This study focused on describing the necessary information related to pathway
mechanisms, pathway characteristics, and pathway databases feature annotations. Various difficulties
related to data storage and data retrieval in biological pathway databases are discussed. These focus
on different techniques for retrieving annotations, features, and methods of digital pathway databases
for biological pathway analysis. Furthermore, many pathway databases annotations, features, and
search databases were also examined (which are reasonable for the integration into microarray
examination). The investigation was performed on the pathway databases, which contain human
pathways to understand the hidden components of cells applied in this process. Three different
domain-specific pathways were selected for this study, and the information of pathway databases was
extracted from the existing literature. The research compared different pathways and performed
molecular level relations. Moreover, the associations between pathway networks were also evaluated.
The study involved datasets for gene pathway matrices and pathway scoring techniques. Additionally,
different pathways techniques such as metabolomics and biochemical pathways, translation, control,
and signaling pathways and signal transduction were also considered. We also analyzed the list of
gene sets and constructed a gene pathway network. This article will serve as a useful manual for
storing a repository of specific biological data and disease pathways.