We were invited to visit by Sarah Ayling, Crop Genomics and Diversity Group Leader at TGAC, who is our collaborator within the transPLANT project. She witnessed the progress of our work introducing phenotypic standards between transPLANT partners and the promotion of the results beyond the project.

Could you explain what the transPLANT project is?

transPLANT is a European project aimed at the provision of a trans-national infrastructure for plant genomic science. The actions undertaken in transPLANT include setting up common standards for data exchange; the development and unification of computational tools and procedures for plant researchers; and the creation of a common entry point to partners' plant-oriented databases. One of the hot topics here is interoperability - having your data and tools compatible with others increases your chances of obtaining better results, or at least making it faster and cheaper, and it also makes it easier to establish collaborations.

What are the benefits establishing a shared system for recording experimental data?

It is essential to publish experimental data (both the collected measurements and, more importantly, the metadata, i.e. description of the biosources, experiment design, conditions, treatments and identification of samples) in order to support published research papers and to make studies searchable, comparable and reproducible. Any system that supports collecting the data and sharing it in a recognised/standard format can be useful to improve the quality of research.

Are there any recurring problems when trying to establish such a shared system?

Collecting experimental data is a huge challenge mainly due to its diversity and size. Due to the quantity of data, instead of building a big centralised data repository, there are a number of smaller local data centres scattered among data producers. Making the data that is exported from these different repositories compatible, can be problematic, especially if they record a different set of metadata, use different terminology or produce a different output format. To address this in the transPLANT project, we have been working on recording the minimal amount of data by carrying out a plant phenotypic experiment and a format for phenotypic data exchange based on ISA-TAB, ‘ISA-TAB For Phenotyping’.

How did you determine what the minimum information recorded for a plant phenotypic experiment should be?

First, we analysed the existing minimum information recommendations, especially those that have been accepted by the research communities, their plant-specific variants and the data we had from our own and our partners' experiments. Then we identified the areas that are covered well by the existing solutions and the gaps in the market. We compiled this into a list defining the basic information needed necessary to know about an experiment which is a proposition of ‘Minimum Information About Plant Phenotyping experiment’ (above), published on the BioSharing website.

What is the future for transPLANT?

The project is due to finish in August 2015. Most of the solutions, tools and resources developed will be supported by the partners and accessible to all plant researchers. A continuation of the project in collaboration with ELIXIR is possible in the future.