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Inversely, many pathway names do not contain obvious pathway-related keywords (e.g. "RNA degradation" [KEGG PATHWAY: hsa03018]).
From many background experiments, we realize that relying only on best hits can result in some noise, since many pathway names in the list x may not have any related pathway names in the list y.
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For many pathways, specific names are gradually established and used within the community in order to avoid repeated descriptions of molecular details for the convenience of communication.
To analyze the agreement of the pathways in different databases, we only look at the pathway names in different databases, and calculate how many pathways two databases have in common.
Canonical pathway names are from Ingenuity Systems.
The general pathway name is chosen as the shortest pathway names from among the identified related pathways.
This is necessary because gene/protein names are frequently nested in pathway names [ 9].
As input MESSI accepts metabolite KEGG IDs or pathway names.
Many of the topic words are either part of the labelled pathway name or are closely related terms.
In this framework, many known pathways are collected from literatures to construct a combined pathway, named 'reference pathway', which only considers chemical transformations without distinguishing the difference of organisms (Fig. 1A, left).
The global village simply has too many pathways.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com