CerealsDB: A community resource for wheat genomics

Lead Research Organisation: Earlham Institute
Department Name: Research Faculty

Abstract

CerealsDB ( http://www.cerealsdb.uk.net/) is one of the most highly accessed wheat web sites with over 5,000 unique accesses per month.

The reasons for CerealsDB's success are clear; it provides the community with sequence and single nucleotide polymorphism (SNP)-based information in a form accessible to and understandable by non-experts.

While CerealsDB is successful, to remain of value to its users, it needs to develop in conjunction with the community's expectations. In addition, CerealsDB needs to expand its remit to include further interaction with other web sites such as the internationally based Wheat Initiative. This development is new to this application as in our previous work we developed tools specifically for the UK community rather than the global wheat community. However, although our previous work did focus on the UK community, the easy to use style of CerealsDB has already resulted in the web site becoming international recognised, with many of its users being from non-UK organisations.

In this further development, CerealsDB will continue work with UK users to develop sequence and SNP-based resources; however, it will also extend its horizons to include interactions with international web-based resources and the exploitation of genomics resources such as the wheat reference sequence. This extension to its remit will result in an expanded audience for CerealsDB and more extensive tools and datasets being made available to the community.

Technical Summary

"A community resource for wheat functional genomics" was one of the first projects to be funded by the BBR initiative. The resources enabled Bristol and Rothamsted Research to develop "CerealsDB" and "Monogram". CerealsDB and Monogram are accessed directly or via other web sites such as the Wheat Improvement Strategic Program (WISP), the International Wheat Initiative and GrainGenes. CerealsDB hosts tools and resources to access and analyse sequence and SNP-based datasets for wheat (Triticum aestivum) and related species. CerealsDB assists breeders and academics in exploring the wheat genome and selecting strategies for genotyping and marker assisted selection. CerealsDB includes a database in excess of 100,000 varietal SNPs, of which several thousand have been validated and mapped on one of three mapping populations. CerealsDB also contains information on DArT markers and Expressed Tagged Sequences (ESTs), and was the first site to host the 5x genome sequence for the variety Chinese Spring released in 2010. Since launch, CerealsDB has been updated regularly, with the last update on the 1st May 2013 with the addition of a further ~1,500 mapped SNP markers and a mapping function which assigns unmapped SNPs to putative homoeologous specific chromosome arms.

To ensure that CerealsDB remains on of the most useful wheat-based web sites and to increase the communities awareness of the resources hosted, we intend to develop CerealsDB to included further tools such as an expanded SNP/genotype database, including iSelect and Axiom based datasets along with facilities to identify and characterise functional SNPs. In addition, new releases will include graphic tools to enable breeders and academics to link mapped and non-mapped SNPs/genes across a variety of wheat related species. Finally, although CerealsDB has always been designed to be easy to use, we will provide training across the range of activities included within the web site.

Planned Impact

The BBSRC web site states that "BBSRC is the principal funder of food-related research in the UK and has food security as one of its key strategic drivers." In the UK wheat is, by a significant margin, the most valuable arable crop and therefore not surprisingly the status of the UK wheat crop is a national issue often reported in the press. While BBSRC funds a large number of wheat-related projects, for the most part, it is the translation of this research into wheat varieties with increased yield or improved qualities such as improved bread making qualities that provides the impact required by BBSRC if it is to deliver its strategic objectives. Translation of wheat research in line with BBSRC's strategic priorities, almost always involves either mapping and cloning genes or crossing alleles of interest into elite varieties. In all cases, since its launch, CerealsDB has helped researchers to achieve impact by providing wheat geneticists with unencumbered sequences and SNP-based information which is easy to access and free from IP or MTAs.

The development of CerealsDB has led to strategic changes in the approaches taken by various wheat breeders, for instance many regard the development of CerealsDB as a significant factor in their decision to convert their marker labs to the SNP-based markers.

In accordance with BBSRC strategy to achieving impact, Prof. Edwards has actively engaged with industry, for instance through the CIRC program and via his participation in a BBSRC science interchange programme with Advanta-Nickerson (now Limagrain) Seeds to exchange technologies and ideas. In addition the university base of the Bristol group and the institutional base of TGAC allows each to incorporate its research directly into undergraduate, post-graduate and post doc teaching. This approach has been remarkably successful and has resulted in numerous young researchers being placed within agricultural institutes or companies as PhD students, researchers or employees.

