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First brassica data training at EI

We hold the first training session on making the most of the Brassica Information Portal (BIP) developed by the Jurkowski Group and collaborators.

September 22, 2016

The Earlham Institute (EI) released the first Brassica Information Portal (BIP), an open-access web repository for brassica data and a tool for collaborative trait-genotype analysis.

To train users, EI held a workshop on 7 September to show researchers how to utilise BIP’s different mechanisms for uploading brassica trait and experimental population data.

Held after the RIPR project (led by Ian Bancroft, University of York) consortium meeting, participants included consortium members (University of Nottingham and Rothamsted Research, industry partners such as BIOGEMMA) and local research scientists from across Norwich Research Park from JIC and IFR.

It’s all about the data.

During the workshop, attendees learned to submit an experimental plant population using a simple Ruby tool. Even those with little or no experience in programming were mastering the task in hand and were greatly satisfied to see their mock-data appear in the BIP database.

After the experimental plant population was submitted, participants used the Brassica Information Portal’s interface to submit their trial data. The BIP handles population data and trial data submission separately; metadata on the background of the plants used in the trial is submitted in the population submission; and metadata on the trial setup is submitted in the trial submission. Here, the trait measurements are also submitted.

Working in pairs, participants could chose from several mock datasets - encouraging teamwork and project collaboration, which is often the case in data research, with many partners, each performing certain experiments. The BIP reflects this common practice in its structure and allows to link different data trials to one project (for example, the multi-Institute RIPR project).

The training will help benefit the plant science community.

Brassica information portal training

How it worked.

All datasets were similar enough so that the participants could help each other along the way. These datasets all told a certain research scenario. For example:

  • Collaborator 1 and 2 perform a phenotyping experiment on a certain group of lines
  • All project members agree on a certain experimental setup and set off collecting data from their polytunnel-grown plants
  • Collaborator 1 measures the contents of some biochemical compounds within the plants, while collaborator 2 measures visual traits.
  • Now they have generated their data and are ready to submit it to the BIP.
  • The mock material was similar to what a scientist would normally use to record and keep their data

At the end of the two-hour workshop, everyone had successfully submitted their mock- data and left well equipped to kick-off real brassica data submissions for their plant research projects.

What they thought.

“Our group is part of a consortium that uses several populations developed within OREGiN and we think it is really useful to have a platform to share resources. We produce a lot of phenotype data for gene discovery; it would be sad not to share our data, as phenotyping is quite time and money intensive. Having a repository for trait data that is accessible for everyone is great for the Brassica community. We need our data to be made available to everyone but would still like to have it quarantined for a limited time."

“The BIP developers and workshop providers have been very, very helpful! The programme content gave me insight into how the database works. Now I understand better how we can submit our data in the future.The workshop clarified how it is possible to engage with the database for those who are not doing any (bio)informatics."

Dr Henk-jan Schoonbeek - CropGenetics (JIC)

Annemarie Eckes (Jurkowski Group) who organised and led the workshop, said: “BIP is a repository for Brassica crop trait data, aimed to help the Brassica community make their trait data publicly available and accessible using controlled vocabulary standardised data formats. This will, ultimately, enhance data discovery through meta-analysis and the application of associative analysis tools to advance Brassica crop improvements. “

“The workshop was intended to give our first group of scientists a practical session on using data upload mechanisms to the BIP. Now that they have learnt the concept, we are looking forward to receiving and hosting their real datasets.”

The brassica information portal workshop material can be accessed here.

Should you have missed the opportunity to participate, you can do the workshop in your own time. Instructions are on the website, good luck!

Article author

Annemarie Eckes

Research Assistant - Data Curation/Plant Phenotyping

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