QTLNetMiner: Mining Candidate Gene Networks From Genetic Studies of Crops and Animals

Lead Research Organisation: Rothamsted Research
Department Name: Computational & Systems Biology

Abstract

Discovering which genes determine a particular biological trait in crops, animals or humans is a very important finding. There are many applications of such knowledge including: identifying new biomarkers for animal or human diseases which can lead to new diagnostics; designing screens for new drugs, and helping to select new varieties of crop or livestock animals with improved productivity or resistance to stresses such as disease. Searching for these candidate genes in a crop or animal genome is, however, like searching for a needle in a haystack and gathering the evidence that supports the choice of one gene over another is even more daunting. This is because the evidence is scatted among different internet databases and in incompatible forms that are not easily linked together or integrated. One very important class of information used by biologists to begin their search for candidate genes is genetics. Classical genetics methods use studies of populations and families and employ statistical methods to identify the most likely genome segments that are known as Quantitative Trait Loci (QTL). The nature of complex traits, however, means that many QTL may be identified for a particular trait. For example, a recent study in Brassica napus identified 47 QTLs which were relevant for seed yield and studies in pig have discovered in total more than 400 QTLs related to fatness. For many years, the study of complex traits in crops and livestock animals has been an important adjunct to their improvement through selective breeding. Until recently, the focus on mapping of QTLs has been based on genetic maps constructed using relatively small numbers (hundreds) of genetic markers separated by quite large genetic distances. By linking the genetic maps with newly obtained genome sequence information it is now possible to list the genes that underlie each QTL. These studies show that typical QTLs in both plants and animals generally encompass quite sizeable parts of the genome - typically several hundred genes. While genetics improves the chances of finding the right gene (or genes), reducing the options down from 22,000 or so found in a typical genome, to hundreds genes for a particular QTL, it is still a daunting and expensive task to evaluate candidate gene in the laboratory. Furthermore, as is becoming apparent in diseases such as cancer, a complex phenotype may be the consequence of groups of seemingly independent genes interacting through a network of different biological relationships. The software we plan to develop in this project builds on previously-funded BBSRC research in which we have developed general methods for integrating different sources of biological information and exploring the relationships among genes and proteins using network-based approaches. Our methods help biologists mine the networks of information and interactions among genes in order to make better-informed judgments about which gene or gene networks are involved in a particular trait. In this project we will further develop the software and adapt our methods to create prototypes of biologist-friendly web sites for four species representing important crop and farm animal species where genetics and QTL data can be combined with other data resources, including the scientific literature. These species have been chosen because of their importance to the BBSRC and national priorities around improving the security of our food and energy (bioenergy) supplies. In particular, we will develop integrated data and network biology resources as web sites for use by the farm animal research community; thus translating the applications of our data integration research into a new area of BBSRC-funded biology. In addition to developing several novel resources for biologists, we wish to demonstrate that the Ondex data integration platform can be adapted to new areas of biological research in a cost-effective manner.

Technical Summary

The Ondex data integration platform uses graph based methods to integrate biological data sources based on concepts of semantic mapping. In a novel development of the Ondex system we will create a client-server application framework based on Web Services and a lightweight Ondex user interface and visualisation framework (QTLNetMiner) that will support biologists mining genetics and genomics data resources for the networks of information and interactions that can be used to select functional candidate genes from QTL studies. We will re-use and substantially adapt components from the Ondex data integration framework developed in a BBSRC SABR project to create integrated knowledge bases constructed from genetics, genome sequence, trait and gene function ontologies, protein family and biochemical pathway and enzyme function information together with Medline abstracts for four sequenced species of agronomic interest. We have selected the tree species Poplar (used as a model for Willow as a bioenergy crop) and three livestock species (Pig, Cow and Chicken) to demonstrate that our data integration methods and software architecture can be adapted to completely new areas of biology in a cost effective way. Our objective will be to create four separate novel biologist-friendly web resources as working prototypes that will enable users to search the crop and livestock genetics datasets using searches based on visualisation of QTL data using a third-party application (GViewer), keyword and regular expression and through inference over the network of relationships in each species-specific knowledge base. The subnetworks retrieved will be displayed using a new and extended web-enabled version of the Ondex client application and this will allow the user to perform visualisation and interactive analysis of the relevant subsection of the knowledgebase to support network-based evaluation of the sets of positional candidate derived from genetics studies.