The facilities offered by CerealsDB are unique. We know that this because our users tell us. Although CerealsDB is international recognised as being a primary source of wheat sequences and SNP-based markers, we believe that by adding the facilities described, Bristol will ensure that it increases its international profile and continues to provide a valuable (almost) one stop shop for wheat functional genomics. In so far as we are aware no similar commercially available resources exist, however, it is important to note that our web site is used by both academic and the industrial sectors with several companies relying on it for a substantial part of their business and many of our improvements have been carried out at the suggestion of the UK wheat breeding sector.

Publications

10 25 50
 
Description As part of the grant remit to extend access to datasets, we set up instances of iRODS (https://irods.org/) which is an open source data management software tool to allow for easy sharing of data allowing for federation between different institutions. It also allows for metadata to be associated with the files within the datasets enable richer searching and data mining. We developed two software tools to add functionality to iRODS: eirods-dav (https://github.com/billyfish/eirods-dav), is a tool to interact with both iRODS and Apache httpd web servers (https://httpd.apache.org/), to allow for easy sharing of iRODS-hosted data from a standard web interface. This took an existing open source solution, davrods (https://github.com/UtrechtUniversity/davrods), and greatly extended it by adding a number of features. These were the ability to greatly modify the page layout to make it more user-friendly, expose the metadata for viewing, searching and editing and adding a REST API to allow for programmatic access to the underlying data and metadata. The second tool, iRODS Bash Completer (https://github.com/TGAC/irods_bash_completer), allows the iRODS client icommands to have auto-complete functionality within a Linux/Unix/Mac operating system which makes for a much more user-friendly experience for users accessing the datasets from a command line.

We created the Grassroots infrastructure which is an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected.

We developed the ability for services to be linked together so that the output results from one service can be parsed automatically to generate an already populated set of parameters for another service so that the user does not have to copy and paste results and can run the subsequent service with a single click or command from within a script.

A number of Grassroots web services were added to the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/webservices.php) which, since they conform to the Grassroots API, can interact with other Grassroots servers such as the one at Earlham Institute. This gives a REST API to allow developers to access the data hosted at CerealsDB such as SNP, contig or phenotype information programmatically.
Exploitation Route The Grassroots infrastructure wraps up both industry-standard software tools and our own custom developed tools with a consistent API, using as many standard schemas and ontologies as possible. As such it allows services and datasets to be distributed across different institutions with the Grassroots infrastructure taking care of connecting them together. Identical services running on different datasets in different institutions can be federated together. So, from a user's point of view, they appear as a cohesive set of tools and data available at one point of entry, with only one web service and a single set of search parameters to populate to query all of the distributed data. This means that when searching for data to use across a number of disparate web services, users do not need to go to each of these Grassroots-powered services in turn, but only visit one of them to get a consistent view over a community's datasets.

The linked service functionality means that we can build services that are linked automatically, helping users gain access to suitable tools and workflows following searches within the Grassroots infrastructure. For example, following a BLAST search for sequence similarity, users are presented with automatically generated links to go from the BLAST results to the full scaffold in which any given hit occurs, or to run Polymarker (http://www.polymarker.info/), an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid species for any given SNP.

We have undertaken collaborations with other institutions whenever possible for the benefit of the wider academic and breeder communities, such as adding wrappers around the data stored in the SeedStor system at https://www.seedstor.ac.uk/ provided by the Germplasm Resources Unit at the John Innes Centre to provide both a map-based Grassroots service as well as a REST API for programmers to access which has already been successfully integrated into their publicly-available tools by the CerealsDB team at the University of Bristol.


These improvements to functionality and user experience will help researchers gain access to a greater breadth and depth of information related to not only CerealsDB but also related projects such as Designing Future Wheat, or which CerealsDB is a key information resource.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)

URL http://www.cerealsdb.uk.net
 
Description We have undertaken collaborations with other institutions whenever possible for the benefit of the wider academic and breeder communities, such as adding wrappers around the data stored in the SeedStor system at https://www.seedstor.ac.uk/ provided by the Germplasm Resources Unit at the John Innes Centre to provide both a map-based Grassroots service as well as a REST API for programmers to access which has already been successfully integrated into their publicly-available tools by the CerealsDB team at the University of Bristol. These and other improvements to functionality and user experience have helped researchers gain access to a greater breadth and depth of information related to not only CerealsDB but also related projects such as Designing Future Wheat, of which CerealsDB is a key information resource. As CerealsDB is an open resource, commercial scientists have access to this information for (pre-)breeding experiments, providing a route to generating impact and revenue across the translational spectrum.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)
Impact Types Cultural,Economic

