COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform

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Accessibility to biological data has been hindered by lack of standards, lack of awareness of the benefits and pathways to releasing data that is described by those standards, and lack of services whereby data can be analysed, published and retrieved easily. Recently, there has been a large commitment by the BBSRC to push for open access data and publishing to further bioscience research in the UK. However, barriers still exist that prevent scientists from openly depositing their data and metadata, which comprise a lack of interoperability between metadata annotation services, data repositories, data analysis platforms and data publishing platforms. As such, plant scientists might not: be aware that the services exist; have the expertise to use them; see the value in properly describing their data.
This project aims to build COPO, the software infrastructure required to reach the level of interoperability that plant researchers need to describe their data using community-recognised ontologies, seamless bi-directional data flow to relevant repositories, and then publish these data for open access. COPO will manage the hardware infrastructure at TGAC to deliver a consistent robust staging area and database that will support unique accessioned artefacts representing the corpus of data and metadata a user wants to expose. The resulting marked-up datasets processed and published using COPO will allow greater potential integrative analysis using existing tools such as iPlant and Galaxy.
New Application Programming Interfaces (APIs) will interconnect existing tools and services, and by developing new RESTful user interfaces that wrap up these APIs, COPO will be a single point-of-entry for plant researchers to disseminate their data all the way from generation to publication. By federating the TGAC iRODS data grid system with others, e.g. Texas Advanced Computing Center's iPlant installation, access to worldwide analytical infrastructure and data will be facilitated.

Impact Summary
Academic, Economic and Commercial Impacts
With the renewed interest and push from all areas of bioscience to promote publicly available research, the COPO project will be a pioneering national and international effort to facilitate sharing of all aspects of plant research to the public. COPO aims to be the vehicle to bring together the tools required to harmonise open plant omics research. This sector has obvious ties with industry. Public domain omics-based bioscience is relevant and important input into industry internal research and discovery activities. To make such bioscience data truly reusable and ensure scientific robustness, it must be uniformly annotated, allowing not only integration through equivalence of terminology but also by increasing efficiency in data production and re-use, and allowing correct interpretation by means of the context provided by their metadata. A collaborative platform for frictionless bioinformatics built with and for the academic and industrial community is long overdue. Alongside data processing, industry also works on finding solutions for integration and management of large 'omics data sets, e.g. efforts like the Pistoia Alliance. Together with COPO industry partners (Eagle Genomics) we will develop use-cases for the platform in industry, propose acceptance criteria required for commercial use, supply technical advice/support on meeting acceptance criteria, evaluate the platform on 3rd party infrastructure, and maximise knowledge exchange and commercialisation.

COPO and the standards community
Expertise and knowledge gained throughout the lifetime of the project and beyond will be disseminated through a variety of channels. The presence of a direct link with the plant science community (through GARNet, UK Plant Sciences Federation (UKPSF)) is key to the success and adoption of the platform and associated standards. The project will have a continuous dialogue, through face-to-face events as well as online tools and social media, between those working on the platform and the plant bioscience community. The several letters of support show a clear interest in working together, using and adopting a platform that implicitly confers standards compliance. COPO will provide a solution to overcome the challenges in standards fragmentation by (i) fostering development, acceptance and implementation of reporting standards that are immediately suitable for plant research, and (ii) limiting the range and variability of standards. This will have a direct impact on the development and maintenance costs for commercial and academic software developers of standards-compliant products.

Societal impacts
Historically there has been reluctancy to adopt some of the standards and open-data principles in the plant bioscience community, especially in the field of food sustainability and security, so openness and transparency in these areas are vital to continue improving the public perception. The presentation of the research data will play a key role in opening the dialogue with the general public and will contribute to the development of stronger links with sectors in society (such as school teachers) that are less familiar with the scientific activities in plant research and the beneficial impact this has in their lives. It is widely recognised that the shortage of expertise and skill in biomathematics and informatics across the world is a major risks for a future development of key areas in life sciences. The objectives of this proposal will help to attract talented staff to work with the COPO partners, and offer alternative career paths.