DFW - Designing Future Wheat - Work package 4 (WP4) - Data access and analysis

Lead Research Organisation: Rothamsted Research
Department Name: Unlisted

Abstract

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.

Publications

10 25 50
 
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 During the year, we have provided BBSRC Swindon office with a google.doc site, 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.

Established (with Rob Davey as chair at EI) the Data Coordination Task Force (DCTF) to bring together researchers from all work packages, and external stakeholders, to initialise the coordination efforts required to ensure that project data flows smoothly from experiment to the DFW repository and gets shared within the project and to the community in a timely way. Meetings have been held each month since the beginning of the project.
Contributed as part of DCTF activities to the developments of data standards and data collection templates for recording data about DFW field trials, genotypic and plant phenotypic data. This also included organising an internal workshop in February 2018 to discuss the MIAPPE standard and its application to DFW datasets. Subsequently provided feedback to MIAPPE team to improve capture of field experiment metadata which fed into to MIAPPE 1.1.

Hackathons have been organised twice per year that bring together DCTF, WP4 developers and scientists from other work packages to further integrate resources from different DFW partners and to prototype solutions for data submission systems.

In Nov 2019 a DCTF hackathon at Rothamsted was used to test interoperability of APIs to KnetMiner, Ensembl plants and CerealsDB. The same hackathon further developed the field trial registration system and metadata collection strategy with RRes trial managers and statisticians, and EI Grassroots developers.

The KnetMiner wheat knowledge graph has been updated with latest database snapshots including Ensembl Plants Release 45, wheat publications from PubMed and new GWAS data from both wheat and Arabidopsis experiments.

Wheat bioinformatics resources including Ensembl Plants, WheatIS, The Triticeae Toolbox, Wheat-expression and Grain Genes have developed integrations into Wheat KnetMiner knowledge graph

Open access RDF-SPARQL and Neo4j-Cypher endpoints for wheat and Arabidopsis KnetMiner graphs have been deployed on CyVerse UK virtual machines.
Started to develop a new collaborative knowledge discovery platform for scientists to save, edit and share query-specific knowledge networks generated by KnetMiner. This will greatly benefit collaboration between DFW scientists and the dissemination of DFW data..

We are working towards the major release of KnetMiner 4.0 with user accounts and knowledge collaboration. We will be able to monitor the usage of KnetMiner more accurately and provide bespoke features in the future.
Exploitation Route The main outputs of this award are focused on providing software and data for the wheat community, comprising biologists, bioinformaticians, breeders, and external stakeholders.

We have developed our software in a general way and release it all with a open source licenses so that it can easily be used by others as part of plant bioinformatics projects, but also in other domains. We have made the KnetMiner network visualisation tool - KnetMaps - available as a BioJS component to increase the interoperability and re-usability of KnetMiner as part of our API development (Singh et al., 2018)

An important aspect of our approach is to define application programmer interfaces (APIs) that facilitates use of our software and our data resources.

The new KnetMiner APIs have increased interest from external users including the Cornell T3 resources, the INRA WheatIS system. This is in addition to future plans to exploit within WP4 with Ensembl Plants and the JIC wheat-expression team.

In 2019, We have been part of two successful grant proposals including a BBSRC BBR (follow on from DiseaseNetMiner) and a strategic LoLa grant that will give us additional resources for KnetMiner code and application development such as diseases, chemistry and pan-genomics.

While publicly funded KnetMiner resources (such as wheat) will remain completely free and open we have started exploring a subscription model for KnetMiner users that would cover the compute and storage cost of other KnetMiner instances and provide additional funds to improve the platform and better support the growing number of end users without depending on public funding. A new KnetMiner homepage is being designed with new branding and a modern look & feel.

We have submitted a joint BBSRC-NSF/BIO proposal with the MGRAST team at University of Chicago to develop "A FAIR.AI knowledge discovery resource for microbial communities and their functional properties" (Nov 2019). We have submitted a BBSRC BBR-GCRF proposal to develop KnetMiner 2.0 for mining pangenomic knowledge networks of crop phenotypes and diseases (Nov 2018). We are expecting two research papers and one software note to be published on our R&D work on KnetMiner. Academic partners such as IRRI in Philippines or INRA in France are interested to connect KnetMiner and our knowledge networks with their own genetics or genomics resources. In addition to the academic activities, we are in contact with several companies who have shown interest or are evaluating the use of in-house versions of KnetMiner deployed with their own private datasets.
Sectors Agriculture, Food and Drink,Environment,Healthcare

 
Description KnetMiner website user statistics (Google Analytics) 2017/2018: 1,520 unique users 2018/2019: 1,823 unique users 2019/2020: 2,821 unique UI users 2019/2020: 3,591 unique API users Geo: 37% of users are from the UK Average session duration lasted 4:32 minutes We have run training courses to scientists from academia and industry at EMBL-EBI, the Wheat Bioinformatics Workshop in Bologna and were invited to present KnetMiner at PAG2018 and PAG2019. Organising the Integrative Bioinformatics (2018) at Rothamsted provided a platform for engagement with the European applied bioinformatics community and awareness of DFW informatics resources and tools being developed at Rothamsted and the Earlham Institute. The new KnetMiner APIs have increased interest from external users including the Grain Genes, Cornell T3 resources, and the INRA WheatIS system. This is in addition to work involved in WP4 to integrate with Ensembl Plants and the JIC wheat-expression team. We have made the KnetMiner network visualisation tool - KnetMaps - available as a BioJS component to increase the interoperability and re-usability of KnetMiner as part of our API development (Singh et al., 2018) We made important progress towards FAIR knowledge graphs for wheat gene information using RDF and Neo4j.The work was published and presented at the Integrative Bioinformatics conference at Rothamsted (Brandizi et al., 2018) and the SWAT4LS conference (Brandizi et al., 2018). KnetMiner RDF and Neo4j endpoints for wheat and Arabidopsis are available on CyVerse UK. Several companies from the Agrifood sector are in discussions with Rothamsted about access or licensing of KnetMiner for use in wheat and other crop research. The new Docker-based deployment provides a simple technology stack to deploy KnetMiner in the AWS Cloud. We have started exploring a business model with the RRes KEC team and lead adopters.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Societal

 
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 08/2017 
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 06/2022
 
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 11/2019 
End 10/2024
 
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 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 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/
 
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 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-LucJannink 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 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 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 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 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 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 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
 
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 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 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,
 
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 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 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 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
 
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
 
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 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 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 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 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 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