COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform
Lead Research Organisation:
Earlham Institute
Department Name: Directorate Office
Abstract
We live in a digital age where we increasingly rely on interconnected resources in our daily lives. Biological science, due to the very nature of the complexity of worldwide research avenues, is typically fragmented. Even though scientific information is published in peer-reviewed articles, it is often badly described and, until very recently, often unavailable to the general public because of journal licensing issues and expensive subscription costs.
The field of bioinformatics (the analysis and management of biological data using computational methods) produces many freely available tools for data analysis and exposure that are incredibly useful to researchers. However, these tools often do not interoperate well, meaning that great effort is spent attempting to convert or tweak datasets to fit with other tools that further bioinformatics processes, hindering timely accurate reusable research. Couple this with the lack of descriptive information noted earlier, and knowledge that can be vital to one researcher, team or community can become at least unreproducible (thus letting others confirm findings) at worst unusable.
Life scientists are people focused on investigating biological processes. This requires a lot of time, effort and fastidiousness in experimental observation, data collection and analysis. Typically for life scientists, more time is spent on the former: defining and publishing experimental methods and results. The latter, i.e. the data behind these results, is usually badly defined and largely unpublished. For computer scientists, the story is reversed - the focus is on getting to the data. This platform will bridge the gap between these two groups by providing tools and training to both life and computer scientists in the plant bioscience field, in order to help them get their data into the right formats and described uniformly for open research.
To do this, the management, interoperability and curation of scientific datasets is key. Researchers need clear guidance and help to:
- Manage their data in a concise relevant way that allows immediate reuse by others: Generating data is only one part of the picture. To back up scientific findings, data needs to be made available to others to allow the same degree of rigour and peer review that is enforced for published material. This is not an easy task because the tools and resources required to describe data well and to make data available are typically designed for the computer scientist.
- Let them analyse their data easily: Large software development projects like Galaxy provide access to complex analytical tools - we are not aiming to reinvent the wheel in this regard. We aim to engage and collaborate with these existing providers to develop and exploit interfaces to these specialised software projects, so to let descriptive tools and analytical tools communicate efficiently.
This project will address these issues directly, providing tools for storing, annotating and sharing valuable information as well as promoting clear guidance, training. Overall this promises to be a major boost to UK plant sciences research.
This project aims to promote and build links between scientific knowledge and the tools used to generate that knowledge, addressing the lack of descriptive information about underlying data. By doing so, we will provide a platform comprising both existing tools and novel interoperability processes, allowing researchers easy access to methods of describing their work, feeding directly into analytical software, thus promoting clear and robust best practices in science.
Open science is vital to the future generation of researcher, especially to realise the goals of transparent knowledge sharing. This project will remove the barriers that restrict researchers in making their findings freely available to everyone in a consolidated seamless easy-to-use fashion.
The field of bioinformatics (the analysis and management of biological data using computational methods) produces many freely available tools for data analysis and exposure that are incredibly useful to researchers. However, these tools often do not interoperate well, meaning that great effort is spent attempting to convert or tweak datasets to fit with other tools that further bioinformatics processes, hindering timely accurate reusable research. Couple this with the lack of descriptive information noted earlier, and knowledge that can be vital to one researcher, team or community can become at least unreproducible (thus letting others confirm findings) at worst unusable.
Life scientists are people focused on investigating biological processes. This requires a lot of time, effort and fastidiousness in experimental observation, data collection and analysis. Typically for life scientists, more time is spent on the former: defining and publishing experimental methods and results. The latter, i.e. the data behind these results, is usually badly defined and largely unpublished. For computer scientists, the story is reversed - the focus is on getting to the data. This platform will bridge the gap between these two groups by providing tools and training to both life and computer scientists in the plant bioscience field, in order to help them get their data into the right formats and described uniformly for open research.
To do this, the management, interoperability and curation of scientific datasets is key. Researchers need clear guidance and help to:
- Manage their data in a concise relevant way that allows immediate reuse by others: Generating data is only one part of the picture. To back up scientific findings, data needs to be made available to others to allow the same degree of rigour and peer review that is enforced for published material. This is not an easy task because the tools and resources required to describe data well and to make data available are typically designed for the computer scientist.
- Let them analyse their data easily: Large software development projects like Galaxy provide access to complex analytical tools - we are not aiming to reinvent the wheel in this regard. We aim to engage and collaborate with these existing providers to develop and exploit interfaces to these specialised software projects, so to let descriptive tools and analytical tools communicate efficiently.
This project will address these issues directly, providing tools for storing, annotating and sharing valuable information as well as promoting clear guidance, training. Overall this promises to be a major boost to UK plant sciences research.
This project aims to promote and build links between scientific knowledge and the tools used to generate that knowledge, addressing the lack of descriptive information about underlying data. By doing so, we will provide a platform comprising both existing tools and novel interoperability processes, allowing researchers easy access to methods of describing their work, feeding directly into analytical software, thus promoting clear and robust best practices in science.
Open science is vital to the future generation of researcher, especially to realise the goals of transparent knowledge sharing. This project will remove the barriers that restrict researchers in making their findings freely available to everyone in a consolidated seamless easy-to-use fashion.
Technical Summary
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.
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.
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
- Earlham Institute (Lead Research Organisation)
- University of Manchester (Collaboration)
- University College London (Collaboration)
- CyVerse (Collaboration)
- Newcastle University (Collaboration)
- Polish Academy of Sciences (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- ELIXIR (Collaboration)
- Rothamsted Research (Collaboration)
- Heriot-Watt University (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- DivSeek International (Collaboration)
- CGIAR (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- Hewlett Packard Enterprise (HPE) (Collaboration)
- UNIVERSITY OF DUNDEE (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
Publications
Williamson HF
(2021)
Data management challenges for artificial intelligence in plant and agricultural research.
in F1000Research
Waterhouse R
(2021)
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
in F1000Research
Shaw F
(2020)
COPO: a metadata platform for brokering FAIR data in the life sciences
in F1000Research
Sansone; R
(2015)
COPO: Aiding the journey from data to publication in the plant sciences
Ramírez-González RH
(2018)
The transcriptional landscape of polyploid wheat.
in Science (New York, N.Y.)
McMullan M
(2018)
The ash dieback invasion of Europe was founded by two genetically divergent individuals.
in Nature ecology & evolution
Leonelli S
(2017)
Data management and best practice for plant science.
in Nature plants
Johnson D
(2021)
ISA API: An open platform for interoperable life science experimental metadata.
