Cascading biochemical reactions occurring within a cell and carried out in a specific sequence are called a biochemical pathway. Numerous distinct pathways co-exist within a cell and they are quite elaborate because of the many participants involved.We are providing a way of bringing the wealth of information contained in major pathway databases into your model - as a way to speed up the process of building a biomodel and, more important, as a way of annotating vCell entities.
The process begins with a keyword search in the Pathway Commons Database - which will result in a list of pathways.
The chosen pathway can be imported in a table which will display the entities (interactions and physical entities) it consists of.
Furthermore the user can choose the entities of interest and add them to a collection whose content can be displayed as a diagram or in a tabular format. Detailed information about each entity is at this point available.
As a last step, the user can choose which entities will be made part of the biomodel through a linking process.
While working on other topics, click at any time on the Pathway tree item or on its children in the Navigation Panel to return to displaying pathway entities.