 
Title Grassroots Genomics grid infrastructure 
Description Integrative research requires extensive multi-level approaches to enrich and expose data and workflows so that informatics infrastructures can process them effectively. The Grassroots Infrastructure is developed at the Earlham Institute (EI) to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public datasets in the plant sciences. Its lightweight reusable software stack comprises: an iRODS data management layer to provide structure to unstructured filesystems, with Elasticsearch indexed metadata and Davrods exposed WebDAV APIs; interfaces to interact with local or cloud-based analysis platforms; an Apache web server layer to deliver content and provide access to public programmatic interfaces; services such as: BLAST search on multiple databases across different sites; a mapping tool showing pathogen samples with temporal and spatial data. It can be run locally or packaged in virtual containers and deployed on a variety of hardware thus representing a decentralised system, allowing information generators to retain control over their resources but allowing interconnected resources to access each other consistently. As such, Grassroots represents EI's contribution to the Wheat Initiative Wheat Information System (WheatIS) project, formalising the infrastructure as the federated UK WheatIS node involving partners from the University of Bristol, the European Bioinformatics Institute, Rothamsted Research, and the John Innes Centre. We are currently working on lightweight mechanisms to expose underlying grid architecture using WebDAV, standardised APIs such as the Breeding API (BrAPI) and schemas such as Frictionless Data and BioSchemas to enable greater interoperability with a variety of existing services, and integration with data analysis platforms such as CyVerse and Galaxy. 
Type Of Material Data handling & control 
Year Produced 2014 
Provided To Others? Yes  
Impact This infrastructure powers the handling and release of the wheat genomics data arising from EI's flagship wheat programmes, as well as aggregating previously published datasets. Currently we have a BLAST service running on top of this infrastructure, but we are currently building federation options into the platform with the iRODS data grid software. The CerealsDB project at the University of Bristol is a widely used and vital resource for the wheat community, and the Bristol group are deploying the Grassroots infrastructure to facilitate integration of the resources held there with the resources at EI. The Field Pathogenomics project (BBSRC IPA funded project BB/M025519/1) is also powered by the Grassroots platform, enabling a fast and informative web-based user interface based on data collected by the project relating to wheat yellow rust epidemiology. 
URL https://wheatis.tgac.ac.uk/grassroots/api/
 
Description Wheat Information System (WheatIS) 
Organisation Cold Spring Harbor Laboratory (CSHL)
Country United States 
Sector Charity/Non Profit 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Zentrum Munchen
Country Germany 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
Sector Public 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of Bristol
Country United Kingdom 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of California, Davis
Department UC Davis College of Biological Sciences
Country United States 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Description Wheat Information System (WheatIS) 
Organisation University of Western Australia
Country Australia 
Sector Academic/University 
PI Contribution The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.
Collaborator Contribution All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.
Impact This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/
Start Year 2011
 
Title API for SeedStor 
Description API for https://www.seedstor.ac.uk to improve the programmatic access. Used in the Grassroots Infrastructure and CerealsDB. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2018 
Impact Grassroots Infrastructure and CerealsDB can now query SeedStor programatically instead of browsing the web page. 
URL https://github.com/TGAC/grassroots-seedstor-api
 
Title EI wheat data portal 
Description A BLAST server dedicated to wheat genomes, powered by the Grassroots API and freely available to the public and hosting a large number of previously published and newly generated genomes of wheat varieties. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact This portal has served over 7100+ page visits, and run more than 11000 BLAST jobs from users in 31 countries, allowing them early access to full wheat genomes even before publication. Notably, this software was the main route of dissemination of the TGAC v1 Chinese Spring 42 wheat genome prior to its inclusion in Ensembl Plants. 
URL https://wheatis.tgac.ac.uk/grassroots-portal/blast
 
Title EIRods-DAV 
Description Eirods-dav provides access to iRODS servers using the WebDAV protocol and has a complete REST API for accessing and manipulating metadata from within a web browser. It adds a substantial amount of functionality to the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Eirods-dav leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact The software is now used to host the Designing Future Wheat data portal. 
URL https://opendata.earlham.ac.uk/wheat
 
Title Eirods-dav 
Description Eirods-dav provides access to iRODS servers using the WebDAV protocol and exposes a REST API for accessing and manipulating metadata from within a web browser. It adds a substantial amount of functionality to the original Davrods module written by Ton Smeele and Chris Smeele, which is a bridge between the WebDAV protocol and the iRODS API. Davrods leverages the Apache server implementation of the WebDAV protocol, mod_dav, for compliance with the WebDAV Class 2 standard. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Eirods-dav is used to allow web-based access to a selection of files and research data released to the public by the Earlham Institute such as the Triticum Aestivum assemblies. It is used by the Grassroots Infrastructure to allow access to data produced by the Designing Future Wheat project. The Eirods-dav application runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/data/
 