in GigaScience
Description | The major impact this year has been the formal inclusion of COPO into the Darwin Tree of Life project, where COPO is now in use as the main sample collection metadata deposition system for the whole project. This is a considerable achievement. This has resulted in growth of user base of the platform and has gathered interest from other projects. For example, COPO is in the recommended list of tools for the Earth Biogenome Projects, as per an upcoming white paper that highlights best practices for existing and future EBP efforts. COPO is also being modified to accept symbiotic sample relationships so it can be used for the Wellcome Sanger institute's Aquatic Symbiosis Genomics project. We have garnered interest further afield, where COPO is one of the proposed metadata capture tools for the Austratlian AgReFed national agricultural programme where PI Davey now sits on their Technical Advisory Board. COPO has continued to be used by the EI CSP to submit data from the strategic programme into core public data repositories such as the EMBL-EBI ENA and the EI CKAN installation. We have improved the COPO deployment process hosted on the CyVerse UK infrastructure, where changes to COPO code result in automated building, testing and deployment to development servers. Using a containerisation approach like Docker makes COPO transferable between different hardware configurations allowing for dynamic scaling of the installation. New installations can be setup by populating a configuration file and running simple terminal commands. This is a potential route of new installation for projects such as the Darwin Tree of Life, as appropriate. This work has resulted in a BBSRC BBR grant submission partnering with EBI and Sanger to expand development. |
Exploitation Route | We are continuing to work within the UK Darwin Tree of Life project, where we have developed the sample collection schemas (the "sample manifest") which set out the rigorous requirements for project metadata capture. These schemas can be uploaded into COPO, validated, and the metadata brokered into the downstream tools for tracking and public release at the Sanger and EBI respectively. COPO is fully open source, and we have received interest in the project from companies as well as research organisations to respond to their data management needs. We are continuing to work with the Designing Future Wheat partners to use COPO as the data brokering platform for DFW data. We successfully undertook a funded collaboration with the CIMMYT Big Data platform to develop COPO to be the main data brokering platform for 15 CGIAR centres globally. We will now be involved in a new collaboration as part of the ELIXIR CONVERGE effort to harmonise data and metadata capture and dissemination, as well as working with other key EU data management experts to integrate COPO into plant dataset lifecycles through the ELIXIR Plant implementation study. Harmonised metadata attribution is becoming a pressing need in the life sciences to ensure that data adheres to the FAIR principles, allowing researchers better access to a wider array of data. |
Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Environment Pharmaceuticals and Medical Biotechnology |
URL | https://copo-project.org |
Description | Due to COVID, we have not been able to present COPO at any public conferences. The Darwin Tree of Life (DTOL) work has continued with excellent results, where COPO is the main metadata ingestion route for the whole project. Due to this success, COPO is also used for the Aquatic Symbiosis Genomes project, and we have been involved in the European Reference Genome Atlas (ERGA) pilot project where COPO is playing the same role. This has been a major undertaking that has placed COPO into a hugely visible and important role. The ELIXIR Biodiversity working group published a paper in F1000 on how Biodiversity metadata is handled across key EU projects through ELIXIR. We have developed sample description modules in COPO for the Darwin Tree of Life project where the platform is in production use to collect all sample data for that project. COPO has brokered almost 250 datasets into the public archives this reporting period. COPO has over 400 registered users, has submitted over 28000 samples into public repositories, comprising over 34000 data files. To date, over 10000 samples have been submitted as DTOL Biosamples to which the sequencing data can be linked and made publicly available. As a result of the ERGA pilot work, we have been included in a Horizon Europe bid to fund the whole ERGA project. |
First Year Of Impact | 2017 |
Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Pharmaceuticals and Medical Biotechnology |
Impact Types | Economic |
Description | FAIRsharing, FAIR Cookbook and ISA resources are core to ELIXIR data management services |
Geographic Reach | Europe |
Policy Influence Type | Influenced training of practitioners or researchers |
URL | https://elixir-europe.org/sites/default/files/documents/annual-report-2020.pdf |
Description | Interview with Environment Adviser from the UK Parliamentary Office of Science and Technology |
Geographic Reach | National |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Impact | Contacted by UK Parliament to contribute to a POSTnote (short document to advise ministers on a given topic) on genebanks and Digital Sequence Information as a result of my recent election to the DivSeek Board of Directors. I was interviewed to provide information around current international policies on DSI and how future UK involvement might be shaped around open licencing/MTAs of DSI datasets. |
URL | https://www.parliament.uk/postnotes |
Description | FAIRplus |
Amount | £3,996,150 (GBP) |
Funding ID | 802750 |
Organisation | European Commission |
Department | Innovative Medicines Initiative (IMI) |
Sector | Public |
Country | Belgium |
Start | 01/2019 |
End | 01/2022 |
Description | ISA-InterMine: accelerating and rewarding data sharing |
Amount | £1,174,660 (GBP) |
Funding ID | 208381/A/17/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 07/2018 |
End | 07/2021 |
Title | CGCore v2 Improvements |
Description | As part of the collaboration between the EI COPO project and the CGIAR Big Data Platform, we worked with CGIAR and Crop Ontology developers to improve the CG Core v2 schema for describing CGIAR digital outputs. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Globally, this work will affect all CGIAR Data Managers and users of the COPO platform to deposit data into CG Centre repositories. |
URL | https://github.com/collaborative-open-plant-omics/cgcore_schema |
Title | Continued improvements to the ISA toolkit |
Description | Started in 2003 and first released in 2007, the ISA tools have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community. Short description of the developments and achievements of the resource over the last year: • Awarded Wellcome Trust funds (2018-2021), as collaborative project with the University of Cambridge's InterMine team to link the two resources and reward researchers for annotating and publish FAIR data; also, ISA is embedded in two ELIXIR Implementation Studies, on a Plant-focused data validation and on metabolomics. • With the uptake of ISA-Galaxy tools (https://github.com/ISA-tools/isatools-galaxy) and integration with the Galaxy Framework, ISA has struck a major milestone by showcasing how prospective data management can be done, demonstrating a full deposition workflow to Metabolights and creating training material (10.7490/f1000research.1115757.1). • Jupyter notebooks (https://github.com/ISA-tools/dtp-isa-exercises) have been developed as teaching material to showcase the use of ISA-API in various context to undergraduate and postgraduate courses on data readiness. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Community use and impact is tracked via the ISA Commons, which currently has over 40 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. For example, ISA is used by the University of Oxford' GigaScience and underpins Springer Nature's Scientific Data data journal, supporting intelligent data sharing and credit; ISA is used to describe the experiment and to provide browse and search functionality for Scientific Data's content (http://scientificdata.isa-explorer.org). The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: o EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. o BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. o ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. o ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. |
URL | http://isa-tools.org |
Title | Continued improvements to the ISA toolkit and the new Datascriptor component |
Description | Started in 2003 and first released in 2007, the ISA tools (http://isa-tools.org) have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community (https://www.isacommons.org). Key work over the last year is the development of a new component, the Datascriptor: https://datascriptor.org, as part of the Wellcome Trust award (2018-2021), a collaborative project with the University of Cambridge's InterMine team. Leveraging our experience and links with the communities, we are designing an open-source web-based tool - part of an ecosystem of existing annotation and authoring systems - to help researchers to use community standards to describe their (meta)data at the source, and capitalize on their effort to accelerate the creation of a data article. In addition major advances have been made to the ISA API also working with the ELIXIR Plant and Metabolomics communities. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Community use and impact is tracked via the ISA Commons, which currently has over 40 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. For example, ISA is used by the University of Oxford' GigaScience and underpins Springer Nature's Scientific Data data journal, supporting intelligent data sharing and credit; ISA is used to describe the experiment and to provide browse and search functionality for Scientific Data's content (http://scientificdata.isa-explorer.org). The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: (i) EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. (ii) BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. (iii) ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. (iv) ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. |
URL | https://datascriptor.org |
Title | Continued improvements to the ISA toolkit: the new graphql interface and RDF representation of ISA. |
Description | The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Started in 2003 and first released in 2007, the ISA tools (http://isa-tools.org) have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community (https://www.isacommons.org Key work over the last year is the development of two new components, graphql interface to query ISA documents and a RDF representation of ISA in obo, sdo or wikidata (as part of the Wellcome Trust award, 2018-2021), a collaborative project with the University of Cambridge's InterMine team. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Community use and impact is tracked via the ISA Commons, which currently has over 50 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: (i) EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. (ii) BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. (iii) ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. (iv) ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. |
URL | https://github.com/ISA-tools/isa-api |
Title | Improvements to the COPO system |
Description | COPO is a computational system that attempts to address the challenges of making data FAIR by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share it with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible. Building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Improvements to the COPO user interfaces and underlying code which have resulted in more data being submitted to public repositories through the system. The CGIAR CGCore v2 implementation is complete and undergoing testing to document and provide improvements. The Darwin Tree of Life project has chosen to use COPO as its main sample metadata submission route. |
URL | https://github.com/collaborative-open-plant-omics/COPO |
