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It cannot deal with branched pathways or with sets of query reactions.
In previous publications (Croes et al., 2006; Faust et al., 2009; van Helden et al., 2002), we investigated different ways to apply two-ends path finding to predict metabolic pathways from a pair of query reactions or compounds.
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A major focus of our efforts has been the development of ranking functionality that combines the candidate document information retrieved by the various text mining-based search systems into a list ordered in a way where documents most likely to be relevant to the query reaction are presented first.
Reactions within a given number of steps from a reaction in a pathway : This query searches for reactions that are n reactions away from a given reaction in a pathway.
Reactions within a given number of steps from a reaction in the metabolic network : This query searches for reactions that are n reactions away from a given reaction in the network.
The first is an advanced, Java-based chemical editor for drawing chemical structures, queries and reactions.
SharePoint 2010 software has the ability to connect to various databases (SQL Server, Oracle, DB2) [3], thereby enabling SharePoint software to not only query compound, reaction, and chemical inventory databases but also external databases by using web services and Accelrys Pipeline Pilot Text Miningg) capabilities [4].
In this way the web developer can choose between the "classical" and new editor look, determine whether query or reaction input should be enabled, how the stereochemistry should be handled, whether nitro or related groups should appear in polar form or with symmetrical pentavalent nitrogen atoms (often a source of serious disagreement between cheminformatics experts) and so on.
Reactions involving a metabolite in a pathway : This query searches for reactions that involve a given metabolite in a specified role in a particular pathway.
The query mechanism for reactions was enhanced to enable searching for KEGG IDs, reactants and genes.
Surprisingly, a Eudravigilance system (i.e., a data processing network and management system for reporting and evaluating suspected adverse drug reactions) query resulted in the finding of two records that involve cases of TdP associated with its use (57).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com