DiseaseNetMiner - A novel tool for mining integrated biological networks of host and pathogen interaction

Lead Research Organisation: Rothamsted Research
Department Name: Computational and Analytical Sciences

Abstract

Modern society is increasingly under threat from a plethora of microscopic fungal pathogens, which cause diseases in agricultural and horticultural crops, and in farmed animals. Many of these diseases cause a significant, detrimental impact on global and local food security. Furthermore, there is a worrying tendency for pathogens to become more aggressive towards their hosts, to cause more disease (increased virulence) and for the anti-fungal chemicals (called fungicides) that are often used to control fungal pathogen outbreaks to become less effective.

In the recent past, (during the genomics era) scientists have developed technologies to sequence and assemble all the chromosomes of an organisms and predict the gene content (i.e. obtain their complete genome blueprints). Now, in the post-genomic era, next generation sequencing technologies have been developed and this has led to an explosion of more genomic data alongside a wealth of gene expression, protein expression, genetic and biological data, which are used by scientists to describe pathogen-host interaction phenotypes and disease outcomes. However, for many scientists with expertise in biology, biochemistry or genetics, this 'omics' data explosion is often seen as a burden, 'an infinite data soup of varying qualities' that only those with specialist computing-based interpretation skills (called bioinformatics), but often only minimal specialist biological knowledge, can penetrate. Therefore, new computer based tools urgently need to be developed to allow researchers to connect, explore and compare all the large and small-scale datasets available for pathogenic species that cause diseases. Once we fully understand how fungal pathogens cause disease, and how the host species try to defend themselves, will it be possible to manipulate these processes and mechanisms and go on to devise new ways to reduce disease levels and thereby improve global food security.

In this project, we will develop a novel software tool, called DiseaseNetMiner, which will be user-friendly and can be used by many different types of scientists to explore integrated biological networks that can predict processes controlling the disease-causing abilities of fungal pathogens. DiseaseNetMiner will deliver understandable outputs from diverse and complex large-scale data inputs. DiseaseNetMiner will allow researchers without specialist bioinformatics skill to explore and compare this wealth of existing data from multiple species with their own latest cutting-edge results to permit rapid progress and new discoveries. This fundamental tool will effectively connect different data types and then return the results in an accessible, explorable, as well as scalable, format that can be easily manipulated, displayed and interrogated. DiseaseNetMiner will create a novel research environment from which new scientific insights and biological discoveries can be made.

The UK research community has been at the very forefront of research and discovery in this field. The initiative we propose will be an exceptionally useful and cost-effective way of ensuring that the leadership shown by the UK research community will continue in the decade ahead. We expect this to yield outcomes with huge impact in our field and beyond, to meet the grand challenges of our age.

Technical Summary

DiseaseNetMiner will provide a user-friendly tool for candidate gene prioritisation and hypothesis generation from large host-pathogen knowledge networks. To ensure efficient and cost-effective delivery, we will make use of the free and open-source Ondex and QTLNetMiner frameworks that we have previously developed at Rothamsted Research. DiseaseNetMiner will include significant, new functional advances and provide a timely and novel tool for the plant and fungal research communities.

Objective 1: Use Ondex to integrate public multi-omics datasets, phenotype information, homology data and functional gene annotations for the key fungal model species S. cerevisiae, N. crassa and A. nidulans, and the pathogenic fungi F. graminearum and Z. tritici. This will deliver a semantically integrated knowledge network (graph data warehouse) of interlinked fungal species that we will provide access to through the QTLNetMiner web application (FungiNetMiner).

Objective 2: Create a novel, combined pathogen-host network by integrating an existing wheat-arabidopsis-rice knowledge network and the new fungal network based on annotations to cross-species ontologies, curated pathogen-host interaction databases, text-mining using gene names and disease/phenotype ontologies, and a statistical correlation approach using data from dual long time-series RNA-seq experiments of infected plants. This knowledge network is estimated to have about 750,000 nodes and 4,000,000 edges including all wheat, Arabidopsis and fungal genes.

Objective 3: Develop the DiseaseNetMiner web application by extending the QTLNetMiner client-server framework to fully support combined plant-pathogen networks and user-provided SNP/GWAS input data. This will require the development of new graph queries to explore combined plant-pathogen networks and novel tools to visualise SNPs within biological interaction networks and to include SNP consequences in the QTLNetMiner gene prioritisation algorithm.

Planned Impact

Modern society is increasingly under threat from a plethora of fungal pathogens, many of which
have a significant, detrimental impact on food security. In the post-genomic era, the explosion of 'omics, genetic and phenotypic data is often seen as a burden, 'an infinite data soup of varying qualities' that only those with specialist bioinformatics skills, but often only minimal specialist biological knowledge, can penetrate.

In this 15 month pilot project, we will focus on the development of new in silico tools to assist scientists based in academic, industry, NGOs and /or government departments to connect, explore and compare large-scale fungal and plant datasets to identify the various generic and species-specific biological processes that control pathogenesis, fungicide resistance and avirulence, while connecting this information to the general growth and development of eukaryotic organisms. The new tool, called DiseaseNetMiner, will allow researchers without specialist bioinformatics skills to explore and compare this wealth of existing data from multiple species, with their own latest cutting-edge results to permit rapid progress, new insights and new discoveries.

