COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform
Lead Research Organisation:
University of York
Department Name: Biology
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Planned Impact
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.
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.
Organisations
Publications
Johnson D
(2021)
ISA API: An open platform for interoperable life science experimental metadata.
in GigaScience
| Description | Co-organised plant user workshops to test the COPO platform with data provided by UK plant researchers (via GARNet and UKPSF) working with genomics, phenomic, proteomic and metabolic datasets. These workshops helped to validate the COPO platform, highlight bugs, provide training in the platform and generate additional user requirements and suggestions for the the extension and use of the COPO platform - Contributing to Objectives 1, 2, and 4. Promotion of the COPO platform within the international DivSeek community that is focused on increasing the access, re-use and annotation of data associated with plant germplam. Activities included inclusion and presentation of COPO at DivSeek events (such as those held at PAG), involvement of COPO in DivSeek working groups. These activities helped to link COPO with relevant international data standards and annotation projects, involvement with relevant DivSeek Initiative working groups on data compatibility and generated opportunities to train people in the use of the platform. Contributing to Objectives 1,2 and 4 Active collaboration with the Research Data Alliance (RDA) specifically the Agriculture Data Group. Activities include attendance at RDA meetings and conference to promote awareness of COPO, to understand the wider 'environment' in which COPO sits and help to ensure it interacts with and is aware of appropriate initiatives with in the RDA activities. Contributing to Objectives 1,2 and 4 Facilitated interaction with the plant researchers and data managers at the international CGIAR Centres. Activities include presentations and attendance at workshops and events such as PhenoharmonIS and PAG. These activities helped to widen the test user group beyond the UK, created opportunities to train people in the use of the platform and provided data sets beyond the initial scope of COPO project generating ideas for future development and collaboration. Contributing to Objectives 1,2 and 4 Taken together activities undertaken by York/Warwick provide users and datasets to test and validate the COPO platform increased awareness of the COPO project at the national and international level brought international activities involved in data management and annotation to the attention of the COPO development team aligned the COPO platform with relevant international efforts in meta data, data standards and data management helped to ensure that data that submitted, annotated and described via COPO is compatible and useful to wide range of users and accessible and reusable in the future |
| Exploitation Route | Help make the COPO platform appropriate for plant scientists and increase awareness of the platform |
| Sectors | Agriculture, Food and Drink |