Title | MIAPPE specification and tools |
Description | Minimum Information About a Plant Phenotyping Experiment is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE specification comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment, and software to validate, store and disseminate MIAPPE-compliant data. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | MIAPPE is a logical standard - but there are specific implementations of tools designed to support its use and application, for example, in the ISA-tools framework. We are working with the developers of the Plant Breeding API (BRAPI) to ensure the compliance of BRAPI with the MIAPPE standard, and to coordinate future developments. |
URL | http://www.miappe.org/ |
Title | COPO Linked Data database |
Description | The COPO docoument-based database runs on the MongoDB engine, providing a flexible and semantically-aware storage mechanism for recording and disseminating linked research objects. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | No |
Impact | The database powers the COPO user interface, and the underlying source code and business logic layers are available to the public via GitHub. Once the COPO project is live in production, we will be releasing staged dumps of this database at regular intervals for anyone to use the information contained within. |
URL | https://github.com/collaborative-open-plant-omics/COPO/tree/master/web/src/dal |
Title | The Earlham Institute CKAN Digital Repository |
Description | The CKAN digital repository has been set up as part of WP3 of Earlham Institute's CSP to hold all EI strategic publications alongside any supplementary datasets and information. This gives the public and researchers immediate access to EI's BBSRC funded research through open access routes where available. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | We have buit scripts to find and make available open access versions of all EII published research, either as preprints or as journal articles. We also supply any supplementary information as appropriate to aid information dissemination. The EI CKAN runs within Earlham Institute's CyVerse UK National Capability. |
URL | https://ckan.earlham.ac.uk |
Description | CyVerse US/UK Partnership |
Organisation | CyVerse |
Country | United States |
Sector | Private |
PI Contribution | The COPO project team brings the expertise on working with disparate metadata standards, and also provides the platform (through COPO web application) for interoperable metadata interactions with CyVerse. This promotes the use of CyVerse not only to researchers at EI, but to a broader community of plant scientists internationally. |
Collaborator Contribution | CyVerse UK provides and supports the necessary infrastructure relied upon by COPO. It is also positioned, in the near future, as one of the analysis platforms supported by COPO. The continued collaboration with CyVerse will keep promoting these objectives, by providing improved applications and better workflows to support researchers relying on both systems. |
Impact | Participated in a hackathon to discuss ideas for improved metadata interoperability between COPO and CyVerse platforms. This led to outcomes including: developing services in COPO for exposing data objects stored in CyVerse; advancing discussions and potential ideas for large file transfer and manipulation via CyVerse. |
Start Year | 2016 |
Description | DivSeek Partnership |
Organisation | DivSeek International |
Sector | Learned Society |
PI Contribution | I bring infrastructure expertise to this partnership, influencing and impacting policy to provide computational and training capacity to other DivSeek partners. I promote the range of infrastructure projects that are developed in my group at EI, but also solutions developed at other centres that can contribute to the DivSeek consortium. Partners are exposed to EI projects such as COPO, Grassroots (Wheat Information System, CerealsDB, marker design), CyVerse UK and Galaxy, through working group communications and meetings at international conferences such as PAG and RDA. I lead the Data Standards for Interoperable Tools working group, and we aim to collate community-suggested standards and tools, and advise the partnership and their stakeholders in best practice for delivery of sustainable and interoperable infrastructure. |
Collaborator Contribution | The DivSeek consortium contributes expertise and knowledge exchange in advances in crop diversity, improving our networking and understanding of challenges and potential solutions to social, structural, and biological problems. With over 66 global partners including EI, this is a powerful and highly respected group of research institutes that are working together to enable a step change in efficiency of interactions, leading to improved crop diversity research and data sharing. |
Impact | EI is a founding partner of DivSeek, and Dr Davey leads one of the new working groups, "Data Standards for Interoperable Tools" (http://www.divseek.org/standards/) |
Start Year | 2015 |
Description | ELIXIR Biodiversity Working Group |
Organisation | ELIXIR |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Drs Davey and Shaw attended the first ELIXIR Biodiversity working group meeting in Milan 2020. Davey gave a talk on UK efforts to track biodiversity data, for example with the COPO platform. |
Collaborator Contribution | ELIXIR initiated this working group and invited member ELIXIR nodes to attend. |
Impact | Main outcome is building the community with a view to submitting an implementation study around biodiversity data. |
Start Year | 2020 |
Description | ELIXIR Interoperability Platform and ISA |
Organisation | ELIXIR |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | ISA is part of the ELIXIR Recommended Interoperability Resources (RIRs) to facilitate interoperability and reusability of life science data and support the principles of FAIR data management. |
Collaborator Contribution | The ELIXIR Recommended Interoperability Resources have been selected by external panel of reviewers, based on the selection criteria published in the Call for RIR application, which measure how they facilitate scientific research and how they improve FAIRness of life science data. |
Impact | ISA is and will continue to be used by and further developed with ELIXIR communities, especially with Plant and Metabolomics use cases. |
Start Year | 2018 |
Description | ELIXIR Metabolomics Community |
Organisation | ELIXIR |
Department | ELIXIR UK |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | My team has contributed ISA-related work to the ELIXIR Metabolomics use case, activities and reports. |
Collaborator Contribution | We have gained more visibility for the ISA work and now ISA-Tab is a formal format used by the Galaxy analysis toolkit for metabolomics applications. |
Impact | The ISA framework as the basis for the metadata standards used by this ELIXIR Metabolomics Community and the tools are embedded in the EBI MetaboLights databases, as well as in other international metabolomics resources. |
Start Year | 2017 |
Description | ELIXIR Metabolomics Community |
Organisation | ELIXIR |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | My team has contributed ISA-related work to the ELIXIR Metabolomics use case, activities and reports. |
Collaborator Contribution | We have gained more visibility for the ISA work and now ISA-Tab is a formal format used by the Galaxy analysis toolkit for metabolomics applications. |
Impact | The ISA framework as the basis for the metadata standards used by this ELIXIR Metabolomics Community and the tools are embedded in the EBI MetaboLights databases, as well as in other international metabolomics resources. |
Start Year | 2017 |
Description | ELIXIR Plant Use Case |
Organisation | ELIXIR |
Department | ELIXIR UK |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | My team has contributed ISA-related work to the ELIXIR Plant Science use case, work and report. |
Collaborator Contribution | We have gained more visibility for the ISA work and COPO activities. |
Impact | ISA is used by the BRAPI and there is an ISA implementation of the MIAPPE specification. |
Start Year | 2016 |
Description | ELIXIR Plant Use Case |
Organisation | ELIXIR |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | My team has contributed ISA-related work to the ELIXIR Plant Science use case, work and report. |
Collaborator Contribution | We have gained more visibility for the ISA work and COPO activities. |
Impact | ISA is used by the BRAPI and there is an ISA implementation of the MIAPPE specification. |
Start Year | 2016 |
Description | ELIXIR Plants Community |
Organisation | ELIXIR |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | By actively being part of the ELIXIR Plants Community it has opened up the possibilities for future projects. Including offering our services and tools (COPO, CyVerse, Grassroots etc) for use in ongoing and future implementation studies. |
Collaborator Contribution | Other community members have incorporated our tools/services into their plans for future work |
Impact | ELIXIR Plant Services Roadmap 2020-2023: doi 10.7490 |
Start Year | 2020 |
Description | ELIXIR UK Node |
Organisation | Earlham Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | Heriot-Watt University |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | Newcastle University |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | Rothamsted Research |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Birmingham |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Cambridge |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Dundee |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Edinburgh |
Department | Edinburgh Genomics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Edinburgh |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Liverpool |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Manchester |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR UK Node |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Help create the ELIXIR UK Node |
Collaborator Contribution | Contribute to the creation of the ELIXIR UK Node |
Impact | Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized. |
Start Year | 2012 |
Description | ELIXIR plant community - COPO listed as a copre plant service |
Organisation | ELIXIR |
Department | ELIXIR UK |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | COPO has been listed, together with a number of other resources, as a core plant service. As COPO is a live service, it;s effectively already contributing to the plant science community improving metadata annotation and submission to repositories processes. |
Collaborator Contribution | the ELIXIR plant community has been working on standardized practices to improve the output quality of the research. They recognize data hygiene as a driver, and therefore identify core resources to address researchers to. |
Impact | this is an ongoing collaboration, the main output would come from the standardization of practices across the research domain and diminished time resources requested from scientist in the metadata and submission processes |
Start Year | 2020 |
Description | HPE AI workshop 2019 |
Organisation | Hewlett Packard Enterprise (HPE) |
Country | United Kingdom |
Sector | Private |
PI Contribution | We worked with HPE staff to organise and host an AI Workshop at EI. We opened the course up for national delegates to attend and discover more about how AI and Machine Learning techniques can be applied to biological research data. |
Collaborator Contribution | HPE provided the trainers and staff to teach the materials. |
Impact | We will continue to work with HPE to supply our institutlonal HPE equipment. We have also put forward HPE as a potential partner in the upcoming DTP3 bid. |
Start Year | 2019 |
Description | Hanna Cwiek - 2 month visit : MIAPPE and ISA |
Organisation | Polish Academy of Sciences |
Department | Institute of Plant Genetics |
Country | Poland |
Sector | Academic/University |
PI Contribution | Members of my team, namely Philippe Rocca-Serra and Alejandra Gonzalez-Beltran has assisted Hanna in her ISA-related work. |
Collaborator Contribution | Dr Hanna Cwiek from the Poznan Institute of Genetic Research in Poland (in Pawel Krajewski's team) visited my team to work on ISA and MIAPPE, helping to refine ISA tools relevant to plant science and COPO activities. |
