Comparing classical pathways and modern networks: towards the development of an edge ontology.
Pathways 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 (HTP) experiments offer standardized networks that facilitate topological calculations. Combining these perspectives, classical pathways can be embedded within large-scale networks and thus demonstrate the crosstalk between them. As more diverse types of HTP data become available, both perspectives can be effectively merged, 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 and well-defined edge ontology is necessary and propose a prototype as a starting point for reaching this goal.
Lu
Long J
LJ
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
Sboner
Andrea
A
Huang
Yuanpeng J
YJ
Lu
Hao Xin
HX
Gianoulis
Tara A
TA
Yip
Kevin Y
KY
Kim
Philip M
PM
Montelione
Gaetano T
GT
Gerstein
Mark B
MB
D000818:Animals; D016208:Databases, Factual; D006801:Humans; D015398:Signal Transduction; D049490:Systems Biology / Q000639:trends