DFW - Designing Future Wheat - Work package 4 (WP4) - Data access and analysis
Lead Research Organisation:
Rothamsted Research
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
In WP4, the large-scale genomic, phenotypic and regulatory datasets emerging from the DFW WPs, will be annotated, integrated and disseminated to generate critical reference resources supporting interpretation and driving new avenues of investigation. These activities will comprise the UK contribution to the international Wheat Information System (WheatIS), a unified global infrastructure for wheat biology being developed under the auspices of the G20 International Wheat Initiative. Wheat resources and information generated within the DFW programme will be presented in an easily accessible form, allowing ready access for UK and international plant researchers not directly working on wheat.
Planned Impact
unavailable
Organisations
- Rothamsted Research (Lead Research Organisation)
- University of Tennessee Institute of Agriculture (Collaboration)
- Cornell University (Collaboration)
- University of Bologna (Collaboration)
- ELIXIR (Collaboration)
- University of Zaragoza (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- Genestack (Collaboration)
- Lawrence Berkeley National Laboratory (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
Publications
Adamski N
(2019)
A roadmap for gene functional characterisation in wheat
Adamski NM
(2020)
A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.
in eLife
Alabdullah AK
(2019)
A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization.
in Frontiers in plant science
Balaur I
(2017)
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.
in Bioinformatics (Oxford, England)
Brandizi M
(2022)
Integrative Bioinformatics - History and Future
Brandizi M
(2024)
A walkthrough in Agronomy Data Modelling with AgriSchemas
| Title | KnetMiner Promo Video |
| Description | Short 1-min clip to promote KnetMiner |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| Impact | Over 250 views on YouTube. Used in presentations. Positive feedback. |
| URL | https://www.youtube.com/watch?v=ASfEUBCbjDA |
| Title | KnetMiner Video/Webinar - May 2021 |
| Description | KnetMiner Knowledge Graphs and Use Cases |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2021 |
| Impact | Linked on KnetMiner website and can serve as a demo for new users. |
| URL | https://youtu.be/RTMTEODbLbU |
| Title | Lightdrawings of networks by Hugo Dalton |
| Description | When science meets art, or new meets old. KnetMiner has inspired the artist Hugo Dalton. He has created lighdrawings of our networks and has projected them on old sculptures to bring them back to life. |
| Type Of Art | Artwork |
| Year Produced | 2018 |
| Impact | Our work has been displayed for 3 months to visitors of the Fitzwilliam Musuem. |
| URL | https://www.instagram.com/p/BflFDaHlwdv/ |
| Title | Slideshare Presentation of Knetminer |
| Description | This is online presentation introducing the knetminer software application. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2017 |
| Impact | It helps with presentation to potential collaborators. |
| URL | https://www.slideshare.net/KeywanHassaniPak/knetminer-overview-oct-2017 |
| Title | Video Introducing KnetMiner |
| Description | A short 90-sec clip introducing KnetMiner to the general public. What is it? Who developed it? Who uses it? |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2017 |
| Impact | Video inspires general public, students and scientists visiting the KnetMiner website. |
| URL | https://www.youtube.com/watch?v=4aOv5QXqvLI |
| Description | We have provided BBSRC Swindon office with a Google Spreadsheet, which lists all our DFW outputs (including data access sites, germplasm generated, datasets generated, publications, and public engagement activities as they occur). This document is updated by us on a regular basis. All the objectives during the DFW reporting period have been met, and many exceeded. All the committees within DFW are running well including the key data coordination task force (DCTF) and Breeder's toolkit committees. Chris Rawlings co-chaired the Data Coordination Task Force (DCTF) and meetings have been held every month since the project start, despite COVID. This has meant we have increased our rate of data sharing for key data types, including field trials, omics and variation datasets, and publications. KnetMiner has matured from version 1.0 in 2018 to version 5.7 in 2024. The KnetMiner knowledge graph for genes, gene networks and traits has grown to 1.5 million nodes and over 7 million relationships. DFW omics datasets have been integrated into the knowledge graph along with latest genomics and literature data for wheat and model organisms. Wheat bioinformatics resources including Ensembl Plants, WheatIS, The Triticeae Toolbox, Wheat-expression and Grain Genes have developed integrations into Wheat KnetMiner knowledge graph. The development of KnetMiner has been a key activity to underpin gene discovery and hypothesis generation in DFW. The KnetMiner paper was published in the high impact Plant Biotech Journal in 2021 and has been cited 99 times (as of March 2025). KnetMiner had over 5,500 unique users in 2023 and over 450 users have registered on the platform. A major achievement has been the standardization of our data modelling using RDF and Neo4j, and their graph query languages (SPARQL, Cypher) to improve scalability, interoperability and reusability of our knowledge graphs. We have developed KnetMiner APIs in collaboration with wheat bioinformatics resources including Ensembl Plants, WheatIS, The Triticeae Toolbox, Wheat-expression and Grain Genes. We have improved the KnetMiner web interface based on user feedback and released at least one major update each year. The latest KnetMiner 5.7, released in January 2024, included many enhancements to user workspaces, gene search, gene set enrichment analysis, network visualization etc. Our software and data integration approaches have matured and are readily available now to be applied to other plant species. |
| Exploitation Route | The main Rothamsted Bioinformatics output of this award has been integrated software and data to enable better gene discovery and trait analysis in wheat. The wheat KnetMiner platform provides biologists, bioinformaticians and breeders easy access to crop genome knowledge graph including DFW data. The funding has helped to integrate various wheat bioinformatics resources including KnetMiner, Ensembl Plants and WheatIS to streamline their navigation. The KnetMiner software components were developed in a general way so that they can be used for other species and application domains. For example, we received new contracts to build KnetMiner resources for other crops and joined a global effort to develop a COVID-19 KnetMiner to provide medical researchers with quick and intuitive access to all documented linkages between genes, medicines, and the virus. The resource was featured in Nature among other AI tools to tame the Coronavirus literature. In 2024, KnetMiner Ltd was established and we are in the final stages of completing the spin-out from Rothamsted Research. |
| Sectors | Agriculture Food and Drink Environment Healthcare |
| URL | https://knetminer.com/ |
