Metabolomics Use cases

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Specification of use cases can help us to extract functional requirements of the DWH. For an explanation see [Wikipedia Use-Cases]. We have used [ArgoUML] to construct the use case diagram, but feel free to describe the use-cases in any other way.

Use Case 1: Quality Control

Use case name: preprocessing GC-MS data, evaluation of QC strategy (1)

Goal: process raw data to make it suitable for statistical analysis and evaluate QC strategies

Summary: starting from raw data the following preprocessing steps are necessary to create a datamatrix consisting of peak area or peak heights for each sample and peak number combination. In this process the following steps are envisioned:

  • Baseline correction
  • Alignment of chromatographic profiles of different samples
  • Peak / variable extraction (peak picking or deconvolution or …)
  • Internal Standard correction
  • Correction for Quality Control samples

Principal actor: technician (chromatographist) or statistician (data analyst)

Sequence diagram:

Sequencediagram usecase1.png

Diagram source files (XMI-format)

Use Case 2: Sharing Data between scientists

Use case name: sharing data between scientists

Goal: provide a central facility where information can be stored and retrieved


Principal actor: scientists looking for details. Authentication details are propagated from the user to the workflow, to allow the latter to access the database.

Sequence diagram:


Use Case 3: Expert Validation

Use case name: validation of results by an expert

Goal: the database facility must be able to store all minimal reporting standards and beyond


Principal actor: scientists looking for details

Sequence diagram:


Use Case 4: Running a Sample Measurement

Use case name: running a metabolomics experiment

Goal: allow to find sample information and storage of RAW metabolomics data


Principal actor: analysist who performs a metabolomics experiment

Sequence diagram:


Use Case 5: Interacting with System

Use case name: Signal outliers

Goal: Allow user to interactively add outlier info


Principal actor: analysist who performs a metabolomics experiment

Sequence diagram: