use_stories.md

use case stories for causal statements in molecular biology

1. Find direct regulatory interactions of a gene product or complex

2. Find indirect regulatory interactions of a gene product or complex (CausalR, SignaLink)

3. A user wants to find the biochemical mechanism of a regulatory event between gene products:

4. State of regulating gene product ?

5. Activity (biochemical) / modification

   1. Activity of regulating gene product
   2. Modification to regulated gene product
   3. regulated activity of regulated gene product

6. Levels of gene product

   1. Expression
   2. transcriptional
   3. translational
   4. stabilization

7. localization

8. A user want to find the provenance of an assertion about a regulatory interaction

9. A user wants to know the location of the regulatory interaction

10. subcellular (GO)

11. cell (CL)

12. tissue (Uberon?)

13. SignaLink: Starting from a member of a known signaling pathway, find all e.g. http://signalink.org/protein/P42003

14. SignaLink: Starting from a regulatory network, find processes that regulate the network, via some specified gene product

15. SignaLink: Find regulatory interactions that function in cross-talk to/from some specified pathway

16. CausalR: To find key regulators of input gene/gene-product sets (regulation may be direct or indirect)

17. CausalR: Reconstruct regulatory networks (direct regulatory interactions preferred).