| Description | KnetMiner is used within DFW at RRes, EI and JIC and has a wider international user base (28% China, 15% US, 13% UK). KnetMiner helps to integrate DFW datasets with published knowledge and make DFW easily accessible. KnetMiner has become a full ELIXIR-UK service in 2021 and is one of the key FAIR resources in the ELIXIR Plant Science community. The KnetMiner website usage (wheat, rice, Arabidopsis, COVID-19) has grown year by year since the beginning of the DFW funding. 2018: 1,520 unique users; 2019: 1,823 unique users; 2020: 2,821 unique users; 2021: 5,270 unique users; 2022: 5,729 unique users. The main KnetMiner 2021 publication has been cited 64 times (March 2024). The KnetMiner APIs are used by major plant bioinformatics databases such as Grain Genes, Cornell T3, and the INRA WheatIS system. This is in addition to work involved in WP4 to integrate KnetMiner with Ensembl Plants and the JIC wheat-expression atlas. The integrations with external providers generate ca 40,000 pageviews per year. We have made major progress towards making our knowledge graphs FAIR using standard schemas, ontologies and graph databases (RDF, Neo4j) which has started to lead to new collaborations with bioinformatics and computer science groups. We have modernized the KnetMiner deployment using Docker to facilitate on-premise or cloud deployment. Several companies from the Agrifood sector and government funded plant research organizations are in discussions with Rothamsted about collaborations and licensing of KnetMiner for use in wheat and other crop research. In 2021, we have undertaken a KnetMiner proof of concept project with the Virtual Laboratory of Plant Breeding (VLPB http://vlpb.nl) which is a pre-competitive consortium of plant breeders. They have evaluated the value of KnetMiner to their businesses. This has included virtual workshops and knowledge exchange events and has led to future opportunities. We have presented KnetMiner at the New Scientist Live 2022 event in London. In November 2023, we have established the KnetMiner spin-out company. KnetMiner Ltd is an innovative software and services company that accelerates agricultural genomics through the integration of comprehensive knowledge graphs (KGs) and the latest advancements in artificial intelligence (AI), particularly through the use of Large Language Models (LLMs). Our objective is to significantly improve the efficiency of identifying crucial genes for crop resilience when exposed to both biotic and abiotic challenges, directly contributing to the global imperatives of food security and sustainable agriculture amid climatic challenges. |
| First Year Of Impact | 2012 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education |
| Impact Types | Societal Economic |
| Description | Bioinformatics to advance wheat breeding |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Trained researchers to use evidence-based practices in biological decision making. |
| URL | http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding |
| Description | 16ALERT |
| Amount | £283,383 (GBP) |
| Funding ID | BB/R000662/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 08/2018 |
| Description | A FAIR community resource for pathogens, hosts and their interactions to enhance global food security and human health |
| Amount | £557,820 (GBP) |
| Funding ID | BB/S020020/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 06/2023 |
| Description | AgroServ: Integrated SERVices supporting a sustainable AGROecological transition |
| Amount | £13,000,000 (GBP) |
| Funding ID | 10054008 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 04/2023 |
| End | 05/2028 |
| Description | ELIXIR Community-led Implementation Study - Increasing Plant data findability and reuse beyond ELIXIR (UK-2021-Plants) |
| Amount | € 19,000 (EUR) |
| Organisation | ELIXIR |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 05/2023 |
| Description | HPC Infrastructure |
| Amount | £4,070,456 (GBP) |
| Funding ID | IGP-23-024 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2023 |
| End | 11/2025 |
| Description | What determines protein abundance in plants? |
| Amount | £3,354,456 (GBP) |
| Funding ID | BB/T002182/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 10/2025 |
| Title | Additional file 2 of Beyond the one-way ANOVA for â omics data |
| Description | Lipidomics model assessment. Table containing the overall assessment of statistical significance and the model fitted for each lipid under both RFM and MRF. (PDF 8 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Beyond_the_one-way_ANOVA_for_omics... |
| Title | Additional file 2 of Beyond the one-way ANOVA for â omics data |
| Description | Lipidomics model assessment. Table containing the overall assessment of statistical significance and the model fitted for each lipid under both RFM and MRF. (PDF 8 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Beyond_the_one-way_ANOVA_for_omics... |
| Title | AraKNET Release 42 - Feb 2019 |
| Description | Integrated database of Arabidopsis genome, genotype, phenotype, omics and homology information. Available through www.knetminer.org or as RDF and Neo4j graph databases. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | It takes away the pain of connecting data from multiple sources and finding useful clues in data. A task that can take biologists weeks or months, can be done in a few minutes using the resource. |
| URL | http://knetminer.rothamsted.ac.uk/Arabidopsis_thaliana/ |
| Title | AraKNET Release 45 - Oct 2019 |
| Description | Release 45 of the Arabidopsis Knowledge Graph on OXL, RDF and Neo4j format |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | FAIR data. |
| Title | COVID-19 KG |
| Description | First release of COVID-19 Knowledge Graph for KnetMiner. Available in OXL, RDF and Neo4j format. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Increased citations and collaboration requests for KnetMiner. |
| URL | https://f1000research.com/articles/10-703 |
| Title | New OWL ontology for Bio-knowledge networks |
| Description | BIOlogical KNowledge Network Ontology (BioKNO, pronounced "bio-know") is a lightweight ontology, aimed at representing biological-related knowledge networks. We use it to power the KnetMiner project. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | None available yet. It is largely a data resource used by the knetminer project |
| URL | https://github.com/Rothamsted/bioknet-onto |
| Title | Open API Access Points for RDF/Sparql and Neo4J/Cypher |
| Description | These are public data access points (APIs) for the KnetMiner for Wheat knowledge base on the UK Cyverse infrastructure SPARQL is completely open and can be used anonymously, the Cypher endpoints require user credentials. https://knetminer.org/data is the entry point for them all. SPARQL (http://knetminer-data.cyverseuk.org/lodestar/sparql) Cypher (http://knetminer-wheat.cyverseuk.org:7474/ |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | None yet |
| URL | https://knetminer.org/data |
| Title | RiceKNET Release 42 - Feb 2019 |
