Sentence examples for by the pathway databases from inspiring English sources
For each gene and metabolite a C2Card provides the identifiers assigned to them by the pathway databases (see Figure 1, and Materials and methods).
Next to exploring the genes, EC numbers, and reactions contained in the pathway databases, as described above, C2Cards can also be of direct use in curating the identifiers (IDs) assigned to the genes and metabolites by the pathway databases.
For additional information provided by the pathway databases, e.g., pathway visualization and literature references, a direct link is provided to the original entry of the reaction in the pathway database.
Although not used for comparing metabolites, we also retrieved the InChI and SMILES of metabolites, when provided by the pathway database, as additional information.
In addition, the remaining disease-associated genes were searched for genes that had direct interactions with those generated by the pathway database.
Only pathways present in MetaCyc can be automatically incorporated into the pathway database by Pathway Tools [ 25].
We then constructed a functional linkage network by integrating the microarray dataset with the pathway database of Kyoto Encyclopedia of Genes and Genomes (KEGG).
While reviewing the database management systems used by the signaling pathway databases, it is observed that most of the databases are based on flat file schema.
However, it requires the commitment and the support of a broad community to construct an initial consensus network and to extend it with new knowledge from domain experts, the scientific literature, and as captured by the various pathway databases.
The gene regulatory network of BDE47 was constructed on the basis of the information provided by the KEGG pathway database and visualized.
