7.12.1. Competency questions for the Ontology ROBOT use case¶

General Questions

How to identify relevant public domain ontologies suiting our needs? (Might be out of scope for ROBOT)
How to establish an ontology covering all terms that are included in the actual data to be represented?
How to merge the internal ontology with publicly available ontologies?
How to remove terms from the resulting ontology that are not needed?
How to guarantee consistency of the final ontology?
How to identify differences in comparison to a previous version of the resulting ontology?

Questions without specifying compounds or genes

Identify all data generated from tissues taken from patients suffering from a specific disease.
Identify all data generated from a specific tissues obtained from mouse models that are related to a specific disease.
Identify all data generated from lung tissue taken from patients suffering from a lung disease that is not related to oncology.
Identify all data generated from primary cells whose origin is the lung.
Identify all data generated from celllines whose origin is the lung.

Questions including single genes or gene sets

What is the expression of PPARg / growths factors in lung tissue from IPF patients?
What is the expression of PPARg / growths factors in primary cells obtained from lung tissue from healthy subjects?
What is the expression of PPARg / growths factors in all available tissues obtained from healthy subjects?

Questions including compound or treatment information

Identify all data generated from primary cells treated with a kinase inhibitor.
Identify all data from patients treated with a specific medication.
Identify all data generated from cells / celllines that have been treated with compounds targeting a member of a specific pathway.
What is the expression of PPARg in lung tissue upon treatment with a specific compound in patients suffering from a specific disease.