| Description | Integrated database of rice genome, genotype, phenotype, omics and homology information. Available through www.knetminer.org or as RDF and Neo4j graph databases. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | It takes away the pain of connecting data from multiple sources and finding useful clues in data. A task that can take biologists weeks or months, can be done in a few minutes using the resource. |
| URL | http://knetminer.rothamsted.ac.uk/Oryza_sativa/ |
| Title | Wheat KG release 55 - March 2023 |
| Description | Wheat genome knowledge graph data using data snapshots as of February 2023. It can be accessed via public SPARQL and Cypher graph endpoints. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Provides integrated data for advanced bioinformatics data analysis |
| Title | Wheat Knowledge Network - Release Nov 2017 |
| Description | Integrated database of wheat genome, genotype, phenotype and homology information (Hassani-Pak et al, 2016) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This database powers the KnetMiner application |
| URL | http://knetminer.rothamsted.ac.uk/ |
| Title | Wheat Tilling population mutants mapped into Ensembl Plants |
| Description | In July 2018 the new IWGSC Wheat RefSeq v1.0 assembly was made publicly available to the scientific community in Ensembl Plants. This was the first time this assembly was made fully public and is a great source for ongoing wheat research. Via collaboration with JIC and Rothamsted the wheat TILLING population mutants were |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Value added to wheat genome assembly in Ensembl plants for use by the international community of wheat researchers |
| URL | https://plants.ensembl.org/Triticum_aestivum/Info/Index |
| Title | Wheat genome database |
| Description | Data from the bread wheat Tritium aestivum and related species have been included in Ensembl Plants, an integrative resource offering access to genome scale data from a variety of plant species. Successive improvements to the genome sequence have been accommodated including polymorphism data important for breeding (increasingly, in collaboration with CerealsDB), and the incorporation of the new TGAC 1.0 genome assembly. The database was developed originally with funding from BB/J00328X/1 and development has continued with funding from BBS/E/J/000PR9782. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | The data structure, analysis pipelines and visualisation interfaces have been developed to accommodate polyploid crops in general of which bread wheat is our first example. Ensembl Plants (as a whole) has had 156,037 unique visitors in 2017. |
| URL | http://plants.ensembl.org/Triticum_aestivum/Info/Index |
| Title | Wheat pathogens knowledge network - Release Nov 2017 |
| Description | Knowledge networks of wheat pathogens Fusarium and Zymospeptoria |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Will help to understand wheat diseases |
| URL | http://knetminer.rothamsted.ac.uk/ |
| Title | WheatKNET Release 42 - Feb 2019 |
| Description | Integrated database of wheat genome, genotype, phenotype, omics and homology information. Available through knetminer.org or as RDF and Neo4j graph databases. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | It takes away the pain of connecting data from multiple sources and finding useful clues in data. A task that can take biologists weeks or months, can be done in a few minutes using the resource. |
| URL | http://knetminer.rothamsted.ac.uk/Triticum_aestivum/ |
| Title | WheatKNET Release 45 - Oct 2019 |
| Description | Release 45 of the wheat knowledge graph in OXL, RDF, Neo4j format |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Used by over 1000 users through the KnetMiner UI and API |
| URL | http://knetminer-data.cyverseuk.org/lodestar/ |
| Title | WheatKNET Release 51 - Nov 2021 |
| Description | Wheat genome knowledge graph data in OXL, RDF and Neo4j graph format. Integration of several data snapshots as of Nov 2021. Underlying dataset used in the freemium wheat KnetMiner. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Integration of a range of datasets relevant to wheat gene discovery and crop improvement. Used by over 100s of users through the KnetMiner UI and API. |
| URL | http://knetminer-data.cyverseuk.org/lodestar/ |
| Description | A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls |
| Collaborator Contribution | See above |
| Impact | This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls |
| Start Year | 2018 |
| Description | COVID-19 International Research Team |
| Organisation | Lawrence Berkeley National Laboratory |
| Country | United States |
| Sector | Public |
| PI Contribution | Collaboration to build COVID-19 knowledge graphs with scientists from Lawrence Berkeley National Laboratory (KG-COVID-19 group) and Monarch Initiative including Justin Reese, Deepak Unni and Chris Mungall |
| Collaborator Contribution | Knowledge exchange on best practices and data standards for developing knowledge graphs |
| Impact | https://knetminer.com/COVID-19/ https://pubmed.ncbi.nlm.nih.gov/33196056/ |
| Start Year | 2020 |
| Description | Carlos Bobed - rdf2pg - University of Zaragoza |
| Organisation | University of Zaragoza |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Development of a new generation rdf2neo tool, to support the conversion of RDF to multiple property graphs, in a modular way. |
| Collaborator Contribution | Open-source code contributions |
| Impact | https://github.com/Rothamsted/rdf2pg |
| Start Year | 2020 |
| Description | Cornell University - T3 integration |
| Organisation | Cornell University |
| Department | College of Agriculture and Life Sciences |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This is a software and data interoperability collaboration. We are ensuring that wheat data and software resources developed in DFW, in particular at Rothamsted in the KnetMiner activity can interoperate with resources in the Cornell Triticae Toolbox (T3). |
| Collaborator Contribution | technical expertise, access to APIs. |
| Impact | T3 wheat data is incorporated into Knetminer for wheat and visualized alongside DFW data as an integral part of the integrated knetminer knowledge graphs. Knetminer APIs and the KnetMaps app enables the T3 website to reference Knetminer vizualizations of genes in the T3 resource |
| Start Year | 2018 |
| Description | GeneStack |
| Organisation | Genestack |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are collaborating in an Innovate UK funded Feasibility Study to translate our bioinformatics software and methods to a commercial cloud based software platform and investigating future commercial licensing. |
| Collaborator Contribution | They are providing the expertise to integrate our software into their platform |
| Impact | Too soon to report outputs |
| Start Year | 2016 |
| Description | GeneStack |
| Organisation | Genestack |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are collaborating in an Innovate UK funded Feasibility Study to translate our bioinformatics software and methods to a commercial cloud based software platform and investigating future commercial licensing. |
| Collaborator Contribution | They are providing the expertise to integrate our software into their platform |
| Impact | Too soon to report outputs |
| Start Year | 2016 |
| Description | Jean-Luc Jannink lab at Cornell |