Impact | Possible paper on the work done |
Start Year | 2017 |
Description | Integration of COPO and CGCore Schemas and Associated Repositories |
Organisation | CGIAR |
Country | France |
Sector | Charity/Non Profit |
PI Contribution | We have developed a proof-of-concept platform to streamline metadata attribution and dataset deposition into CGIAR repositories using the BBSRC-funded COPO software. Drs Etuk and Shaw, two Research Software Engineers in the Davey group at Earlham Institute and the original core developers, have implemented various new features into COPO to allow CGIAR Data Managers to harmonise and streamline the submission of CG-relevant metadata and data into the CG digital data repositories. All software and infrastructure is hosted within the CyVerse UK cloud. We have: - Implemented support of CG Core v.2.0. (http://repo.mel.cgiar.org/handle/20.500.11766/4764) metadata annotation of various data types, including publications, produced at the CGIAR institutes via the existing COPO wizard system. - Implemented support of submissions of annotated objects to institutional instances of the following repositories: dSpace (https://www.duraspace.org/dspace/), CKAN (https://ckan.org/) and Dataverse (https://dataverse.org/). - Designed and implemented a mechanism within COPO which controls which users can submit to which repositories. - Implemented support the annotation of variables within data sets (i.e. column headings; experiment condition descriptors etc) with terms and URIs from ontologies or controlled vocabularies/trait dictionaries (AGROVOC and GACS). |
Collaborator Contribution | CGIAR have provided coordination contributions with key members in the CG Centres to gather feedback on developed elements, as well as provided funds to allow a core CGCore metadata schema developer to travel to EI and work with Drs Etuk and Shaw to improve the CGCore schema. |
Impact | This collaboration has seen rapid development of key functionality in the COPO platform to support CG centre Data Managers. This has required technical skills to develop the software, biocuration expertise provided by CGIAR to improve and refine the CGCore metadata schema, ontology expertise from the Bioversity team in Montpellier, and coordination expertise from Dr Davey (EI) and Medha Devare (CGIAR). Software and Technical Products (Webtool/Application - Collaborative Open Plant Omics (COPO) (2017)): All software code developed is open source and can be found within the COPO Github repository: https://github.com/collaborative-open-plant-omics/COPO |
Start Year | 2018 |
Description | Martin Mueller - 1 week visit to EI: CG Core v.2.0 work |
Organisation | CGIAR |
Country | France |
Sector | Charity/Non Profit |
PI Contribution | Drs Etuk and Shaw worked closely with Martin to refine and integrate the CG Core v.2.0 schema into COPO |
Collaborator Contribution | Martin Mueller worked as a contractor to CGIAR to produce the CG Core v.2.0 schema. He provided a good insight to the workflow of the new schema and how COPO could better support its implementation from the metadata attribution user interfaces to the submission workflow. |
Impact | Full support for the CG Core workflow now implemented and available in COPO. |
Start Year | 2018 |
Title | ASG Submissions in COPO |
Description | Implementing pipeline to create and submit ASG type samples |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | samples from the ASG group can now be contributed to the DTOL project |
Title | ASG submission pipeline |
Description | The Darwin Tree of Life pipeline for metadata validation and samples submission to ENA was used as a baseline to deploy a similar pipeline for the aquatic Symbiont Genome Project. |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | In the first 10 months over 2700 ASG samples were submitted trough COPO |
URL | http://copo-project.org |
Title | Annotation of PDFs and Spreadsheets |
Description | Tools for annotating spreadsheet documents and pdfs with ontology terms from the OLS updated and in some cases implememented. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | Rich metadata can be added and shared to otherwise simple tabular or textual data files. |
Title | Automatic Software Builds |
Description | COPO is now automatically built by Dockerhub when submitting a correctly formatted tag to Github. Notifications are sent from Dockerhub to Slack/Discord when the build completes, which means its now extremely rapid to deploy new code to all COPO servers. |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Bug fixes and new features can be implemented and deployed to COPO live services within 10-20 mins. |
Title | CGCore Schema |
Description | Schema is a template designed to collect all metadata relating to research outputs produced by the CGIAR institutes. Our group helped design the specification. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | This schema is being deployed to the CGIAR centers imminently. Once done, it will form the basis of data collection for 15 research centers around the globe employing in excess of 8000 scientists. |
Title | CGCore Wizard |
Description | Based on the CGCore specification, the wizard is an implementation of the template in the COPO platform. It enables researchers to actually record the metadata relating to CGIAR research objects. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | Researchers from the CGIAR institutes will be able to record their metadata based on the CGCore schema. CGIAR encompasses 15 institutes worldwide employing over 8000 researchers. |
URL | https://copo-project.org/copo |
Title | CKAN Workflow for data deposition |
Description | In collaboration with the CGIAR centers, we developed a workflow for depositing heterogeneous data into the CKAN repository along with appropriate metadata extracted from CGCore metadata fragments. CKAN is an open source, mature federated solution for storing, sharing and disseminating data objects and metadata. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | This will allow COPO to be the main access point of metadata annotation and data deposition for the CGIAR institutes. This is a major conglomeration of research stations around the globe responsible for many agricultural advances in the developing world since the end of the second world war. From this work, we can expect to broker tens of thousands of documents, data sets or other research objects from CGIAR researchers. |
Title | COPO - release of real time stats and histogram |
Description | for ease reporting and assessment of impact graphs and stats are now visible in the COPO website |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | easier reporting to board and in presentation |
Title | COPO - release of validation and pipeline for DTOL SOP version 2.3 and ASG 2.3.1 |
Description | COPO was updated to successfully validate the new version (2.3 for Darwin Tree of Life and 2.3.1 for Aquatic Symbiont Genome project) of manifests |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | DTOL and ASG communities successfully updating their SOPs and using COPO as a metadata validation, metadata storing and submission broker |
Title | COPO - samples updates for ERGA and acceptance of rejected samples |
Description | ERGA users can amend previously uploaded manifest as long as validation pass. DTOL/ASG and ERGA managers are also now able to accept previously rejected samples (that may have been rejected by mistake or that have been amended and became acceptable). |
Type Of Technology | Webtool/Application |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | The ability for users to perform updates, albeit only in some scenarios hugely reduced the burden both on the COPO team and the ERGA coordinators in dealing with custom support requests. Similarly the possibility for managers to correct errors from the interface reduce the number of custom requests of support to the COPO team, that can instead develop new features |
URL | http://copo-project.org |
Title | COPO - taxonomy edge cases validation |
Description | COPO validation of DTOL/ASG manifests was updated to take into account edge cases in species for which NCBI doesn't return a genus, a family or either |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | This has allowed to successfully return errors for manifest not allowed to be submitted in the context of the DTOL and ASG projects, and to successfully validate samples from taxa that do not have an allocated family |
URL | http://copo-project.org |
Title | COPO -ERGA manifest validation and submission |
Description | COPO was adopted as a validation and submission metadata broker by the ERGA (European Reference Genome Atlas) community. Separata profile type, user group and validation for the project were developed and released |
Type Of Technology | Webtool/Application |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | The ERGA community has been using COPO since January and received funding for further research having been able to prove the feasibility of the project |
URL | http://copo-project.org |
Title | COPO API |
Description | HTTP rest methods for accessing sample information. |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | This is the mechanism by which the Sanger STS pulls sample information, which is then used by many other DToL partners. |
Title | COPO Stats Generator |
Description | Daily stats for COPO samples, profiles, data files and users are collected, stored and available as lists in the API |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | up to date figures and graphs are always available for COPO reporting |
Title | COPO developer documentation |
Description | Extensive development documentation has been created or updated descrihbing how to deploy and use the COPO system. |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Allows potential system administrators to deploy an instance of COPO themselves. Also required as comments in a paper under review expressed that there was not enough information to deploy COPO. |
Title | Collaborative Open Plant Omics (COPO) |
Description | COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories. COPO facilitates the links to data analysis platforms such as CyVerse UK and Galaxy. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces. This improvement output represents the beta release of the COPO platform in 2017. |
Type Of Technology | Webtool/Application |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | COPO has been added to the ELIXIR-UK roadmap for ELIXIR core data services, and is currently being used by EI and JIC researchers to deposit real, large scale sequencing datasets into the European Nucleotide Archive. COPO is also being investigated as a potential data entry tool for the CGIAR Big Data project, and this will be explored in a joint EAGER submission with CIMMYT. COPO has also been selected to act as one of the data ingestion pipelines for data arising from the Designing Future Wheat programme, depositing open data into the Grassroots repository. COPO is also being included in grant submissions to assist vertebrate and wheat communities in effective metadata management. COPO runs within the CyVerse UK National Capability infrastructure. |
URL | https://copo-project.org |
Title | Collaborative Open Plant Omics (COPO) software |
Description | COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories and to facilitate links to data analysis platforms. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces. |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | The software is in an early stage, but functional for deposition of data to a small number of repositories. As such we are not yet ready for end-user testing. However, we are collaborating with Cyverse US (was iPlant Collaborative) to investigate the use of COPO as the brokering system for their Data Commons. |
URL | https://github.com/collaborative-open-plant-omics/COPO |
Title | Creation of Deployment architecture |
Description | The deployment architecture is based on Docker Swarm hosted on the CyVerse UK virtual infrastructure. This provides a robust and dynamic deployment system allowing load balancing between virtual servers, whilst providing convenience and security. |
