Release 2.1.1
I'm actually quite excited about this update. The user will now be able to save a generated pathway for both further reference to view/share and
will be able to incorporate the generated pathway in other future pathway searches. The pathways page now contains both an index view of
biochemical pathways (for now the same portion of the Calvin Cycle) and an index view of the user generated pathways. The user generated pathways index view will show the name and
graphic representation of the start and end molecules of the pathway and a description of the pathway. The user may save/approve a new pathway after the pathway has been
generated by clicking the "Approve" button and filling in any desired Notes. The primary benefit of this new feature is that it will allow the pathway generator to grow. As more pathways
are discovered (be it from a third party reaction database, new reactions introduced to the local database, etc.) the pathway search will become more powerful and have more data points
from which to generate better/more efficient pathways.A very simple example of using the new persistence of generated pathways is to look at a pathway search for the reaction of converting cyclohexanol to cyclohexanone. Exploiting the ability to search the online Rhea DB for a reaction, we are able to find that the reaction Cyclohexanol Dehydrogenase will work. We are now given the option to approve the reaction. Once we do it will be saved and we may add it to the reactions we can query locally, using the MolGen Reactions search. We will then no longer need to query the Rhea DB for this particular reaction. Once the pathway is approved it will also show up in the index view of My Pathways.
Standards - At this stage room has been left for any standards deemed necessary in the future for approving proposed/generated pathways. I am anticipating a plethora of requirements, so obviously the approval process may be redesigned multiple times.
Controls - Pathways may now be approved and added to the library of known pathways by clicking the "Approve" button on a generated pathway. They may then be viewed in the My Pathways link on the Pathways page. Options for which source(s) to use for a pathway search may now be defined at the URL level by adding the parameter "?options=" followed by one or more of "Calc" (for Pathway Calculations), "Reac" (for local MolGen Reactions), and "RheaDB" (to use the Rhea DB).
Future considerations - It is evident that a tutorial and instructional documentation are becoming increasingly necessary. Also, I hope to add a more complex example of combining different sources used in a pathway search soon. The pathways index view will be expanded to allow more sophisticated navigation as well as search. Finally, the User Pathways section of the Pathways index view will be expanded to include pathways created by other users as well.