| Organisation | Cornell University |
| Department | School of Integrative Plant Science |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have built KnetMiner APIs for the Jannink lab at Cornell which they use to link their The Triticeae Toolbox (T3) database of wheat genetics into KnetMiner knowledge graphs. |
| Collaborator Contribution | The Jannink lab have provided us with public wheat GWAS data that we have integrated into our wheat knowledge graph. |
| Impact | The key output that has resulted from this partnership is a more efficient way or working for wheat scientists and breeders through the new interconnected KnetMiner-T3 resources. |
| Start Year | 2018 |
| Description | KnetMiner ELIXIR-UK Service |
| Organisation | ELIXIR |
| Department | ELIXIR UK |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We applied for KnetMiner to become a full ELIXIR-UK service. |
| Collaborator Contribution | Following the Scientific Development Group meeting, which was held on 3rd September 2021, we are delighted to tell you that KnetMiner scored 1 - which means the panel considered that this service meets all the ELIXIR-UK criteria and is Infrastructure ready and we are delighted to include it as an ELIXIR-UK service. |
| Impact | Invitation to participate in ELIXIR Implementation Study for Plant Sciences. Invitation to join a EU HORIZON-INFRA grant proposal. |
| Start Year | 2021 |
| Description | MIAPPE metadata for DFW Phenotypes |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | This has been an interaction with the wider group of MIAPPE standards team, but largely with Cyril Pommier at INRA Versailles to improve the recording of field-based phenotyping metadata so that the MIAPPE standard evolves into something that DFW can adopt fully. |
| Collaborator Contribution | They have visited Rothamsted several times and participated in a project workshop in February 2018 |
| Impact | DIscussions and contributions have led to changes to the MIAPPE standard which has now been updated .. |
| Start Year | 2018 |
| Description | Priya Ranjan - University of Tennessee |
| Organisation | University of Tennessee Institute of Agriculture |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Knowledge exchange for building KnetMiner for a new plant species and accessing the data pro grammatically |
| Collaborator Contribution | Testing and providing new use cases |
| Impact | No outputs yet |
| Start Year | 2020 |
| Description | University of Bologna - Tuberosa |
| Organisation | University of Bologna |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | This collaboration with Roberto Tuberosa's group was to rank genes in 100s of QTL using a Neo4j wheat knowledge network. It was testing the gene ranking methods that we have developed and to demonstrate the potential of knetminer to this group. |
| Collaborator Contribution | The collaborators provided data and expertise of wheat genetics. |
| Impact | Research is still ongoing and no impact yet evident |
| Start Year | 2018 |
| Description | WheatIS Group interaction with INRA Versailles |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | At INRA Versailles, URGI group is the technical hub of the WheatIS bioinformatics team. We are working with them to better integrate knetminer with the developing WheatIS infrastructure. |
| Collaborator Contribution | The URGI group have been contributing expertise and access to software interfaces. |
| Impact | To early in the collaboration for impact to be recognised |
| Start Year | 2018 |
| Title | KnetMiner trademark |
| Description | Trademark application for KnetMiner and KnetBuilder |
| IP Reference | |
| Protection | Trade Mark |
| Year Protection Granted | 2022 |
| Licensed | No |
| Impact | Protection of KnetMiner and KnetBuilder names. |
| Title | COVID-19 KnetMiner |
| Description | KnetMiner search engine for COVID-19 research data and literature. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | Invited to join the COVID-19 International Research Team. Featured in Nature article. New collaborations with US. |
| URL | https://knetminer.com/COVID-19/ |
| Title | Docker Images for KnetMiner (bare, base, knetminer) |
| Description | This is a containerised version of KnetMiner for Cloud deployment - particularly for use in the Cyverse UK environment |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | None yet |
| Title | KnetBuilder 3.0 |
| Description | New release of our data integration platform KnetBuilder |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | in a recent POC - companies were able to use KnetBuilder to integrate their own data on-premise. |
| Title | KnetBuilder 5.0 |
| Description | Software to build knowledge graphs for KnetMiner from a range of data types. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Interest by several commercial and academic organisations. |
| URL | https://github.com/Rothamsted/knetbuilder/releases/tag/5.0 |
| Title | KnetMaps |
| Description | KnetMaps is a BioJS component for the interactive visualization of biological knowledge networks. It is well suited for applications that need to visualise complementary, connected and content-rich data in a single view in order to help users to traverse pathways linking entities of interest, for example to go from genotype to phenotype. KnetMaps loads data in JSON format, visualizes the structure and content of knowledge networks using lightweight JavaScript libraries, and supports interactive touch gestures. KnetMaps uses effective visualization techniques to prevent information overload and to allow researchers to progressively build their knowledge. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | This has enabled integration with other software and database projects relating to plant genome information. These include our collaboration with Cornell University Triticae Toolbox resources. |
| URL | http://knetminer.rothamsted.ac.uk/KnetMaps/. |
| Title | KnetMiner 4.0 |
| Description | KnetMiner 4.0 was released with a new feature to save gene networks to KnetSpace |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | User experience is more awarding now. Increased number of users. Increased number of citations. |
| URL | https://knetminer.com/news/knetminer-4-release.html |
| Title | KnetMiner 5.0 |
| Description | Major new release of the KnetMiner webapp for gene-based exploration of biological knowledge graphs. New features and various enactments. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Increased number of users and POCs |
| URL | https://github.com/Rothamsted/knetminer/releases/tag/5.0 |
| Title | KnetMiner 5.6 |
| Description | Next iteration of KnetMiner with new and enhanced functionality |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Wheat researchers are now able to search and visualise genomics and literature data more easily. |
| URL | https://github.com/Rothamsted/knetminer/releases |
| Title | KnetMiner 5.7 |