Title Grassroots API 
Description The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact The Grassroots API powers the public BLAST service that runs at TGAC, predominantly for the currently available wheat assemblies including the recently released TGAC v1 w2rap assembly (in preparation). We have served over 4000 unique users with over 6000 BLAST jobs since November 2015. It also underpins the Field Pathgenomics project (BBSRC IPA award 2015, PI - Saunders D., TGAC/JIC fellow), a web portal that represents the detection and subsequent phenotyping and genotyping of the wheat yellow rust pathogen. The site aims to enable researchers and breeders to track rust epidemics over variety and time, allowing for a more proactive approach to wheat crop breeding and farming. Finally, we are working with the CerealsDB group at Univ. Bristol to deploy the Grassroots infrastructure alongside the CerealsDB web portal, allowing a federation of searching, datasets, analysis and dissemination of markers, genotypes and associated feature and literature information. 
URL https://wheatis.tgac.ac.uk/grassroots/api/
 
Title Parental Genotype Service 
Description The Parental Genotype Service works with data from various cross-parental breeding lines with associated genotypic markers along with which parent is responsible for their presence in the child line. It can accept various queries across this data, 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact As part of a collaboration with Paul Wilkinson at the University of Bristol and Luzie Wingen at the John Innes Centre, it is used as part of a QTL web service available from the CerealsDB website. 
URL http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/select_QTL.php
 
Title The Grassroots Infrastructure 
Description The Grassroots software is an open source "as-a-Service" stack that powers a number of data dissemination and analysis activities at EI, and other sites such as CerealsDB at the University of Bristol. We have continued to develop the functionality within the software stack to share crop-related datasets. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Grassroots has previously been used to host the Field Pathogenomics project website and Yellow Rust map, the EI wheat BLAST service, the CerealsDB federation project, and the multi-scale improvements to the Polymarker marker design software. Recently, Grassroots has been put forward as the main data repository and metadata catalogue for the Designing Future Wheat project, and has started to host data from this project, the Open Wild Wheat Consortium, and 5 new wheat genomes from EI. The Grassroots service runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/
 
Title iRODS filename completion tool for BASH 
Description This is a tool to allow the iRODS client icommands to have auto-complete functionality within Bash as is the case with normal mounted filesystems. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact For people using the iRODS client icommands, it allows time to be saved as instead of having to type out the full paths which is error-prone and time-consuming, they can simply press the tab key to get all current matching filenames taking into account any characters that they may have already entered. 
 
Description Building infrastructure for open science - British Computer Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited speaker at the Advanced Programming Group annual Christmas lecture
Year(s) Of Engagement Activity 2015
URL http://www.bcs.org/category/18516
 
Description CerealsDB Workshop for end users 
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 Academics and breeders attended to get overviews and tutorials of the tools available within CerealsDB, Grassroots and Ensembl Plants. This gave them an opportunity to discover how these tools might be useful for them as well as giving feedback to us, as the developers of these platforms, to help plan useful future work.
Year(s) Of Engagement Activity 2018
 
Description Data Stewardship in the Life Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I spoke at the "Challenges and Opportunities in Plant Science Data Management" workshop on the subject of data management in the life sciences.

Open data and integrative data sharing are fundamental factors in order to address the challenges of modern data-intensive science. There is a clear need to develop and maintain community-focussed, semantically-aware data stewardship and management platforms, such as COPO, that are able to cope with the description and sharing of potentially huge datasets arising from the life sciences. Once made available, it is not sufficient to assume that researchers around the globe have requisite skills and resources to analyse these data. Therefore, we need to provide large-scale data analysis environments that are fit for purpose, incorporating state-of-the-art interfaces and programmatic layers to meet broad end-user requirements, such as CyVerse and Galaxy. Finally, this can only happen when there are community-led efforts into implementing solutions for data standardisation, best practice, and FAIR data policy. We are now only just starting to take advantage of groundbreaking opportunities to make integrated data a reality, and thus enabling scientists to store, manage, and share their data as a first-class citizen of the scientific process.
Year(s) Of Engagement Activity 2017
URL http://app.core-apps.com/pag_2017/event/e2bec353017762d275ce250c23e011e6
 
