7.12.1. Competency questions for the Ontology ROBOT use caseΒΆ

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 diseas