| Description | KnetMiner 5.7 includes minor enhancements and bug fixes. We have made small changes to the user search limits incentivizing users to register for a free account by offering higher gene list limits to registered users. Additionally, the API and backend have seen upgrades for better performance and usability. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | KnetMiner 5.7 signifies our last major release at Rothamsted Research. In November 2023, we have established the Knetminer spin-out company to build the next generation of the KnetMiner SaaS platform with a team of experienced designers, developers, data scientists and bioinformaticians. While we remain committed to open source, to safeguard our IP and our expanding customer base, 5.7 is our final completely open-source version. |
| URL | https://knetminer.com/knetminer-5-7_newspost/ |
| Title | KnetMiner v1.0 |
| Description | Helps users to analyse biological experiments and put finding into the context of published knowledge. Follow the link to see the release notes. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Accelerates gene discovery and plant breeding. |
| URL | http://knetminer.rothamsted.ac.uk/ |
| Title | KnetMiner v2.0 |
| Description | KnetMiner is a web app for gene mining and knowledge discovery. Follow the link to see the release notes. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Improved interoperability through web APIs |
| URL | http://knetminer.rothamsted.ac.uk/ |
| Title | KnetMiner v2.1 |
| Description | Improved search term suggestions and text highlighting. See release notes. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Improved usability of KnetMiner. |
| URL | http://knetminer.rothamsted.ac.uk/ |
| Title | KnetMiner v3.0 |
| Description | Major new release of KnetMiner with improved usability and interoperability. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Better Gene List & Genome Region Search. You have a list of genes and no clue what they do? Just paste your gene ids/names into the Gene List box (without any keyword) and let KnetMiner provide a summary of all information it has for your genes, their location, enriched linked terms and allow you to view their knowledge network. Genes wont be ranked and only paths from gene to trait and phenotype nodes will initially be shown. If you combine your gene list with keywords, KnetMiner will be able to rank your gene list based on relevance and highlight the most interesting paths of the knowledge network. New Web API access. KnetMiner knowledge networks can now be searched and visualized through API calls. For example, check out the MFT gene in araknet, wheatknet or riceknet. Adding a keyword argument to the URL will do some smart filtering and display the most interesting paths connecting genes and keywords (see example). You can embed similar code snippets into your own website. Smart Publication filtering. Some genes are linked to hundreds of papers. KnetMiner will now only show the most recent 20 publications in Gene View (Evidence box) and in Network View. This change will help you to get quicker to most recent research papers and has significantly improved the KnetMiner loading time. Deploy your own KnetMiner with Docker. KnetMiner is now available as a Docker image that can be easily deployed on your own server or in the AWS Elastic Beanstalk. To host your own private or public KnetMiner, you will need to create or clone one of the existing my_species (see example) folder. You can build your own my_species knowledge network or ask us to build one for you as a service. |
| URL | https://github.com/Rothamsted/knetminer/releases/tag/v3.0 |
| Title | KnetMiner v3.1 |
| Description | Minor improvements and bug fixes |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Benefits KnetMiner end users and developers |
| URL | https://github.com/Rothamsted/knetminer/releases/tag/v3.1 |
| Title | KnetMiner v3.2 |
| Description | Minor improvements and bug fixes |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Benefits to KnetMiner end users and developers |
| URL | https://github.com/Rothamsted/knetminer/releases/tag/v3.2 |
| Title | Knetminer Builder Update |
| Description | This is a software tool that is used to automatically construct knetminer instances and is being applied to all crop instances including wheat. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This enables regular updates to the knetminer instances when new component datasets are released. |
| URL | https://github.com/Rothamsted/ondex-knet-builder/releases/tag/v1.2 |
| Title | New KnetMiner API |
| Description | New KnetMiner API for gene based queries against a Neo4j database with knowledge graphs for cereals, vegetable, brassica and ascomycota genomes. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Impact | This will allow better integrations of KnetMiner data with other platforms, and provide new collaborations with AI and data science academic and industry users. |
| URL | https://api.knetminer.com/ |
| Title | OWL Ontology for Bioknowledge Networks |
| Description | This ontology is used as part of a suite of tools to represent knetminer knowledge networks using RDF |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Making knetminer systems shared through semantic web technology will facilitate sharing and access to the data from other tools. |
| URL | https://github.com/Rothamsted/bioknet-onto |
| Title | Ondex to RDF Exporter |
| Description | Ondex components and applications that are necessary for building genome-scale knowledge networks used in projects like KnetMiner. It includes the Ondex base, CLI, workflow engine and a set of plugins (parsers, mappers, transformers, filters and exporters) that are relevant for building genome-scale knowledge networks |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | It is part of a suite of tools that help knetminer networks, including those developed for wheat, be shared through linked open data methods. |
| URL | https://github.com/Rothamsted/ondex-knet-builder/tree/master/modules/rdf-export-2 |
| Title | Ondex-Knet-Builder v2.1 |
| Description | Command line based workflow engine for building knowledge graphs in OXL and RDF format. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Improvements to several data loaders. |
| URL | https://github.com/Rothamsted/ondex-knet-builder/releases/tag/v2.1 |
| Title | RDF to Neo4j converter |
| Description | RDF-Neo4 Converter and config to load KnetMiner data |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Exports our biological knowledge networks into formats that can be more easily re-used. |
| Title | Wheat KnetMiner - Release Nov 2017 |
| Description | Wheat KnetMiner - Release Nov 2017. Added disease related RNA-seq studies and wheat GWAS data. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Helps wheat researchers in gene discovery and knowledge visualization. |
| URL | http://knetminer.rothamsted.ac.uk/Triticum_aestivum/ |
| Title | Wiki page: Deploying and Developing KnetMiner with Docker |
| Description | This is documentation for how to develop and deploy KnetMiner using Docker |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Impact | None |
| URL | https://github.com/Rothamsted/knetminer/wiki/8.-Docker |
| Company Name | Knetminer Limited |
| Description | KnetMiner develops software that helps scientists search and analyze large volumes of biological literature and data to better understand complex traits and diseases. |
| Year Established | 2023 |
