After another round of consultations with ISA-Team the following changes were introduced in the phenotyping configuration and in the example files:

• Declaration of Sample Name moved to study file.
  Assay file should start with Sample Name column which references declaration of samples from the study file. Samples can correspond directly to sources (if no factors and protocols applied), or can represent a combination of sources and factors. Further analysis-specific factors can be added in the assay file.
• Assay Name column added to assay file.
  Derived Data File changed to ‘Assays by Traits‘ format.
  The column Assay Name identifies rows in the assay file, and links them to the observations in Derived Data File, which implies a change of Derived Data File column names – instead of ‘Samples by Traits‘ it becomes a ‘Assay by Traits‘ matrix.
  Introduction of Assay Name column allows for specification of more levels of the processing of the plant material, i.e., there can be also an Extract Name and Labeled Extract Name columns defined after the Sample Name (and before Assay Name).
• Introduction of another Protocol REF, Normalization Name and Data Transformation Name.
  In order to comply with the general ISA-Tools configuration and allow usage of ISA-validator for phenotyping ISA-Tab files, we have adopted the recommendations of ISA-Team regarding these columns:
  Protocol REF should be used to describe in all transitions of data from one node to another (Source Name > Sample Name > Extract Name > Labeled Extract Name > Assay Name), and to specify data processing for Derived Data File.
  Normalization Name and Data Transformation Name should proceed all derived data files. Unlike Protocol REF, they are not linked to any broader description in the investigation file, nor can take parameters. They can be either just symbolic names or more elaborated descriptions in this very column, or stay empty.
• File naming convention.
  ISA-Tab prefixes (i_, s_, a_) in names of file types were corrected; other-then-standard ISA files do not include them now.

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