Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology

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dc.creatorLu, Long J.
dc.creatorSboner, Andrea
dc.creatorHuang, Yuanpeng J.
dc.creatorLu, Hao Xin
dc.creatorGianoulis, Tara A.
dc.creatorYip, Kevin Y.
dc.creatorKim, Philip M.
dc.creatorMontelione, Gaetano T.
dc.creatorGerstein, Mark B.
dc.date2007-06-01
dc.date.accessioned2026-07-07T08:03:54Z
dc.date.available2026-07-07T08:03:54Z
dc.descriptionPathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely, modern high-throughput experiments give rise to standardized networks facilitating topological calculations. Combining these perspectives, we can embed classical pathways within large-scale networks and thus demonstrate the crosstalk between them. As more diverse types of high-throughput data become available, we can effectively merge both perspectives, embedding pathways simultaneously in multiple networks. However, the original problem still remains - the current edge representation is inadequate to accurately convey all the information in pathways. Therefore, we suggest that a standardized, well-defined, edge ontology is necessary and propose a prototype here, as a starting point for reaching this goal.
dc.description30 pages including 5 figures and supplemental material
dc.identifierhttps://arxiv.org/abs/0706.0194
dc.identifierhttp://arxiv.org/abs/0706.0194
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/129756
dc.subjectMolecular Networks
dc.titleComparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology
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