I am new to bioinformatics and have a problem that I am sure almost everyone has faced or is facing. I know that my question is an over simplification, but any pointers in the right direction would be much appreciated.
I would simply like to query (compare/contrast/word search/etc.) multiple biological pathways.
I have used Cytoscape and imported pathways from databases/tools such as Reactome, KEGG, STRING, Agilent Literature search, but the two main limitations are:
1. Limited pathways to choose from
2. Interactions are not well defined
3. Difficult to compare large number of pathways on specific parameters
Does a tool/database exist that incorporates more pathways and detailed interactions? GO annotations and more descriptions on the single gene/molecule itself would not be helpful. I am focusing mainly on the interactions in the pathway.
I can't imagine having to manually annotate or even create 1000s of pathways. I also know that this is not a unique problem, so creating a database or tool would probably be redundant.
How have any of you solved the problem of getting a greater number of detailed pathways?
Giving names of any other tools/database, areas of research, etc. would be helpful.