Description Data, Data, Data Everywhere (Pint of Science talk, Norwich) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Davey delivered a talk as part of the Norwich 2017 Pint of Science series about the challenges and solutions for modern data management in the life sciences, including recent data developments, high-performance computing, and software tools.
Year(s) Of Engagement Activity 2017
URL https://pintofscience.co.uk/event/crops-crystals-and-computers-technology-for-food-security
 
Description Divseek Working Group - Data Standards for Interoperable Tools 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As part of the "DivSeek - Addressing the challenges and opportunities for information and data sharing associated with plant germplasm" session at PAG, I spoke about the DivSeek Data Standards for Interoperable Tools Working Group. This WG will promote best practice in data sharing in the plant sciences, through the use of open and interoperable software powered by the adoption of open standards, i.e. programmatic interoperability standards (APIs), controlled vocabularies, trait dictionaries, metadata standards, and ontologies. We aim to highlight gaps in interoperability that impede workflows important to the communities supported by DivSeek partners, by liaising with research development groups, other DivSeek working groups, and consortia with relevance to DivSeek. We will educate and train data generators about standards and the tools and resources that use them, in order to promote and foster standards-compliance for long-term open data stewardship.
Year(s) Of Engagement Activity 2017
URL https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/26202
 
Description Down The Tubes! Talk at the Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Davey gave a talk on the internet and data science entitled "Down The Tubes!" at the 2018 Norwich Science Festival.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/down-the-tubes/
 
Description Engagement with Industry - KWS UK Ltd 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Mr Bian and Miss Minotto showed EI CyVerse infrastructure and Grassroots Infrastructure's features, including data sharing to the staffs from KWS UK Ltd: Ed Byrne, Janina Dordel, Andreas Menze and Vipul Patel.
Year(s) Of Engagement Activity 2018
 
Description Grassroots Infrastructure and the Wheat Information System (Genome 10K & Genome Science 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mr Bian and Dr Tyrrell presented a poster at Genome 10K & Genome Science 2017 conference.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Grassroots Infrastructure and the Wheat Information System (RDA Interest Group on Agricultural Data (IGAD), Barcelona) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Davey delivered a talk about the Grassroots software infrastructure for the dissemination of wheat data through federation and integration of storage and compute e-infrastructure.
Year(s) Of Engagement Activity 2017
URL https://www.rd-alliance.org/rda-interest-group-agricultural-data-igad-pre-plenary-meeting-3-4-april-...
 
Description Integrative Bioinformatics 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Gave a workshop about the Grassroots Infrastructure and COPO to end users.
Year(s) Of Engagement Activity 2018
 
Description PhenoHarmonIS Workshop 
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 given about the tools and data available within the Grassroots Infrastructure and how it uses standards to describe crop-based experimental data
Year(s) Of Engagement Activity 2018
URL https://sites.google.com/a/cgxchange.org/cropontologycommunity/2018-phenoharmonis
 
Description RDA Wheat Data Interoperability Working Group meeting, RDA Plenary, Barcelona 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Wheat Data Interoperability Working Group aims to provide a common framework for describing, representing linking and publishing Wheat data with respect to open standards.Such a framework will promote and sustain Wheat data sharing, reusability and operability. Specifying the Wheat linked data framework will come with many questions: which (minimal) metadata to describe which type of data? Which vocabularies/ontologies/formats? Which good practices? Mainly based on the the needs of the Wheat initiatiative Information System (WheatIS) in terms of functionalities and data types, the working group will identify relevant use cases in order to produce a "cookbook" on how to produce "wheat data" that are easily shareable, reusable and interoperable. This meeting saw the maturation of the Working Group into a Maintenance Group, showing that we have moved from an inception phase to an implementation phase, promoting the outputs of the WG (the Wheat Data Interoperability guidelines) to users.
Year(s) Of Engagement Activity 2016
URL https://www.rd-alliance.org/group/agricultural-data-ig-igad-wheat-data-interoperability-wg-agriseman...
 
Description Visit from Collaborator from University of Bristol; Paul Wilkinson 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Visit from Collaborator from University of Bristol; Paul Wilkinson
Year(s) Of Engagement Activity 2018
 
Description Wheat Initiative group discussion at Plant and Animal Genome conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Discussion of the latest research activities from the Wheat Initiative members.
Year(s) Of Engagement Activity 2019
 
Description iRODS functionality within the Grassroots Infrastructure (iRODS User Group Meeting 2017, Utrecht, The Netherlands) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Tyrrell presented work on the development of the eirods-dav software package for the Grassroots data dissemination platform.
Year(s) Of Engagement Activity 2017
URL https://irods.org/ugm2017/