Type Of Technology | Webtool/Application |
Year Produced | 2018 |
Open Source License? | Yes |
Impact | COPO has over 99% uptime meaning that our users are provided with a reliable and accessible service around the globe and around the clock. |
URL | https://copo-project.org/copo |
Title | Creation of MIAPPE wizard |
Description | Schema implemented in wizard format in COPO to allow collection of plant phenotyping experimental metadata. |
Type Of Technology | Webtool/Application |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | Users can now record their metadata in this format. Phenotyping experiments are an important part of crop science, and to be able to collect full metadata in such a manner as this is very important. |
Title | Creation of institutional repos architecture |
Description | This piece of work allows for the deposition of items to institutional repository instances. This is important since researchers are increasingly looking to looking to smaller scale institutionally hosted instances of off the shelf repository solutions such as Dataverse, CKAN and DSPACE. |
Type Of Technology | Webtool/Application |
Year Produced | 2018 |
Open Source License? | Yes |
Impact | Allows users to enter details of their institutional repo instances and have many users submit there. |
Title | Creation of shared profile architecture |
Description | This allows users to share profiles with other users of their choice to facilitate group editing of metadata. |
Type Of Technology | Webtool/Application |
Year Produced | 2018 |
Open Source License? | Yes |
Impact | This was a much requested feature to allow collaborations between disparate research groups. |
Title | DSPACE repository deposition workflow |
Description | In collaboration with the CGIAR centers, we developed a workflow for depositing heterogeneous data into the DSpace repository along with appropriate metadata extracted from CGCore metadata fragments. DSpace is developed by DuraSpace and is widely used in academia to deposit and disseminate research objects. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | This will allow COPO to be the main access point of metadata annotation and data deposition for the CGIAR institutes. This is a major conglomeration of research stations around the globe responsible for many agricultural advances in the developing world since the end of the second world war. From this work, we can expect to broker tens of thousands of documents, data sets or other research objects from CGIAR researchers. |
Title | DToL Supervisor View |
Description | DToL Supervisors can see samples which are pending, accepted or rejected. Pending samples can be accepted or rejected. If accepted, a background task compiles all samples to be accepted, sends them to ENA for biosampling and then makes them available via the API for services such as Sanger STS. |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | This is an integral part of the DToL workflow, and allows supervisory oversight of sample metadata before it enters the DToL ecosystem |
Title | Datascriptor |
Description | From structured dataset to data article. Leveraging our experience and links with the communities, we are now designing an open-source web-based tool - part of an ecosystem of existing annotation and authoring systems - to help researchers to use community standards to describe their (meta)data at the source, and capitalize on their effort to accelerate the creation of a data article. The user will be guided to provide (semi)structured descriptions of the experimental design, and of the post-processed data, to generate, respectively, the Methods and a set of statements to populate the Results section of a manuscript. Datascriptor will work: (i) as a stand-alone tool - for anyone to use - implementing generic metadata models, such as W3C Data Catalog vocabulary; and (ii) as a component of the ISA Tools - for its user communities - implementing the ISA metadata model. To output short sentences from the (semi)structured input, we will evaluate a mixed data-to-text approach using template-based and neural-based (i.e. machine learning) methods. To further enrich the content of the manuscript, Datascriptor will connect to existing authoring systems, including Substance, Texture, Stenci.la and Manuscripts, and export the result in JATS format. Our plans also include an export as a DAR file and in LaTeX format. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | Work has just started, but to ensure continued impact in the stakeholder community, the Datascriptor User Advisory Board includes a core group of existing collaborators: Thomas Lemberger (EMBO Press), Scott Edmunds (GigaScience), Holly Murray ( F1000), Varsha Khodiyar (Springer Nature). |
Title | Deposition workflow to Dataverse Repository |
Description | In collaboration with the CGIAR centers, we developed a workflow for depositing heterogeneous data into the Dataverse repository along with appropriate metadata extracted from CGCore metadata fragments. Dataverse is developed by Harvard university and is widely used in academia to deposit and disseminate research objects. |
Type Of Technology | Webtool/Application |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | This will allow COPO to be the main access point of metadata annotation and data deposition for the CGIAR institutes. This is a major conglomeration of research stations around the globe responsible for many agricultural advances in the developing world since the end of the second world war. From this work, we can expect to broker tens of thousands of documents, data sets or other research objects from CGIAR researchers. |
Title | Dublin Core Integration |
Description | Dublin core schema and implementing wizard created allowing researchers to record metadata for their outputs in this community standard format. |
Type Of Technology | Webtool/Application |
Year Produced | 2018 |
Open Source License? | Yes |
Impact | Some users have reported using this feature. Dublin core is a well recognized community standard used by many data producers and repositories. |
Title | ENA sequence read submission manifest |
Description | ENA sequence submissions can be carried out by filling out a spreadsheet and parsing the required metadata out of it |
Type Of Technology | Webtool/Application |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | This should make submissions easier and more reliable, by allowing users to use spreadsheet software to fill out large tables of data. |
Title | ISA API |
Description | Released under the Common Public Attribution License Version 1.0 (CPAL) license, the Investigation Study Assay (ISA) API aims to provide developers with with a set of tools to enable the programmatic construction of ISA objects, validation of objects, and conversion between serialisations of ISA-formatted datasets and other formats/schemas (e.g. data deposition schemas). To facilitate the use of the ISA model (see the ISA-Tab specification - http://www.isa-tools.org/format/specification/) in modern web applications, the model (version 1.0) is represented as a set of JSON schemas, which provide the information the ISA model maintains for each of the objects. JSON is a widely used interchange format that powers much of the web today, and is used by a range of programming languages and platforms. As such, the objective of designing and developing JSON schemas is to support a new serialisation of the ISA-Tab model in JSON format, in addition to existing serialisations in Tabular format and RDF format. The new JSON models can be found here: https://github.com/ISA-tools/isa-api/tree/master/isatools/schemas/isa_model_version_1_0_schemas/core |
Type Of Technology | Software |
Year Produced | 2015 |
Open Source License? | Yes |
Impact | The ISA API is used in a number of projects arising in collaboration with the Oxford eResearch Centre (OERC), notably the COPO project, and is under continued development. |
URL | https://github.com/ISA-tools/isa-api |
Title | ISA Model and Serialization |
Description | The original ISA-Tab specification was published as a Release Candidate document in 2008, documenting the initial work that forms the ISA framework, with a further update in 2009. Since then, we have done work on a new serialization in JSON, ISA-JSON, and abstracted out the data model from both the tabular and JSON formats. |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | Serialisations implemented by several ISA components; the documentation also helps other users to implement ISA formats. |
URL | http://isa-tools.org/2016/10/release-of-the-isa-specs/ |
Title | ISA Python API |
Description | The ISA API aims to provide software developers with a set of tools to help you easily and quickly build your own ISA objects, validate, and convert between serializations of ISA-formatted datasets and other formats/schemas (e.g. SRA schemas). The ISA API is published on PyPI as the isatools package. |
Type Of Technology | Software |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | The vision for the ISA API is to provide a programming library that will become the core for all software tooling that supports the ISA framework. It enables the import of various data formats into an implementation of the ISA Abstract Model as Python objects, and export of ISA content from Python objects back to different serialization formats. |
URL | http://isa-tools.org/2017/01/isa-api-milestone/ |
Title | ISA software suite (built iteratively, component by component) |
Description | The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Built around the 'Investigation' (the project context), 'Study' (a unit of research) and 'Assay' (analytical measurement) data model and serializations (tabular, JSON and RDF), the ISA framework helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable. |
Type Of Technology | Software |
Year Produced | 2010 |
Open Source License? | Yes |
Impact | Growing number of users, as listed at http://isacommons.org; but also of co-developers have and are contributing to the collaborative enhancements. |
URL | http://isa-tools.org/ |
Title | ISA-API Python library |
Description | Project name: ISA-API Project home page: http://github.com/ISA-tools/isa-api Operating system(s): Platform independent Programming language: Python 3 Other requirements: None License: CPAL-1.0 ISA-API, a Python library that supports the creation, editing, parsing, and validatiation of both ISA-Tab and ISA-JSON formats, using a common data model implemented as native Python objects. |
Type Of Technology | Software |
Year Produced | 2018 |
Open Source License? | Yes |
Impact | This provides users with a common interface and interoperable medium between the two ISA formats, as well as conversion to a set of other formats required for depositing data in public databases. |
Title | Parsing and Validation of ASG Sample Manifests |
Description | Automatic parsing, validation and ingestion of ASG (Aquatic Symbiosis Genomics) manifests is now possible. Around 10 different validations are performed on every cell of a manifest (which can easily amount to tens of thousands of cells for a single manifest) |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Integral to the DToL Project, COPO is the entry point for all Sample metadata. |
Title | Parsing and Validation of DTOL Sample Manifests |
Description | Automatic parsing, validation and ingestion of DTOL manifests is now possible. Around 10 different validations are performed on every cell of a manifest (which can easily amount to tens of thousands of cells for a single manifest) |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Integral to the DTOL project, COPO is the entry point for all sample data |
Title | Refactoring TOL validations |
Description | Validations now carried out in a celery task |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | COPO servers are now more available |
Title | SOP 2.3 |
Description | COPO validations conform to 2.3 version of TOL manifest |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Data in the TOL projects is increasingly FAIR |
Title | Submission of DToL samples |
Description | Pipeline for submitting sample metadata to ENA implemented. |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | This allows public access to DToL data, fundamental goal of the project. |
