/
Examples step 2

Examples step 2

Owned by Niek van Ulzen
Last updated: Feb 27, 2025 by Xiaofeng Liao (Unlicensed)
3 min read

Competency questions example

One way to start modeling with the user in mind is to collect to so-called user stories and/or competency questions. Competency questions are questions that the metadata model should be able to answer. In simpler terms, they represent the question: What would you like to search for in the catalogue?

From such user stories and competency questions specific metadata elements can be extracted. Below we provide some examples.

User story

“A researcher in neurology requires MRI scans of patients taken over a span of years, ideally both from patients who eventually developed Alzheimer's disease and those who did not. These longitudinal datasets can help to trace the progression and potential early signs of the disease. The researcher turns to the National Health Data Catalogue that hosts a vast array of medical imaging data from various hospitals and research institutions.”

Competency questions

As a researcher in neurology, using the national catalogue, I would like to:​

  1. Filter datasets that only contain MRI scans, ensuring that I am looking at the right type of imaging data;

  2. Among MRI scans, refine my search search to only include datasets with brain imaging, excluding other parts of the body;

  3. See datasets spanning the last 20 years;

  4. Filter on datasets that are not only about Alzheimer’s disease, but on neurodegenerative diseases in general.

Metadata requirements

From the user story and competency questions a number of metadata elements can be extracted, for example:

  • The first question refers to metadata about the imaging modality. In this case, only MRI scans but not CT or PET scans;

  • The second question points to metadata about the body part. In this case, the brain;

  • The third questions points to metadata about time period;

  • The fourth questions points to metadata about the health theme or disease domain.

 

Such requirements are input for subsequent analysis. In brief, whereas imaging modality is very likely to be imaging domain specific, body part, time period and health theme are expected to be much more general. For eventual domain-specific modeling, it is important to further think about what to capture regarding imaging modality; and to discuss with the Health-RI hub what is or should be part of the generic Health-RI core/health metadata schema.

 

Other examples of imaging competency questions (CQ) and some extracted requirements

CQ

Modality requirement

Body part requirement

Treatment requirement

CQ

Modality requirement

Body part requirement

Treatment requirement

As a research, I want to see how cerebral blood flow changes in dementia subjects

MRI

Brain

 

I want to know how dense breast / breast density can obscure breast cancer

Mammography, Ultrasound

Breast

 

I want to know how smoking increases lung tissue damage caused by COVID-19

CT

Lung

 

I have a conference and need CT scans RIGHT NOW to see how epicardial fat evolves over time

CT

Heart

 

I want to research the effectiveness of brachytherapy in prostate cancer patients

PET

Prostate

Brachytherapy

I want to study how breast cancer patients that receive therapy evolve over time on MRI

MRI

Breast

Neoadjuvant chemotherapy

What is the correlation between cardiac volume and brain infarcts (longitudinally)

CT

Heart, brain

 

Example of Omics competency questions

CQ

What you'd need to look for in the Data Catalog

Which search aspects do you expect to select

CQ

What you'd need to look for in the Data Catalog

Which search aspects do you expect to select

  1. Find a patient with one particular genetic variant

 

 

  1. I want to do a GWAS study of longevity

 

 

  1. I need a reference (proteome?) for a healthy pancreas

 

 

  1. What is the mutation frequency of the P53 gene across all cancer cases

 

 

  1. I want to know the molecular diagnostics for RETT syndrome patients in NL

 

 

  1. I am studying the expression profile of cultured neurons.

 

 

  1. I am looking for de novo mutation rates

 

 

  1. I am trying to find reasons why some patients respond differently to certain drugs

 

 

  1. I need expression data on XXX patients

 

 

  1. I'm studying epigenetics data of XXX

 

 

  1. I am looking for control data as a reference for patients with complications after applying fillers.

transcriptomics data from healthy people skin; different layers of the skin (tissue type) and how the sample was obtained

Transcriptomics (technique; platform)

Tissue type (derms, epidermis)

Biopsy (how and where it was taken)

The question No. 11 can be answered with the current omics metadata schema (bare minimum).

Specifically, following attributes can be utilized: 

Organism <-> human 

Organism part <-> skin 

Sample type – biopsy or tissue (derms, epidermis) 

Measurement type or technology type <-> microarray or sequences 

 

References

A goal-oriented method for FAIRification planning | Research Square

Use of Competency Questions in Ontology Engineering: A Survey | SpringerLink

http://dx.doi.org/10.1007/978-0-387-34847-6_3

 

 

Related content