Planned Impact

The impact plan for this short sTRDF project focuses on promoting the potential benefits to crop and animal pre-breeding and genetics research through using the tools we are developing to exploit integrated bioinformatics data resources and network analysis methods in the translation of knowledge from model species (e.g. Arabidopsis, Human, Mouse) to a better understanding of complex trait biology. This project will develop advanced prototypes that could be extended for the benefit of other crop and livestock species. We are thus creating a proof of principal for a general approach and platform bioinformatics technology that could be deployed more broadly and with the associated increase in impact. We also consider that the resources being created by QTLNetMiner will be a showcase for how data-intensive biology can be exploited for the benefit of plant and animal science. The impact of the project in the crop science community will be addressed through engagement by the Rothamsted group with the commercial and academic partners in the BBSRC Sustainable Bioenergy Centre consortium. The Poplar knowledge base will be used and tested by the Willow geneticists and breeders at Rothamsted. Any potentially valuable candidate genes identified with the willow genetics team would potentially be evaluated for suitable intellectual property protection by Rothamsted or in partnership with PBL Technology. The Rawlings group is also involved with other crop science communities (wheat and brassica) and during this project we will be participating in stakeholder events (e.g. the WGIN and OREGIN genetic improvement networks) where we will look to demonstrate the potential impact of the QTLNetMiner tools and resources. We will be using the working prototypes developed in this project to engage with the livestock and veterinary research communities. The recent incorporation of the Roslin Institute with the Royal (Dick) School of Veterinary Studies provides excellent opportunities to engage with a wider range of animal and veterinary scientists in the private sector. Andy Law will lead this aspect of our impact activities. Roslin scientists have particular sectoral expertise and industry engagement activities, not just with commercial animal breeding companies but with the pharmaceutical sector who use animal models of human diseases in their research programmes. We will work through the Roslin Division of Genetics and Genomics and Business Development Executive to identify where best to focus our outreach activities given the limited resources and duration of this project.

Publications

10 25 50
 
Title KnetMiner overview and demo at PAG 2017 
Description Overview of KnetMiner 
Type Of Art Film/Video/Animation 
Year Produced 2017 
Impact Increased visibility of KnetMiner 
URL https://www.youtube.com/watch?v=PvxHTems3pA&feature=youtu.be&a
 
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 Training video for QTLNetMiner Users - 2015 
Description Training / User support video for QTLNetMiner 
Type Of Art Film/Video/Animation 
Year Produced 2015 
Impact None 
URL https://www.youtube.com/watch?v=1FDCVrlB6G4
 
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 This project has used components of the Ondex data integration framework to develop a web based application that enables crop and livestock scientists to explore the genes that determine complex traits. This will facilitate the discovery of new genes and potentially genetic markers that might be used for breeding.
In 2017 the software was re-branded as KnetMiner.
There are new features in KnetMiner for wheat and also new datasets incorporated into the wheat knowledge graph anticipating future needs in DFW. New features include improved search of gene lists, interactive filtering of search results and improved compatibility of KnetMiner with Cytoscape Desktop. New datasets include wheat gene expression studies from EBI and GWAS data from The Triticeae Toolbox. Wheat specific publications were added to the knowledge graph and abstracts were scanned for gene-phenotype information. In total, 22,315 wheat Gene-TO (Trait Ontology) relations were created based on sentence-based co-occurrences of putative wheat gene names and TO terms in wheat publications.

We have started evaluating more standardised data formats (RDF) and graph databases (Neo4j) for exchanging and searching our genome-scale knowledge networks. Providing more expressive graph query languages and helping us to build web-services for use by other wheat resources such as CerealsDB, Ensembl Plants, Grassroots, WheatIS, T3 Toolbox
Exploitation Route The software is open source and available for download for any user. The current versions of knetminer can be used to help research scientists and breeders understand the genes and networks of proteins involved in complex agronomic traits. The software is generic and it could be used to develop equivalent applications for a range of new crops or livestock species where genetic and genomic data are available.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology

URL http://knetminer.rothamsted.ac.uk/
 
Description The success of this product has led to collaborations with Syngenta and more recently GeneStack. These have led to QTLNetMiner applications for Maize. In the case of GeneStack there is an ongoing collaboration to transfer elements of the QTLNetMiner and Ondex tools into their cloud based bioinformatics software environment. The aim is to offer services equivalent to those in QTLNetMiner to licensees of GeneStack. KnetMiner had over 1500 unique users since April 2017 (+200% compared to previous year) with most coming from the UK (30%), followed by US (24%) and including users from developing countries such as Malaysia (4%), Philippines (2%) and India (2%). The average session duration lasted 5:22 minutes (-35% indication for users can get information faster). We have run a training course to wheat researchers and breeders at the Wheat Bioinformatics Workshop in Bologna and since have started a collaboration with the Tuberosa group to rank genes in wheat QTLs using KnetMiner and our new Neo4j graph database. We were invited to present KnetMiner at PAG2018 and had follow-up interactions with the Quesneville group at INRA to add KnetMiner to the federated WheatIS index.
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)
Impact Types 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 Finding Value in Complex Biological Data - Integrated 'omics FS
Amount £22,973 (GBP)
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 04/2016 
End 10/2017
 
Description Tools and resources development fund: call 2
Amount £128,467 (GBP)
Funding ID BB/N022874/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2016 
End 03/2018
 
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 KnetMiner Instance for Arabidopsis 
Description KnetMiner instance for Aradidopsis 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Publication in press 
URL http://knetminer.rothamsted.ac.uk/Arabidopsis_thaliana/
 
