Figure 1.
Schematic Illustrating the Biological Pathway Building Process
Pathway curators initially mine information (Step 1). The mining process can be initiated by two broad pathway building objectives: (a) DDO wherein a list of genes and/or proteins are obtained by high-throughput experiments such as microarray, mass spectrometry or (b) KDO wherein a broad topic of interest is chosen and then the knowledge concerning this topic is mined from resources such as the primary literature and knowledgebases. Information from the mining process is assembled (Step 2), using pathway building tools, into a pathway, which, following many iterations of feedback from domain experts (Step 3) and refinement (Step 4), leads to the desired specific annotated pathway.
Table 1.
A List of Databases, Classified Based on the Type of Information Represented, Commonly Used during a Biological Pathway Construction
Figure 2.
Example of KDO Pathway Assembly: Signal Transduction Pathways Involved during Infection due to Pathogens such as Virus, Bacteria in Mammalian Dendritic Cells
Starting from a broad topic of interest—infection in mammalian dendritic cells—using the resources in Table 1, this network of pathways was built.