| Impact | The company has been established to leverage new types of funding and revenue to sustain the product development and maintenance of KnetMiner in the long term. We are in the final stages of finalising the IP license (March 2025). |
| Website | https://knetminer.com/ |
| Description | 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 | The Alan Turing Institute (ATI) hosted a workshop in partnership with the BBSRC-funded Designing Future Wheat research programme to explore the potential for innovative applications of data science and artificial intelligence to address problems relevant to the UK wheat community. 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. See here for more information https://www.turing.ac.uk/collaborate-turing/data-study-groups. We hope to encourage wide participation from data scientists and the UK wheat community, including stakeholders from industry and government. Problems considered within scope for the workshop include, but are not limited to: wheat genomics and genetics, phenotyping, breeding, GxExM interactions, agronomy, wheat pests and disease interactions, impacts of climate change, sustainability and wheat as part of a healthy diet. We particularly want to encourage participation from members of the wider data science community who consider that they have relevant skills or experience that could be brought to bear on the areas listed above and might be interested to be involved in future DSGs as a challenge owner (Early Career Researcher) or as a potential PI. |
| Year(s) Of Engagement Activity | 2020 |
| Description | BMGF CIMMYT - UK Wheat Research Workshop - August 2017 |
| 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 | A workshop was organised by the Bill and Melinda Gates Foundation between key CIMMYT investigators and Designing Future Wheat Investigators to explore areas of common interest to help network links and to identify areas of common interest. Possibilities of future collaborative projects were explored. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Better Data for a Better World - Imperial College Student Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This was an invited presentation and discussion with post-grad students at Imperial College on the "Ethics of Automation". |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.slideshare.net/mbrandizi/better-data-for-a-better-world-238896153 |
| Description | Bioinformatics for Plant Biology Course 2018 - KnetMiner training |
| 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 | EBI Training course on Plant Bioinformatics |
| Year(s) Of Engagement Activity | 2018 |
| Description | Blog - The rise of the genomes |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Blog article about the highlights of the Plant and Animal Genomes Conference in San Diego |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.rothamsted.ac.uk/articles/rise-genomes |
| Description | Blog post on FAIR Knowledge Graphs |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A blog article by Marco Brandizi describing the power of standardised and FAIR knowledge graphs under the hood of KnetMiner. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://knetminer.com/cases/the-power-of-standardised-and-fair-knowledge-graphs.html |
| Description | Careers Fair |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | This was a careers fair at a local school. Students and Parents attended to learn about career opportunities in agriculture and STEM |
| Year(s) Of Engagement Activity | 2019 |
| Description | Chairing wheat genetics symposium, Tuln, Austria |
| 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 | Chaired a session of Wheat Genetic symposium |
| Year(s) Of Engagement Activity | 2017 |
| Description | Co-organised the Integrative Bioinformatics Symposium 2019 in Paris |
| 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-organised the Integrative Bioinformatics Symposium 2019 in Paris which was attended by 70 scientists. It led to follow-up collaborations with industry and academia. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://symposium.inrae.fr/ib2019/ |
| Description | Conference organiser of PAG San Diego attracting 3800 plant and animal researchers |
| 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 | I am on the organising committee of the largest plant and animal ag genomics conference attracting some 3800 researchers, policy makers, industry etc |
| Year(s) Of Engagement Activity | Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019 |
| Description | DFW Presentation to DEFRA chief science advisor |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | A discussion of the outcomes and impact of WISP and DFW programmes |
| Year(s) Of Engagement Activity | 2019 |
| Description | Designing Future Wheat - connecting data and resources for wheat research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog article in the role of KnetMiner in Designing Future Wheat |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://knetminer.com/cases/dfw-knetminer.html |
| Description | Developing Software Licensing Guidance for BBSRC Scientists |
| 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 | This was workshop to develop guidelines on the most appropriate methods for making software as a research result available to other researchers. It was convened by the BBSRC. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Discussion with KWS about Knetminer interaction/collaborations |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion (Skype) with Andreas Menze (Head of Bioinformatics@KWS) about different modes of interaction/collaboration around KnetMiner |
| Year(s) Of Engagement Activity | 2019 |
| Description | Durum EWG Workshop: Bioinformatics to advance wheat breeding |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A 2-day workshop organised by Roberto Tuberosa and Luigi Cattivelli and attended by 100 wheat breeders, geneticists and researchers to learn about cutting-edge bioinformatics tools and resources available for wheat. The KnetMiner training led to a collaboration with Roberto Tuberosa's lab to identify potential candidate genes in hundreds of wheat QTL using KnetMiner networks and APIs. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding |
| Description | ELIXIR UK All Hands Meeting 2018 |
| 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 | This is a meeting of the UK Node of ELIXIR. Participation provided an opportunity for discussions around the development of standards for sharing metadata from agricultural field trials. This would build on the work of the DCTF. |
| Year(s) Of Engagement Activity | 2018 |
| Description | EMPHASIS |
| 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 | EMPHASIS is a project to develop a European Science Infrastructure (ESFRI) for plant phenotyping. A community workshop was held at Rothamsted in 2018. An important component of the activities of EMPHASIS is the management and sharing of data following agreed national/international standards. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://emphasis.plant-phenotyping.eu/ |
| Description | Enquiry and discussion with CSIRO about cost to develop KnetMiner for sugarcane/sorghum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Presentation to and discussion with CSIRO about cost to develop KnetMiner for sugarcane/sorghum |
