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There are multiple user friendly methods for searching a pathway for query.
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As an entry point, the user can search a pathway using simple filters or the global metabolic map.
Although several heuristic approaches are available using fragment-based chemical similarity searches, they fail to identify exact atom-bond equivalence between the query and target molecules and thus cannot be applied to complex chemical similarity searches, such as searching a complete or partial metabolic pathway.
Many of these potential reasons are due to design decisions we made in an attempt to demonstrate the utility of this approach on a paradigm that could reasonably be expected to scale up to more realistic scenarios, such as searching a chest radiograph for signs of cancer, or surveying a pathway in search of evidence of improvised explosive devices.
Pathway Commons [ 11] is a collection of publicly available pathway data from multiple organisms that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language.
One example is presented in Figure 2, which shows the search of a pathway between 4-nitrophenol and 2-maleylacetate.
We call the converging path from a starting motif candidate to the final consensus motif a motif searching pathway.
The route from original assumed reference motif to the final converged motif is called a motif searching pathway.
McKinney and his colleagues searched this pathway for a weak point.
Gaps in the network were first addressed by searching pathway databases for the missing enzymes and corresponding genes in other organisms whose genome is sequenced (A. thaliana, E. coli, and S. cerevisiae).
The inferred ADR-pathways associations can be used to interpret an observed drug-ADR pair through searching pathways that were associated with the ADR among pathways affected by the drug.
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