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Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

Boué S, Talikka M, Westra JW, Hayes W, Di Fabio A, Park J, Schlage WK, Sewer A, Fields B, Ansari S, Martin F, Veljkovic E, Kenney R, Peitsch MC, Hoeng J - Database (Oxford) (2015)

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.

View Article: PubMed Central - PubMed

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.

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Network models and constituent subnetworks in the CBN database. For each of the six biological processes (marked by circles), the biological networks (marked by stars), and, whenever relevant, subnetworks (marked by lines) describing distinct signaling pathways are listed. Currently, a total of 123 network models with 1–3 different versions each are deposited in the CBN database. Note that even though the endothelial shear stress network was built with the other stress models, its context is exclusively vascular.
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bav030-F1: Network models and constituent subnetworks in the CBN database. For each of the six biological processes (marked by circles), the biological networks (marked by stars), and, whenever relevant, subnetworks (marked by lines) describing distinct signaling pathways are listed. Currently, a total of 123 network models with 1–3 different versions each are deposited in the CBN database. Note that even though the endothelial shear stress network was built with the other stress models, its context is exclusively vascular.

Mentions: Here, we report the causal biological network (CBN) database, a collection of modular, evolving, manually curated, biological expression language (BEL)-scripted causal network models that describe signaling pathways relevant in diseased and nondiseased pulmonary and vascular tissues. Structurally, the CBN collection is organized into the following biological areas (Figure 1): cell response to stress, cell proliferation, cell fate (including DNA damage response, autophagy, senescence, apoptosis and necroptosis), tissue repair and angiogenesis, pulmonary inflammatory processes, vascular inflammatory processes and chronic obstructive pulmonary disease (COPD)-specific networks. Details of these network models have been published previously (7–12).Figure 1.


Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

Boué S, Talikka M, Westra JW, Hayes W, Di Fabio A, Park J, Schlage WK, Sewer A, Fields B, Ansari S, Martin F, Veljkovic E, Kenney R, Peitsch MC, Hoeng J - Database (Oxford) (2015)

Network models and constituent subnetworks in the CBN database. For each of the six biological processes (marked by circles), the biological networks (marked by stars), and, whenever relevant, subnetworks (marked by lines) describing distinct signaling pathways are listed. Currently, a total of 123 network models with 1–3 different versions each are deposited in the CBN database. Note that even though the endothelial shear stress network was built with the other stress models, its context is exclusively vascular.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401337&req=5

bav030-F1: Network models and constituent subnetworks in the CBN database. For each of the six biological processes (marked by circles), the biological networks (marked by stars), and, whenever relevant, subnetworks (marked by lines) describing distinct signaling pathways are listed. Currently, a total of 123 network models with 1–3 different versions each are deposited in the CBN database. Note that even though the endothelial shear stress network was built with the other stress models, its context is exclusively vascular.
Mentions: Here, we report the causal biological network (CBN) database, a collection of modular, evolving, manually curated, biological expression language (BEL)-scripted causal network models that describe signaling pathways relevant in diseased and nondiseased pulmonary and vascular tissues. Structurally, the CBN collection is organized into the following biological areas (Figure 1): cell response to stress, cell proliferation, cell fate (including DNA damage response, autophagy, senescence, apoptosis and necroptosis), tissue repair and angiogenesis, pulmonary inflammatory processes, vascular inflammatory processes and chronic obstructive pulmonary disease (COPD)-specific networks. Details of these network models have been published previously (7–12).Figure 1.

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.

View Article: PubMed Central - PubMed

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