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mibiscreen Data handling

General

We designed data handling for field sample data typical for biodegradation processes. This data includes

  • sample specification data,
  • contaminant concentrations, focusing on petroleum hydrocarbons,
  • hydrogeochemical data and habitat conditions, e.g. redox potential, pH, electron acceptor concentrations, such as oxygen, nitrate, sulfate
  • microbiome data (i.e. the occurrence of DNA and functional genes),
  • metabolite data (i.e. intermediate products of the degradation process)
  • measurements on stable isotope fractions (particularly for hydrogen and carbon within the sample and/or of individual contaminant)

Data has to be provided in a standardized form. Data transformation is implemented in functions performing:

  • loading data from csv or excel files
  • check of input data on
    • correct units provided
    • numerical values
  • standardisation, e.g. of column names to standard names
  • selection of data

A workflow of data handling is illustrated for the Griftpark data in a jupyter-notebook \examples\ex01_Griftpark\example_01_grift_data.ipynb.