New version of the ISA-TAB phenotyping configuration is a consequence of our recent developments in defining minimum information set, according to the opinions expressed in our paper. We have added some environmental information and reordered most of the attributes by grouping them into protocols. Detailed description is given below. The latest implementation of MIAPPE recommendations in the ISA-TAB format can be found here.
We are proposing an ISA-TAB phenotyping configuration that includes the general information about any experiment in Investigation and Study files, and more specific phenotyping-related features in the Assay files:
- Basic Phenotyping Assay – a set of obligatory basic characteristics, common for all phenotyping experiments. You should be able to provide all the information for this assay, irrespective of the type of analysis you are about to describe. Use this assay to start formatting your experiment data, and add more attributes characterising the biosources, experimental design, conditions and treatments according to the needs of each analysis. Consult MIAPPE to be sure that you don’t skip any important information. In the simplest case, you can use the phenotyping configuration with this assay to format and store datasets for which no additional parameters are known, apart from objects names and observed values. Such cases are common, although the scientific value of the observations of phenotypic traits without environmental condition records is low.
- Field Phenotyping Assay – extension of the basic assay for field experiments. Apart from the general attributes, it includes the basic characteristics describing field phenotyping experiment, i.e. sowing, watering, fertilisation, aerial conditions, etc. Each such area is defined as a protocol with a number of parameters that should be provided, e.g. for Aerial conditions protocol specify air humidity, light intensity, day temperature, and night temperature.
Use this assay to format data from field experiments – most of the recommended attributes are already there! Add more attributes to better describe the biosources, specify additional factors, treatments, etc.
- Greenhouse Phenotyping Assay – an extension of the basic assay for greenhouse experiments. Apart from the general attributes, it includes the basic characteristics describing handling of the plants in greenhouse experiments. It differs from the field configuration mainly in the Rooting protocol – you should describe parameters of pots instead of plots.
In this assay most of the recommended attributes for greenhouse experiments are already defined, but you can add more to better describe the biosources, specify additional factors, treatments, etc.
Whichever Assay you choose to start from, consult MIAPPE to find out what other attributes are recommended to record and include in the description of a phenotyping experiment. In the field and greenhouse assay we include most of the obligatory ones that are common to most experiments. In MIAPPE we name also more specific attributes which pertain to some trials only. In such a case, it is important for the correct biological interpretation of your experiment that you add them to the formatted Assay. To do this you can define a new Characteristics (for more detailed description), a new Factor (to underline a simple multi-valued attribute that differentiates between rows), a new Parameter of a Protocol (to add another characteristics of some process or treatment), or a new Protocol (to define another process or treatment), perhaps also described by some parameters.