Title QTLNetMiner Integrated Knowledge Networks 
Description The QTLNetMiner project generated a set of integrated plant genetic and genomics datasets which can be used for candidate gene identification 
Type Of Material Database/Collection of data 
Year Produced 2013 
Provided To Others? Yes  
Impact None 
URL https://ondex.rothamsted.ac.uk/QTLNetMiner/releasenotes/xnets/
 
Title QTLNetMiner for Barley 
Description Instances of QTLNetMiner for Barley research 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Initiated collaboration with IPK Gatersleben which unfortunately did not last 
URL https://ondex.rothamsted.ac.uk/QTLNetMinerBarley/
 
Title QTLNetMiner instance for Maize 
Description QTLNetMiner instance for Maize 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact This has been developed as part of a collaboration with Syngenta which unfortunately has been terminated because of internal re-structuring in the company. 
URL https://ondex.rothamsted.ac.uk/QTLNetMinerMaize/
 
Title QTLNetMiner instance for Wheat 
Description QTLNetminer instance for Wheat 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Leading to discussions about participation in future cross-institute ISP and collaborations with the EBI 
URL https://ondex.rothamsted.ac.uk/QTLNetMinerWheat/
 
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 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/
 
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 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 Visiting Scientist from Institute of Agricultural Biotechnology, Argentina 
Organisation Research Councils UK (RCUK)
Department Institute of Agricultural Biotechnology, Argentina
Country Argentina 
Sector Public 
PI Contribution A visiting scientist participated in software development and built a new knowledge base for QTLNetMiner proving tools to mine QTL intervals in Potato.
Start Year 2012
 
Description WheatIS Group interaction with INRA Versailles 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Public 
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 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 - Knowledge Network Miner 
Description KnetMiner (formerly QTLNetMiner) is a modern software application for interrogating genome-scale knowledge networks to identify direct and indirect relations between genotype and phenotype. 
Type Of Technology Webtool/Application 
Year Produced 2013 
Open Source License? Yes  
Impact KnetMiner has helped to accelerate and speed up candidate gene discovery in plant and crop species. What our users say: "You and rest of the Rothamsted team have created a really intuitive tool that makes genetic discovery fun and efficient." 
URL http://knetminer.rothamsted.ac.uk/
 
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 v2.1 
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 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 Suite 
Description Data integration using semantic integration methods for lifesciences research and systems biology 
Type Of Technology Software 
Year Produced 2010 
Open Source License? Yes  
Impact It led to further research projects and enabled a collaboration with Syngenta 
URL http://www.ondex.org
 
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/
 
Description Connecting Crop Phenotype Data Workshop - PAG 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 Several groups (INRA France, IPK Germany, Cornell University) approached us to develop programmatic interfaces (APIs) for KnetMiner. This will enable and facilitate tool integration and collaboration.
Year(s) Of Engagement Activity 2017
URL https://pag.confex.com/pag/xxv/webprogram/Session4249.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 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 EBI Training Workshop - Integrative 'OMICS 2015, 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We taught data integration and visualisation using Ondex and QTLNetMiner at the European Bioinformatics Institute
Year(s) Of Engagement Activity 2015,2016
URL http://www.ebi.ac.uk/training/events/2015/introduction-integrative-omics
 
Description Industry Workshop - PAG 2017 (California) 
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 Engaged with several food and agri companies that showed interest in the KnetMiner tools and approaches for knowledge mining
Year(s) Of Engagement Activity 2017
URL https://pag.confex.com/pag/xxv/webprogram/Session4338.html
 
Description Introduction to Integrative 'omics 2016 
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 Training workshop in integrative omics software methods. Features both Ondex and QTLNetMiner
Year(s) Of Engagement Activity 2016
URL http://www.ebi.ac.uk/training/events/2016/introduction-integrative-omics-0
 
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 course (EBI 2017 - Introduction to omics data integration) 
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 30 scientists from academia and industry were trained to use KnetMiner for the discovery of genes involved in specific diseases. Audience was very engaged and found our appraoches very useful but also requested some new features that would improve KnetMiner.
Year(s) Of Engagement Activity 2017
URL https://www.ebi.ac.uk/training/events/2017/introduction-omics-data-integration
 
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 SeqAhead - NGS Current Challenges and Data Analysis for Plant Researchers 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Training workshop for academic and commercial plant scientists
Year(s) Of Engagement Activity 2014
URL http://www.tgac.ac.uk/seqahead-challenges-for-plant-researchers
 
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 Systems Biology and Ontologies Workshop - PAG 2016 
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 Workshop for industry and academia on use of plant ontologies for crop research
Year(s) Of Engagement Activity 2016
 
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 Wheat Breeders Workshop 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Bioinformatics and genomics workshop for wheat breeders
Year(s) Of Engagement Activity 2015
URL http://www.tgac.ac.uk/news/240/68/Wheat-breeders-techno-remix/
 
Description WheatIS Workshop - PAG2016 
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 Meeting of the formal Expert Working Group in the Wheat Initiative Information System to report progress and discuss priorities with stakeholders.
Year(s) Of Engagement Activity 2016