DiseaseNetMiner will contain and connect information in a combined network for three well studied fungal species (S. cerevisiae, N. crassa and A. nidulans) and two globally economically important fungal pathogens of wheat crops, namely Fusarium graminearum and Zymoseptoria tritici. This fungal network will be connected to a plant network combining information from Arabidopsis, rice and wheat.

Academics will use DiseaseNetMiner to interrogate and prioritise candidate gene lists for both pathogens by gaining additional annotation from model species, the responses of the host plant and from the occurrence of SNPs. Researchers would then test the function of the most promising candidate genes with reverse genetics experiments. Researchers will use the combined plant and pathogen networks to explore functions of genes and their interactions. Researchers involved in sequencing large numbers of natural or laboratory generated strains of F. graminearum and Z. tritici with subtly different phenotypes, e.g. increased aggressiveness, can use DiseasesNetMiner for the biological interpretation of genome wide association studies. This should reveal the domains, hubs and /or proteins in the network most likely to be causally linked to the phenotypic shift.

In the short term, the agrochemical and plant breeding industries will use DiseasesNetMiner to connect publically-available datasets on pathogens, crop plants and model species to their own proprietary data sets. This will give new insights on where product failure, (agrochemical or resistant wheat cultivar) may be occurring as individual population shift occur or when individual isolates in a population mutate and rise in abundance. In the longer term, these connected data sets, when viewed over yearly time series, will help to guide the identification of novel target sites for intervention and, therefore, guide innovative agrochemical product development and influence disease resistance breeding strategies, such as identifying the most effective R gene stacks.

NGOs and government departments will use DiseaseNetMiner to investigate and predict the possibility of emerging disease threats in the UK and elsewhere by investigating the genomic changes present in newly virulence strains and/ or fungicide resistant strains and go on to provide advice to farmers and the AgriIndustry.

To deliver the above impacts, we plan to develop a community of researchers in the UK and elsewhere to beta test the tools with their own unpublished data, publicise the existence of DiseaseNetMiner to the wider scientific community at national/ international conferences, hold virtual and face-to-face workshops, give seminars to various industries / consortia and complete various media activities.

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 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 grant supported the development of the KnetMiner tool suite for evidence-based gene discovery. KnetMiner Release 2.1 was made available on GitHub and included major improvements to the usability including features such as gene list search, interactive filtering of search results and better compatibility of KnetMiner with Cytoscape Desktop.

We developed a new plugin for KnetBuilder to transform tabular data to knowledge networks. This has helped us to stream-line the data fetching, processing and integration process. The knowledge base was extended with new types of information including gene expression, genetic studies, species specific publications and gene-phenotype information.

We created knowledge networks for two major disease causing wheat pathogens: Fusarium and Zymoseptoria. We made important progress towards making our knowledge networks FAIR by providing RDF, Neo4j and API access.

We organised an international workshop as part of the Integrative Bioinformatics Conference 2018 at Rothamsted which helped us to engage with developers and end-users. We also demonstrated KnetMiner to the wheat pathogenomics group at Rothamsted and received positive feedback.

We were successful building individual crop or pathogen knowledge networks including data from model species, however, the cross-kingdom integration of a combined pathogen-host knowledge network remains a major challenge because of gaps in data and our current technology stack. The curated PHI-base database provided useful information for a small number of proteins (effectors) that can act as a bridge between pathogen and host systems, but more research is needed to predict such interactions for a larger number of effectors and their targets. Equally, a more optimized and standardized graph database technology will be needed in the future to efficiently store and query over 10 million relationships that would exist in a combined pathogen-host knowledge graph.
Exploitation Route Findings from this grant have been taken forward in a new BBSRC BBR grant proposal which aims to address the issues identified around building combined pathogen-host knowledge graphs and also to develop new approaches to integrate chemistry information. We expect our integrated knowledge networks to be accessed by hundreds of users every month using KnetMiner web-app and our new APIs. The tools and resources will enable faster scientific discoveries and lead to citations in research papers. The growing reputation will foster new collaborations with academic partners such as IRRI in Philippines, INRA in France or Cornell in US who are already connecting their resources to KnetMiner and our knowledge networks. 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,Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology

 
Description KnetMiner had 1520 unique users in 2017/2018 (+200% compared to previous year) and 1823 unique users in 2018/2019 (+20% compared to previous year) with most users coming from the UK (32%), followed by US (25%) and including users from developing countries such as China (5%), Malaysia (2%), Philippines (2%) and India (2%). The average session duration lasted 5:22 minutes. 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. We have started exploring different business models for KnetMiner to better support the needs of companies. The KnetMiner app in the commercial Genestack platform provides one possible route to commercialization. The new Docker-based deployment offers companies a simple solution to deploy KnetMiner in their own private cloud (e.g. Amazon EC2). We have run training courses for 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 KnetMiner resources and tools being developed at Rothamsted.
First Year Of Impact 2018
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
 
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 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 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 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 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 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 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 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/
 
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 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 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 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 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 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 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 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 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 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 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