Title | Swagger for API |
Description | Swagger is a documentation/experimentation framework for rest apis. It allows users to both examine and test in real time, an api service. This has been implmented for COPO. |
Type Of Technology | Webtool/Application |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Self documentation and testing of COPO api methods. Has allowed end users to get up to speed with our api quickly and also allowed bugs to be conveniently reported to us with examples. |
URL | http://copo-project.org/api |
Title | Update pipeline |
Description | Updating of existing samples |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | TOL users can now update samples under certain conditions (mainly that samples have not been submitted to ENA) |
Title | Updated COPO frontpage |
Description | New modern design implemented. Designed by our in-house graphic designer and implemented by the COPO development team, COPO now has a fresh look, and shows realtime relevant numbers on the frontpage |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | potential users can now see how much data copo handles. |
URL | http://copo-project.org/ |
Title | Web Guide to COPO |
Description | Visual guide with full screenshots of how to submit various datatypes to COPO |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Allows users to get up and running with COPO. |
Title | interaction with ECS datastore |
Description | work has started to interact with EIs ECS datastore, to enable COPO to access large datafiles created by our researchers |
Type Of Technology | Webtool/Application |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | this will make COPO more useful by hugely reducing the amount of data transfer needed for submissions |
Title | stats and charts in COPO |
Description | D3 based stats and charts created for COPO |
Type Of Technology | Webtool/Application |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Users can inspect things like, number of samples, users, files; as well as inspecting metadata chracteristics in tol data |
Title | tol barcoding |
Description | lookup, acceptance and storing of barcoding data for tol samples |
Type Of Technology | Webtool/Application |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | COPO can interact with and harvest data from the BOLD database to keep an organised collection of barcoding along with sample metadata |
Description | 1st COPO user workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | The Collaborative Open Plant Omics (COPO) consortium workshop brought together a focus group, comprising a small number of experts for 2 days, with an active interest in collecting and managing plant data. During the workshop, we discussed approaches to the description, collection, annotation, standardisation and management of (large) datasets, including requirements for submission to public repositories, current user needs and stumbling blocks. The workshop enabled us to better understand the needs of end users and to generate an overview of how, and what types of datasets, plant biologists are currently generating. This information has helped to guide the COPO consortium as it develops its community platform for data publication and citation. |
Year(s) Of Engagement Activity | 2015 |
URL | http://blog.garnetcommunity.org.uk/copo-2015-meeting/ |
Description | 2nd COPO User Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The Collaborative Open Plant Omics (COPO) consortium workshop brought together a focus group, comprising a small number of experts for 2 days, with an active interest in collecting and managing plant data. During the workshop, we demonstrated the new COPO portal and metadata collection layers of the software, discussed approaches to the description, collection, annotation, standardisation and management of (large) datasets, including requirements for submission to public repositories, current user needs and stumbling blocks. The workshop enabled us to better understand the needs of end users and to deliver feedback to the COPO partners about gaps and recommended software features. This information has helped to guide the COPO consortium as it develops its community platform for data publication and citation. |
Year(s) Of Engagement Activity | 2016 |
URL | http://copo-project.org/agenda_workshop2.html |
Description | Advanced statistical modelling and machine learning for molecular biology |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Workshop to look for synergies between disciplines between AI and molecular biology. |
Year(s) Of Engagement Activity | 2019 |
Description | Attendance at the Biodiversity Genomics 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Rob Davey attended Biodiversity Genomics 2020 which brought together researchers across the world to celebrate the achievements in genome sequencing across the eukaryotic tree of life, explored current challenges and their likely solutions, and looked forward to the coming decade of the application of genomics across the globe. With major projects starting to deliver data at scale, new tools for sequencing and assembling genomes becoming available, and increased awareness of the power of whole genome data in understanding organismal biology and ecosystem processes, Biodiversity Genomics 2020 promised to be a milestone in the effort to "sequence life for the future of life". Continuing the tradition of ambitious, collaborative science Biodiversity Genomics 2020 continues the tradition of previous meetings of Genomes 10k, the Vertebrate Genomes Project, the Global Invertebrate Genomics Alliance, and the Earth BioGenome Project. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.sanger.ac.uk/science/biodiversity-genomics-2020/ |
Description | Attendance at the ELIXIR All Hands 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Attendance at the ELIXIR All Hands representing COPO and possible future collaborations |
Year(s) Of Engagement Activity | 2020 |
URL | https://elixir-europe.org/events/elixir-all-hands-2020 |
Description | Attendance at the ELIXIR-UK All Hands 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Rob Davey attended the ELIXIR-UK All Hands 2020 to take part in discussions about ongoing and possible future collaborations |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.earlham.ac.uk/elixir-uk-all-hands-2020 |
Description | Attendance at the UK-Conference of Bioinformatics and Computational Biology 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Attendance at the UK-Conference of Bioinformatics and Computational Biology 2020 The UK-CBCB conference is designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Rob Davey, Nicola Soranzo, Alice Minotto attended to participate in discussions and to add impact to the ongoing work in bioinformatics |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-2020#About- |
Description | Attendance of the ELIXIR Biodiversity Working Group Face to Face meeting by Rob Davey and Felix Shaw |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Attendance at the ELIXIR Biodiversity face to face meeting, including discussions into how COPO can be used as a platform to submit data |
Year(s) Of Engagement Activity | 2020 |
Description | Attended and Presented a talk at the DFW All Hands 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Rob Davey attended the DFW All Hands 2020 (DFW Annual Meeting) and presented a talk on the work being carried out in WP4 |
Year(s) Of Engagement Activity | 2020 |
Description | BBSRC/NSF/ERA-CAPS workshop on Challenges and Opportunties in Plant Science Data Management at PAG 2015, San Diego, CA, US |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The workshop intended to bring the plant data science community together to discuss data, metadata, tools and policy. Across the plant sciences data of a varying types are being generated, analysed and shared on a daily basis using a wide variety of tools, terminologies and formats. However, without mechanisms to encourage researchers to describe their materials, data, assays, and experimental procedures in an agreed manner it is almost impossible to discover and compare datasets. The workshop showcased researchers working in the areas of data and experimental description; data identification and discovery; data integration and data citation. Dr Davey presented COPO to the audience, and it was well received. Most notably was the opportunity to discuss the platform with a co-speaker Dr Walls, a member of the Univ Arizona iPlant/Cyverse analyst team. She was very interested in COPO as a potential platform to wrap up into Cyverse as a brokering mechanism for their Data Commons. This collaboration is ongoing. Specific information about the presentation can be found here: https://pag.confex.com/pag/xxiv/meetingapp.cgi/Paper/22219 |
Year(s) Of Engagement Activity | 2015 |
URL | https://pag.confex.com/pag/xxiv/meetingapp.cgi/Session/3732 |
Description | BBSRC/NSF/ERACAPS Closed Forum Workshop on Plant Phenotyping at Plant and Animal Genomes (PAG) Conference 2015, San Diego, CA, US |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | BBSRC/NSF/ERACAPS Closed Forum Workshop on Plant Phenotyping at Plant and Animal Genomes (PAG) Conference 2015 Topic areas for breakout groups: (1) Sensors - development and technologies, (2) Standards, and (3) Interoperability. Questions to consider for each topic area: What are the major strengths, weakness and opportunities? What is the biggest challenge facing this area? What would be needed to meet this challenge in order to revolutionize the area and have a lasting impact? Are new tools, technologies or resources needed? Does progress require policy or social change? What education and training is required to meet these challenges? A white paper is in preparation to document the outcomes of the round table workshop. |
Year(s) Of Engagement Activity | 2015 |
Description | Biohackathon; ELIXIR, Paris |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The team participated to several tracks, especially working on ISA for plant and metabolomics community, as well as for use in Galaxy, and the bioschema work. The work carried our continue to embed ISA and FAIRsharing into ELIXIR-driven infrastructure and activities. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.elixir-europe.org/events/biohackathon-2018-paris |
Description | Bioinformatics for Plant Biology |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Hosted by the European Bioinformatics Institute (EBI), the aim of the workshop was to provide an introduction to resources and tools to help manage, discover and analyse genomics data, with a particular focus on cereal genomics. Within this context, an in-depth training session on COPO as a data management tool was delivered. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.ebi.ac.uk/training/events/2018/bioinformatics-plant-biology |
Description | Building infrastructure for open science - British Computer Society |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker at the Advanced Programming Group annual Christmas lecture |
Year(s) Of Engagement Activity | 2015 |
URL | http://www.bcs.org/category/18516 |
Description | CGIAR Big Data Workshop - Naivasha |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Around 60 data managers, developers, and policy makers from the CGIAR research centers attended this workshop to discuss annual progress and direction. COPO was demonstrated and a group of test users was recruited. |
Year(s) Of Engagement Activity | 2018 |
URL | https://bigdata.cgiar.org/event/cgiar-platform-for-big-data-in-agriculture-convention-2018-nairobi-k... |
Description | CGIAR Big Data in Agriculture Convention (Hyderabad) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Demo of latest COPO features to CGIAR data managers. |
Year(s) Of Engagement Activity | 2019 |
URL | https://bigdata.cgiar.org/hyderabad-2019/ |
Description | COPO - A Metadata Platform for Brokering FAIR Data in the Life Sciences |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 100 or so conference attendees saw my talk at Plant and Animal Genomics. |
Year(s) Of Engagement Activity | 2020 |