| Year(s) Of Engagement Activity | 2018 |
| Description | GCC2017 (Galaxy conference) 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk was presented at the international Galaxy bioinformatics tools conference. KnetMiner: an application suite to integrate, search and interactively explore large knowledge networks |
| Year(s) Of Engagement Activity | 2017 |
| Description | Hackathon - Initiating Linked Public Datasets for Agriculture and Food |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This is a proof of concept hackathon to demonstrate the extent and scale at which we are able to connect agriculture and food datasets; using publicly available data from EnsemblGenomes, AHDB recommended list variety trials, PHI-base, Agrimetrics, CerealsDB and other data resources. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ebi.ac.uk/industry/private/industry-workshop/2019/03/initiating-linked-public-data-sets-... |
| Description | Invited speaker at IB2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker at the Integrative Bioinformatics Conference in Poland. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://ib2023.port.org.pl/ |
| Description | Invited talk at the Plant and Animal Genomes Conference, San Diego |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited speaker at the largest agri-genomics conference in the world which attracts over 3,000 participants. Presentation sparked follow-up discussions with the International Rice Research Institute (Philippines) and INRA URGI (France). |
| Year(s) Of Engagement Activity | 2018 |
| Description | KnetMiner 5.0 Release News |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News article describing new features in KnetMiner 5.0. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://knetminer.com/news/knetminer-5-release.html |
| Description | KnetMiner User Workshop in Amsterdam |
| 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 | 20 researchers from a European breeding consortium attended a KnetMiner user workshop in Amsterdam, which sparked questions and follow-on licensing discussions. |
| Year(s) Of Engagement Activity | 2021 |
| Description | KnetMiner training as part of the Wheat Bioinformatics Workshop - Bologna |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a training course and the KnetMiner system was presented to the wheat researchers at the meeting. |
| Year(s) Of Engagement Activity | 2017 |
| Description | KnetMiner training course (EBI 2018 - Introduction to Plant Bioinformatics) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | 30 course participants were trained in using KnetMiner. User requests were collected and addressed in forthcoming release. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Member of the board of the G20 wheat initative |
| 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 | I am a board member of the G20 wheat initiative set up by the G20 agricultural ministers to facilitate coordination of wheat research in the G20 countries. We organise working group to facilitate such coordination, and to identify priorities for funding by funding agencies within the G20 countries |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017,2018 |
| Description | Member of the management board of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World |
| 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 | A management board member of CGIAR wheat programme (CIMMYT and ICARD) to breed wheat for the resource-poor in the developing World |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017,2018,2019 |
| Description | Monogram 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Monogram is the UK national meeting on cereal genetics and genomics. It involves researchers and industry, including breeders. The presentation was on KnetMiner: Gene discovery through data mining and interactive visualization |
| Year(s) Of Engagement Activity | 2017 |
| Description | New KnetMiner website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | New KnetMiner website to better explain our vision and mission. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://knetminer.com |
| Description | News article - Mining mother lode |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release about KnetMiner publication |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.rothamsted.ac.uk/news/mining-mother-lode |
| Description | Organisation a day workshop at Eucarpia meeting , Clermont_Ferrand Paris, with INRA (French) and Proweizen (German ) and CIMMYT researchers |
| 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 worship was to discuss possible collaborations which could lead to bids into the EU for funding |
| Year(s) Of Engagement Activity | 2018 |
| Description | Organised 14th International Symposium on Integrative Bioinformatics (IB2018) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Organised a successful event that brought together experts in the field of integrative bioinformatics. Increased reputation of group and institute as a whole. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://ib2018.eventzilla.net/ |
| Description | Phenotyping Data Standards 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 workshop was convened to discuss the use of an emerging international standard for describing phenotyping datasets - MIAPPE withing the Designing Future Wheat programme. Most of the participants were collaborators in the the project, but a major contributor came from INRA. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at COVID-19 International Research Team |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented COVID-19 KnetMiner to an international team of COVID-19 researchers |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://knetminer.com/COVID-19/ |
| Description | Presentation at Monogram Network meeting 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | http://www.monogram.ac.uk/MgNW2017.php |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.monogram.ac.uk/MgNW2017.php |
| Description | Presentation at the conference for the UK Millers and bakers (NABIM-london) on DFW |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Was asked to provide further information on the coordinated DFW programme |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation on DFW at the DEFRA stakeholders WGIN meeting at RRES |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Request for more information on the programme |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation on WISP/DFW to ACC1 Cereals and Grains conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | The presentation was to inform the cereal grain (rice, maize and wheat) processes community on the step change which has occurred in wheat research and the involvement of WISP/DFW in the step change |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation on WISP/DFW to the BBSRC legume community |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation was to describe how the UK coordinated wheat programme was put together, and the impact the programme has had on the step change which has occurred in wheat research |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation on WISP/DFW to the BBSRC rice community |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation described how the coordinated WISP/DFW UK wheat programme was put together, and the impact the programme has had on the step change which has occurred in wheat research |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation to WGIN Stakeholder Meeting - March 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Title of presentation: From Farm to FAIR - A Data Sharing Infrastructure for Designing Future Wheat This was a presentation on the work of WP4 of DFW to develop tools to collect, integrate and make available data from the project. The stress was on the committment to FAIR data sharing and the challenges that have been addressed. |
