ISA-Tab for Phenotyping

We are proposing ISA-Tab for Phenotyping as a format for phenotypic data exchange.

It is based on ISA-Tab – a hierarchical, general purpose framework to capture and communicate the metadata required to interpret experiments, being developed by ISA team in collaboration with multiple research communities.

ISA-Tab is a text format representation of ISA data model, managing metadata and linking them with corresponding data files. Experiment description in ISA-Tab is organised within a hierarchy of text files characterising Investigation, Study and Assay levels. The content of these files is experiment-specific, however a common set of necessary elements can be defined within particular research domains. Recommendations regarding these elements are contained in ISA-Tab configurations, which can be used to create ISA-Tab files manually or through ISA-Tools Software Suite.

We are proposing ISA-Tab for Phenotyping configuration, featuring basic phenotype attributes defined in MIAPPE. The configuration consists of:

  • an ISA-default Investigation file,
  • a Study file with plant-experiment dedicated protocols, and
  • a Phenotyping Assay file, dedicated to description of numerous heterogeneous variables. The Phenotyping Assay file includes links to data files (raw and derived), and to Trait Definition File, where all phenotypic traits and environmental variables are described.
    There are no restrictions about the format of Raw Data file, it is not obligatory to include it, either. Derived Data files should be preceded by a processing protocol description. By default they should be organised in a ‘Sample per Trait’ matrix.

In the future, the phenotyping configuration will be further extended to better suit the needs of particular phenotyping situations and high throughput phenotyping.

Download the current version of the phenotyping configuration and an example here.

See also:

  • some more datasets in PlantPhenoDB repository (IPG PAS)
  • trials export from GnpIS Ephesis database (INRA)
  • highthoughput image datasets in PGP┬árepository (IPK)

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