Description | COPO 3rd User Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The EI COPO team organised and ran the 3rd COPO User Workshop as a dedicated training event hosted as a satellite event to the Plant and Animal Genome (PAG) conference, in January 2018. We hired conference facilities at the nearby Mariott hotel, and ran a successful 3rd workshop to show recent developments to the platform and to gather feedback about potential improvements to 15 international participants. |
Year(s) Of Engagement Activity | 2018 |
Description | COPO live demonstration at PAG 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Live demonstration of the COPO system during a Digital Tools and Resources stream at the PAG conference. |
Year(s) Of Engagement Activity | 2018 |
Description | COPO training sessions for DTOL |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | We run 2 training session on how to use COPO for Darwin Tree of Life submissions. |
Year(s) Of Engagement Activity | 2020 |
Description | COPO training sessions for DTOL - session 2 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | To teach Darwin Tree Of Life researchers how to use COPO and how to annotate effectively their data to submit as part of the DTOL project, answer any question and doubt they may have had |
Year(s) Of Engagement Activity | 2020 |
Description | COPO: A Data Stewardship Platform for Plant Scientists - Computer Demo session (PAG XXV) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We present Collaborative Open Plant Omics (COPO), a brokering service between plant scientists and public repositories, which enables management, aggregation and publication of research outputs described and integrated using linked data. COPO provides consolidated access to services and disparate information sources via a web interface and Application Programming Interfaces. Users create profiles which represent a logical span of research, such as a grant funding round or PhD project. 'Research objects' comprising a broad spectrum of potential outputs (such as sequence data, images, manuscripts, source code, posters) can be uploaded into the profile. Annotation of these objects with community-supported standards is facilitated using simple user-interface wizards which aim to reduce the complexity of this task, supported by ISA components (http://isa-tools.org/) for metadata interoperability and automated metadata format conversion. COPO uses the Ontology Lookup Service (http://www.ebi.ac.uk/ols) to provide the crucial contextual metadata required for standardised data description. Currently, deposition of both data and metadata to the European Nucleotide Archive for sequence data, and Figshare for data types such as images, posters, and presentations is supported. In the future, we will support more public repositories for multi-omic data submission, and users will be able to search for and pull such data into analysis environments such as CyVerse and Galaxy. We will subsequently track the outputs and associated metadata in COPO, thus creating a provenance trail from data to publication. http://copo-project.org/ https://github.com/collaborative-open-plant-omics/COPO |
Year(s) Of Engagement Activity | 2017 |
URL | https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/23791 |
Description | COPO: Extending the frontiers of "FAIR" Data in Agriculture |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Demonstration of COPO features to Research Data Alliance delegates. |
Year(s) Of Engagement Activity | 2020 |
Description | CUDDEL closing workshop/hackathon, EBI |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Closing workshop of the CUDDEL grant, following up on issues outstanding from the 2017 Hong Kong workshop; discussion to explore the feasibility of making a follow up BBSRC Partnering application in the future. |
Year(s) Of Engagement Activity | 2018 |
URL | https://github.com/ISA-tools/cuddel-mzml2isa-enhance |
Description | CW21 + hackaton partecipation |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Collaborative workshop 2021 is a conference for research software engineers. We discussed changes in work pattern and collaborations due to the pandemic and which ones have been beneficial for our jobs, accessibility and diversity was discussed, with a focus on disabilities. We had collaborative ideas about how to improve the RSE landscape and had a hackaton day to tackle the identified issues. |
Year(s) Of Engagement Activity | 2021 |
Description | Challenges and Opportunities in Plant Science Data Management (Workshop, PAG 2019) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Davey organised the PAG 2019 workshop Challenges and Opportunities in Plant Science Data Management alongside Carolyn Lawrence-Dill from Iowa State University, USA. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.intlpag.org/2019/ |
Description | Darwin Tree Of Life all hands |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | the conference/meeting was meant to share and discuss progresses and next steps as part of the Darwin Tree Of Life project. Multiple working groups had the chance to meet and present their work with improvements on the understanding of the wide process |
Year(s) Of Engagement Activity | 2021 |
Description | Data Brokering for Plant Scientists (DivSeek partner's meeting, PAG 2018, San Diego) |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Delivered a lightning talk to promote the COPO data brokering platform at the annual DivSeek partner's meeting at PAG. |
Year(s) Of Engagement Activity | 2018 |
Description | Data Stewardship in the Life Sciences |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I spoke at the "Challenges and Opportunities in Plant Science Data Management" workshop on the subject of data management in the life sciences. Open data and integrative data sharing are fundamental factors in order to address the challenges of modern data-intensive science. There is a clear need to develop and maintain community-focussed, semantically-aware data stewardship and management platforms, such as COPO, that are able to cope with the description and sharing of potentially huge datasets arising from the life sciences. Once made available, it is not sufficient to assume that researchers around the globe have requisite skills and resources to analyse these data. Therefore, we need to provide large-scale data analysis environments that are fit for purpose, incorporating state-of-the-art interfaces and programmatic layers to meet broad end-user requirements, such as CyVerse and Galaxy. Finally, this can only happen when there are community-led efforts into implementing solutions for data standardisation, best practice, and FAIR data policy. We are now only just starting to take advantage of groundbreaking opportunities to make integrated data a reality, and thus enabling scientists to store, manage, and share their data as a first-class citizen of the scientific process. |
Year(s) Of Engagement Activity | 2017 |
URL | http://app.core-apps.com/pag_2017/event/e2bec353017762d275ce250c23e011e6 |
Description | Data, Data, Data Everywhere (Pint of Science talk, Norwich) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Dr Davey delivered a talk as part of the Norwich 2017 Pint of Science series about the challenges and solutions for modern data management in the life sciences, including recent data developments, high-performance computing, and software tools. |
Year(s) Of Engagement Activity | 2017 |
URL | https://pintofscience.co.uk/event/crops-crystals-and-computers-technology-for-food-security |
Description | Datascriptor hackathon - eLife Innovation Sprint |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Hackathon on the Datascriptor prototype, part of the ISA toolkit. Datascriptor aims to taking the pain out of beginning to write papers, making it easy to automatically generate the parts of a paper that can be easily scaffolded and incentivising reproducible papers by ensuring the scaffolds include well-structured data and metadata. During the online event the prototype was fleshed out by user testing with hands-on use cases. |
Year(s) Of Engagement Activity | 2020 |
URL | https://sprint.elifesciences.org/data-paper-skeleton-tools-for-life-sciences/ |
Description | DivSeek Partner's Meeting (PAG 2019) |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Davey attended the DivSeek Partner's Meeting in the Courtyard Marriott hotel at PAG 2019. |
Year(s) Of Engagement Activity | 2019 |
Description | Divseek Working Group - Data Standards for Interoperable Tools |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | As part of the "DivSeek - Addressing the challenges and opportunities for information and data sharing associated with plant germplasm" session at PAG, I spoke about the DivSeek Data Standards for Interoperable Tools Working Group. This WG will promote best practice in data sharing in the plant sciences, through the use of open and interoperable software powered by the adoption of open standards, i.e. programmatic interoperability standards (APIs), controlled vocabularies, trait dictionaries, metadata standards, and ontologies. We aim to highlight gaps in interoperability that impede workflows important to the communities supported by DivSeek partners, by liaising with research development groups, other DivSeek working groups, and consortia with relevance to DivSeek. We will educate and train data generators about standards and the tools and resources that use them, in order to promote and foster standards-compliance for long-term open data stewardship. |
Year(s) Of Engagement Activity | 2017 |
URL | https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/26202 |
Description | Down The Tubes! Talk at the Norwich Science Festival |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Dr Davey gave a talk on the internet and data science entitled "Down The Tubes!" at the 2018 Norwich Science Festival. |
Year(s) Of Engagement Activity | 2018 |
URL | https://norwichsciencefestival.co.uk/events/down-the-tubes/ |
Description | ELIXIR Data Management Network F2F Meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr. Nicola Soranzo participated to this meeting in Brussels, Belgium, 26/02/2020.This was the second meeting of the new ELIXIR Data Management Network of experts, which is being established as part of Work Package 1 of the ELIXIR Converge project. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.eventbrite.co.uk/e/elixir-converge-kick-off-meeting-tickets-84730383859 |
Description | ELIXIR UK ALL HANDS 2018 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The ELIXIR-UK All Hands Meeting provided updates on recent activities from the ELIXIR UK Node and ELIXIR Hub, alongside discussions of future resources, events and roadmapping breakouts.Dr Davey presented the COPO project and CyVerse UK infrastructure as UK-specific resources that were being developed as national infrastructure for UK researchers. There was much interest from the participants in both projects, and conversations at this event led to the submission of a BBSRC TRDF with Gos Micklem (Cambridge), Dr Davey and Dr Shaw (EI). |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.earlham.ac.uk/elixir-all-hands-2018 |
Description | ELIXIR all hands 2020 - poster: the Cyverse UK cyberinfrastructure offer to support open science and FAIRness |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented a poster to highlight what the CyVerse UK infrastructure is supporting in term of all the services hosted (COPO, grassroots and Galaxy in particular) to improve the FAIRness of the data landscape. We also showed how the data is shared with collaborators trough federation of iRODS instances. |
Year(s) Of Engagement Activity | 2020 |
URL | https://f1000research.com/posters/9-525 |
Description | ELIXIR all hands 2021 participation |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | members of ELIXIR around Europe attended the all hands to discuss progresses in different working groups, data FAIRness, policies etc |
Year(s) Of Engagement Activity | 2021 |
URL | https://elixir-europe.org/events/elixir-all-hands-2021 |