| Year(s) Of Engagement Activity | 2021 |
| URL | http://www.wgin.org.uk/ |
| Description | Press release - KnetMiner re-purposed for COVID-19 research |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Taking time off from their own research, the Rothamsted team repurposed a tool they had originally developed to help crop scientists, to provide medical researchers with quick and intuitive access to all documented linkages between genes, medicines, and the virus. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.rothamsted.ac.uk/news/rothamsted-answers-white-house-call-coronavirus-data-help |
| Description | Press release on KnetMiner software and collaboration with Genestack |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release introducing the KnetMiner software developed in the Hassani-Pak lab at Rothamsted and a recent collaboration to make it available as an App in the Genestack bioinformatics platform. News covered by Rothamsted, Genestack, BBSRC, Aafarmer, Farmbusiness and other websites. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.rothamsted.ac.uk/news/visualising-data-connections-promises-faster-discoveries |
| Description | Revival Exhibition by Hugo Dalton at Fitzwilliam Museum, Cambridge |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Hugo Dalton's lightdrawings were inspired by two major innovations, i.e. Omega3 plants and KnetMiner software, from Rothamsted Research. His light projections were on display at the Fitzwilliam Museum in Cambridge from Nov 2017 - Feb 2018. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | http://www.fitzmuseum.cam.ac.uk/calendar/whatson/hugo-dalton-revival-lightdrawings |
| Description | Rothamsted Research Open Weekend 2018 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Rothamsted Open Weekend "Festival of Ideas" saw 8000 visitors come and hear about our science over 3 days |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.rothamsted.ac.uk/events/rothamsted-festival-ideas |
| Description | Software Evaluation and Licensing - 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentations to an international company, who can't be named for reasons of business confidentiality were made to introduce them to the potential of knetminer as a software platform in their crop science research division. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Software licensing and evaluation - 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This was a small webinar to a company who does not want to be named, but was interested in licensing our knetminer software. The webinar had several company scientists on the call. It led to a small commercial contract that enabled the company to undertake a more extensive in-house evaluation of the software. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Towards Responsible Plant Linkage Workshop - Turing Institute and Exeter University - March 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk Entitled From Farm to FAIR: The Trials of Linking and Sharing Wheat Research Data The presentation presented the range of responsibilities the DFW project has for managing its data so that it can benefit participants in the project, research and industry stakeholders. Also satisfy the needs of the funders. The complexity of the data management task for the project, the approaches we have taken and the challenges of delivering this were also presented. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.exeter.ac.uk/idsai/plantdata/ |
| Description | Training for IRRI Collaborator |
| 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 was a small scale training session over several days for IRRI research staff. The training covered the construction and use of the Bioinformatics software tool Knetminer. |
| Year(s) Of Engagement Activity | 2017 |
| Description | WebEx with Monsanto - KnetMiner presentation and discussion |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Hosted a presentation on Knetminer to potential industry collaborator - Monsanto |
| Year(s) Of Engagement Activity | 2018 |
| Description | Webinar with Monsanto technical team to present and discuss KnetMiner |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Webinar with Monsanto technical team to present and discuss KnetMiner |
| Year(s) Of Engagement Activity | 2018 |
| Description | WheatIS Expert Working Grop |
| 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 expert working group for the Wheat Information System is developing standards and tools to enable the global wheat science community to share data effectively. |
| Year(s) Of Engagement Activity | 2014,2015,2016,2017,2018 |
| URL | http://wheatis.org/ |
| Description | Workshop - Connecting the dots in life science data, part of IB2018 |
| 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 | This was a workshop presenting work we have done on data integration for crop science applications alongside others with similar interest. Keywan Hassani-Pak (Rothamsted Research) Setting the scene: introduction to data integration and KnetMiner Marco Brandizi (Rothamsted Research) Behind the scenes of KnetMiner: towards standardised and interoperable knowledge graphs Mark Needham (Neo4j) Neo4j graph database - Introduction to Neo4j, Cypher and latest developments Kevin Dialdestoro (Genestack) - Deploying private KnetMiner Servers in the cloud |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://imbio.de/ib2018 |
| Description | Workshop for VLPB consortium |
| 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 | Technical workshop for a pre-competitive consortium of plant breeding companies (VLPB). Attended by 20 participants. |
| Year(s) Of Engagement Activity | 2020 |
| Description | member of the G20 wheat Initiative Science board during 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 | The members of the science board discuss how to better coordinate the wheat research activities in the G20 countries |
| Year(s) Of Engagement Activity | 2019,2020 |
| Description | member of the management board of the CGIAR wheat programme (CIMMYT and ICARDA) to breed wheat for the resource poor in the developing world |
| 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 | I offer advice to the management team of the wheat CGIAR programme |
| Year(s) Of Engagement Activity | 2019,2020 |
| Description | member of the organising committee for PAG 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 | Suggest plenary speakers for inviting to speak at PAG 2020 meeting attracting 3000 animal and plant researchers |
| Year(s) Of Engagement Activity | 2019 |