Create templates for select AOPs and COPs

[karafecho]

Per Use Case WG discussion on 01.15.2024

This issue is intended to capture the plan that the Use Case WG developed for creating sample queries and templates for the ROBOKOP UI. The plan builds on work conducted on the prototype to ROBOKOP and reflects work by [Morton et al. (see supplementary materials). [See slide deck and slides 30-33 for additional background on prior efforts in AOPs and COPs.]

Morton et al. published the following AOP and COP:

Kara reproduced the results using the current ROBOKOP question-builder tool and also ran simplified versions of the AOP and COP structured as chemical-gene-disease. See this G-folder.

For the templates, we will create four templates following the general structure of the simple and more complete AOPs and COPs, but we will ask the user to provide the input chemicals and diseases. The templates will not be added to the "load sample queries" drop-down menu in the question-builder tool, but rather will be accessible separately (exact approach TBD), as they will require modification of the UI.

1. AOP template: proposed title - "What adverse outcome pathways (AOPs) may explain the relationship between [chemical exposure X] and [disease Y]"
   ChemicalEntity - Gene - BiologicalProcessOrActivity - PhenotypicFeature - Disease

2. COP template: proposed title - "What clinical outcome pathways (COPs) may explain the relationship between [drug X] and [disease Y]"
   ChemicalEntity - Gene - BiologicalProcessOrActivity - PhenotypicFeature - Disease

3. AOP-simple template: proposed title - "What genes may relate [chemical exposure X] and [disease Y]"
   ChemicalEntity - Gene - Disease

4. COP-simple template: proposed title - "What genes may related [drug X] and [disease Y]"
   ChemicalEntity - Gene - Disease

Important: The templates likely will not support every possible chemical-disease input pair. Thus, we will need to include a disclaimer such as:

"The templates provided here are expected to support many, but not all possible, chemical-disease input pairs. If a query does not return results, it is because those paths do not exist in the ROBOKOP KG for the specified input chemical and disease. In that case, please provide a new chemical-disease input pair."

[EvanDietzMorris]

Adding a reminder for @Woozl here, that the drop downs for these should include specifying the intended entity type in their calls to the name resolver

[karafecho]

@Woozl : Thanks for adding the example AOP and COP templates to the dropdown examples in the UI. Looks good to me, although I might suggest that the query paths are ordered in a more logical manner: n0 -> n1, n1 -> n2, etc. This confused me at first, so my guess is that other users would also find it confusing.

[karafecho]

@Woozl : Perhaps we can also add disclaimer text to the AOP and COP templates, e.g., "Please note that these templates will work with most (but not all) input chemical exposure / drug - disease entity pairs."

Additionally, in the description of the template perhaps add "chemical exposure (n0)" and "disease (n4)"?