Description | ELIXIR-UK ALL-HANDS MEETING 2017 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The ELIXIR-UK All Hands Meeting provided updates on recent activities from the ELIXIR UK Node and ELIXIR Hub, alongside discussions of future resources, events and roadmapping breakouts.Dr Davey presented the COPO project and CyVerse UK infrastructure as UK-specific resources that were being developed as national infrastructure for UK researchers. There was much interest from the participants in both projects, and conversations at this event led to the submission of a BBSRC TRDF with Gos Micklem (Cambridge), Dr Davey and Dr Shaw (EI). |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.elixir-europe.org/events/elixir-uk-all-hands-meeting-2017 |
Description | ELIXIR-UK All Hands meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Showcasing latest work on FAIRsharing and and presentation by Dr. Rocca-Serra of the FAIR Cookbook, as well as discussing how to best connect with other UK resources and those from other Nodes. |
Year(s) Of Engagement Activity | 2021 |
URL | https://elixir-europe.org/events/elixir-all-hands-2021 |
Description | ELIXIR-UK AllHands meeting, Birmingham |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Showcasing latest work on FAIRsharing and ISA, as well as discussing how to best connect with other UK resources and those from other Nodes. |
Year(s) Of Engagement Activity | 2018 |
URL | https://elixiruknode.org/event/elixir-uk-all-hands-2018/ |
Description | ENA Facilities Day - 2017 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a demonstration to promote COPO, as a data brokering and standards promotion platform, at the European Nucleotide Archive (ENA) Facilities Day. The Facilities Day is a meeting of representatives of sequencing facilities to participate in discussions, and to share their views on the impact of ENA as a global sharing platform for sequencing data and how it promotes bioinformatics research. Participants are given the opportunity to exchange ideas directly with ENA project leaders, and influence future developments towards sustaining and improving the ENA service. The ENA is one of the repositories currently supported by the COPO platform. |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.ebi.ac.uk/ena/support/facilities-day |
Description | Earlham Institute - COPO Workshop 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | COPO tutorial for EI staff. |
Year(s) Of Engagement Activity | 2020 |
Description | Giving a talk at the ELIXIR All Hands 2020 Mini Symposium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Rob Davey: Gave a talk at the ELIXIR All Hands 2020 Mini Symposium: FAIRification for knowledge management: COPO: Extending the frontiers of FAIRness in life science data |
Year(s) Of Engagement Activity | 2020 |
Description | I'm a scientist get me out of here, Darwin Tree of Life |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | A class of pupils came together in an online chat to ask scientist and other professionals involved in the Darwin Tree of Life project questions about science, career, general curiosity etc |
Year(s) Of Engagement Activity | 2021 |
Description | ISA presentation to GARnet workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | David Johnson - in my team - gave a presentation on "Data Infrastructures to Foster Data Reuse" at a workshop on Integrating Large Data into Plant Science: From Big Data to Discovery hosted by GARnet (the UK network for Arabidopsis researchers) and Egenis (the Exeter Centre for the Study of the Life Sciences). The workshop was held at Dartington Hall in Devon, South West England, and was well attended by researchers from the plant and biological science community worldwide as well as representatives from industry from organisations such as Syngenta. |
Year(s) Of Engagement Activity | 2016 |
URL | http://isa-tools.org/2016/07/plant-science-takes-a-focus-on-isa/ |
Description | Integrative Bioinformatics workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This event was hosted by the Rothamsted Research, Harpenden, and brought together experts in the field of bioinformatics, computer science, statistics, computational and systems biology to discuss key science and technology platforms to integrate, align and model heterogenous data types to generate meaningful insights from big data and from complex biological systems. The event attracted a wide range of participants (and expertise) both from academia and industry. In particular, key players in the publishing sector (e.g., F1000, Elsevier) were also present to discuss their individual efforts to making science more open. The workshop provided an excellent platform to showcase COPO, and its drive to make research output more open and easily accessible. |
Year(s) Of Engagement Activity | 2018 |
URL | https://ib2018.eventzilla.net/web/event?eventid=2138944931 |
Description | Laying the Foundations; Why are Semantics in Agriculture Difficult? - PAG 2020 talk in Plant Phenotypes workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Davey gave an invited talk to approx 90 attendees at the PAG 2020 workshop "Plant Phenotypes" |
Year(s) Of Engagement Activity | 2020 |
Description | NERC DataTree |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Video to introduce the basic concepts of the FAIR principles, FAIR data management and FAIRsharing. The target audience for Data Tree is NERC funded PhD students and early career researchers, however, Data Tree will be an openly available resource. |
Year(s) Of Engagement Activity | 2017 |
URL | https://datatree.org.uk/ |
Description | Nudge Norfolk Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Workshop to discuss possible collaborations between COPO, AI and regional industrial partners such as farmers and retailers. |
Year(s) Of Engagement Activity | 2019 |
Description | Ontology COP meeting presentation |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Discussions around COPO integration with big data platform's ontology community of practice. |
Year(s) Of Engagement Activity | 2019 |
Description | Organisation and Attendance at the Alan Turing Institute for AI for Wheat Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Rob Davey helped organise the Alan Turing Institute - AI For Wheat Workshop 9th & 10th March 2020 This two day workshop will bring members of the UK wheat community and data science researchers together to identify suitable and exciting biological problems (with associated datasets) that could be further developed and made ready for a future wheat-focussed Data Study Group (DSG). DSGs are week-long intensive interdisciplinary workshops which explore a small number of topics in greater depth to seed longer-term collaborations which could lead to joint publications or research proposals. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.rothamsted.ac.uk/events/ai-wheat-workshop |
Description | Organiser of Challenges and Opportunities in Plant Science Data Management PAG workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Co-organiser of Challenges and Opportunities in Plant Science Data Management PAG workshop, which saw 6 international speakers deliver presentations on various aspects of data management in the plant sciences. Approx 50 attendees. |
Year(s) Of Engagement Activity | 2020 |
Description | Poster presentation: ISAcreate and Galaxy; Galaxy conference, Portland |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | ISA-Tab format is now used by Galaxy tools; the discussion helped ensuring the uptake continue |
Year(s) Of Engagement Activity | 2018 |
URL | https://gccbosc2018.sched.com/event/FEWs/g26-isacreate-a-galaxy-tool-for-prospective-data-management... |
Description | Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation - GROW Colombia UK workshop 2019 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Robert Davey gave a talk on the C3 Biodiversidad ConsortiumProject Coordination and Website |
Year(s) Of Engagement Activity | 2020 |
Description | RDA Wheat Data Interoperability Working Group meeting, RDA Plenary, Barcelona |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The Wheat Data Interoperability Working Group aims to provide a common framework for describing, representing linking and publishing Wheat data with respect to open standards.Such a framework will promote and sustain Wheat data sharing, reusability and operability. Specifying the Wheat linked data framework will come with many questions: which (minimal) metadata to describe which type of data? Which vocabularies/ontologies/formats? Which good practices? Mainly based on the the needs of the Wheat initiatiative Information System (WheatIS) in terms of functionalities and data types, the working group will identify relevant use cases in order to produce a "cookbook" on how to produce "wheat data" that are easily shareable, reusable and interoperable. This meeting saw the maturation of the Working Group into a Maintenance Group, showing that we have moved from an inception phase to an implementation phase, promoting the outputs of the WG (the Wheat Data Interoperability guidelines) to users. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.rd-alliance.org/group/agricultural-data-ig-igad-wheat-data-interoperability-wg-agriseman... |
Description | RSE Career Pathways |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | it was discussed the career path of RSE and the concordat funding bodies have published to provide a progression. Many RSE intervened with the purpose of creating recommendations |
Year(s) Of Engagement Activity | 2021 |
Description | School chat - I'm a scientist get me out of here, Darwin Tree of Life |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | A class of pupils came together in an online chat to ask scientist and other professionals involved in the Darwin Tree of Life project questions about science, career, general curiosity etc |
Year(s) Of Engagement Activity | 2021 |
Description | Support open science and FAIRness through an integrated collaborative platform for life science: CyVerse UK and hosted services |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Elixir all hands meeting. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk delivered at the ELIXIR Biodiversity working group Inaugural meeting - Milan 2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | Organised as part of a new ELIXIR working group to address challenges in biodiversity data management and infrastructure. |
Year(s) Of Engagement Activity | 2020 |
Description | UKRI Artificial Intelligence and Machine Learning workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | UKRI fact finding workshop to ascertain how best to invest and implement UK AI strategy. |
Year(s) Of Engagement Activity | 2019 |
Description | UKRI Darwin Tree of Life Project meeting, London |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Dr Davey travelled to London with other EI staff to discuss strategy for an SPF bid to UKRI for the UK Darwin Tree of Life Project. |
Year(s) Of Engagement Activity | 2018 |
Description | UKRI-BBSRC workshopin computing in the bioscience |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | RSEs professional came together in a consultation with funding bodies, about issues in computing in bioscience, what are the future risk and where improvement is needed. Conversations focused both on technical topic and related topics such as career of RSEs |
Year(s) Of Engagement Activity | 2021 |
Description | Webinar given to Research Data Alliance |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Webinar given to Research Data Alliance members. |
Year(s) Of Engagement Activity | 2020 |
URL | http://aims.fao.org/capacity-development/webinars/copo-extending-frontiers-data |
Description | Workshop on the Genomics of Plant Genetic Resources: |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Rob Davey participated in the DivSeek Workshop on the Genomics of Plant Genetic Resources on 13th January 2021 |
Year(s) Of Engagement Activity | 2021 |
Description | participatio in data management - more than a numbers game event |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | the event fostered a conversation about the use of big data in agriculture. More than the availability of data, it focused on how they can be exploited effectively. |
Year(s) Of Engagement Activity | 2021 |
Description | software licensing workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | the workshop raise awareness about how to choose a license for software, why, and which are the consequences in term of downstream usage by other researchers and industry alike |
Year(s) Of Engagement Activity | 2021 |