deploying the COPD-enhanced biological networks on the NVC website on Bionet (http://bionet.sbvimprover.com) for verification by the scientific community, the set of ‘pulmonary’ networks were agglomerated to yield a more concise set of 50 networks that combined related/complementary cellular pathways. This set of 50 network models is also available in the CBN database as version 1.1 of the network models. The relationships between versions 1.0 and 1.1 are described in a network hierarchy figure (Figure 1) and in the Supplementary data describing all available network models of the CBN database (Supplementary Material). Improvements made to the network models during the NVC-included submission of new pieces of evidence, additional literature publications to support existing network edges, as well as submission of new biological edges with supporting evidence for relationships that were not represented in the original networks. When networks are refined, they are imported into the CBN database as new versions (Figure 3C). Thus, conceptually, Bionet and the CBN platform are linked intrinsically and were developed in parallel so that the CBN database constitutes a repository of all versions of the network models and Bionet contains a single version of the network that is open for crowd verification (Figure 4).Figure 4.
Affiliation: Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA.